Base Composition Characteristics of Mammalian miRNAs

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Bin Wang

2013-01-01

Full Text Available MicroRNAs (miRNAs are short RNA sequences that repress protein synthesis by either inhibiting the translation of messenger RNA (mRNA or increasing mRNA degradation. Endogenous miRNAs have been found in various organisms, including animals, plants, and viruses. Mammalian miRNAs are evolutionarily conserved, are scattered throughout chromosomes, and play an important role in the immune response and the onset of cancer. For this study, the author explored the base composition characteristics of miRNA genes from the six mammalian species that contain the largest number of known miRNAs. It was found that mammalian miRNAs are evolutionarily conserved and GU-rich. Interestingly, in the miRNA sequences investigated, A residues are clearly the most frequent occupants of positions 2 and 3 of the 5′ end of miRNAs. Unlike G and U residues that may pair with C/U and A/G, respectively, A residues can only pair with U residues of target mRNAs, which may augment the recognition specificity of the 5′ seed region.

Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells

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VÊNCIO, ENEIDA F.; PASCAL, LAURA E.; PAGE, LAURA S.; DENYER, GARETH; WANG, AMY J.; RUOHOLA-BAKER, HANNELE; ZHANG, SHILE; WANG, KAI; GALAS, DAVID J.; LIU, ALVIN Y.

2014-01-01

The prostate stromal mesenchyme controls organ-specific development. In cancer, the stromal compartment shows altered gene expression compared to non-cancer. The lineage relationship between cancer-associated stromal cells and normal tissue stromal cells is not known. Nor is the cause underlying the expression difference. Previously, the embryonal carcinoma (EC) cell line, NCCIT, was used by us to study the stromal induction property. In the current study, stromal cells from non-cancer (NP) and cancer (CP) were isolated from tissue specimens and co-cultured with NCCIT cells in a trans-well format to preclude heterotypic cell contact. After 3 days, the stromal cells were analyzed by gene arrays for microRNA (miRNA) and mRNA expression. In co-culture, NCCIT cells were found to alter the miRNA and mRNA expression of NP stromal cells to one like that of CP stromal cells. In contrast, NCCIT had no significant effect on the gene expression of CP stromal cells. We conclude that the gene expression changes in stromal cells can be induced by diffusible factors synthesized by EC cells, and suggest that cancer-associated stromal cells represent a more primitive or less differentiated stromal cell type. PMID:20945389

Turbo Decision Aided Receivers for Clipping Noise Mitigation in Coded OFDM

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Declercq David

2008-01-01

Full Text Available Abstract Orthogonal frequency division multiplexing (OFDM is the modulation technique used in most of the high-rate communication standards. However, OFDM signals exhibit high peak average to power ratio (PAPR that makes them particularly sensitive to nonlinear distortions caused by high-power amplifiers. Hence, the amplifier needs to operate at large output backoff, thereby decreasing the average efficiency of the transmitter. One way to reduce PAPR consists in clipping the amplitude of the OFDM signal introducing an additional noise that degrades the overall system performance. In that case, the receiver needs to set up an algorithm that compensates this clipping noise. In this paper, we propose three new iterative receivers with growing complexity and performance that operate at severe clipping: the first and simplest receiver uses a Viterbi algorithm as channel decoder whereas the other two implement a soft-input soft-output (SISO decoder. Each soft receiver is analyzed through EXIT charts for different mappings. Finally, the performances of the receivers are simulated on both short time-varying channel and AWGN channel.

Turbo Decision Aided Receivers for Clipping Noise Mitigation in Coded OFDM

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Maxime Colas

2008-02-01

Full Text Available Orthogonal frequency division multiplexing (OFDM is the modulation technique used in most of the high-rate communication standards. However, OFDM signals exhibit high peak average to power ratio (PAPR that makes them particularly sensitive to nonlinear distortions caused by high-power amplifiers. Hence, the amplifier needs to operate at large output backoff, thereby decreasing the average efficiency of the transmitter. One way to reduce PAPR consists in clipping the amplitude of the OFDM signal introducing an additional noise that degrades the overall system performance. In that case, the receiver needs to set up an algorithm that compensates this clipping noise. In this paper, we propose three new iterative receivers with growing complexity and performance that operate at severe clipping: the first and simplest receiver uses a Viterbi algorithm as channel decoder whereas the other two implement a soft-input soft-output (SISO decoder. Each soft receiver is analyzed through EXIT charts for different mappings. Finally, the performances of the receivers are simulated on both short time-varying channel and AWGN channel.

HITS-CLIP analysis uncovers a link between the Kaposi's sarcoma-associated herpesvirus ORF57 protein and host pre-mRNA metabolism.

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Emi Sei

2015-02-01

Full Text Available The Kaposi's sarcoma associated herpesvirus (KSHV is an oncogenic virus that causes Kaposi's sarcoma, primary effusion lymphoma (PEL, and some forms of multicentric Castleman's disease. The KSHV ORF57 protein is a conserved posttranscriptional regulator of gene expression that is essential for virus replication. ORF57 is multifunctional, but most of its activities are directly linked to its ability to bind RNA. We globally identified virus and host RNAs bound by ORF57 during lytic reactivation in PEL cells using high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP. As expected, ORF57-bound RNA fragments mapped throughout the KSHV genome, including the known ORF57 ligand PAN RNA. In agreement with previously published ChIP results, we observed that ORF57 bound RNAs near the oriLyt regions of the genome. Examination of the host RNA fragments revealed that a subset of the ORF57-bound RNAs was derived from transcript 5' ends. The position of these 5'-bound fragments correlated closely with the 5'-most exon-intron junction of the pre-mRNA. We selected four candidates (BTG1, EGR1, ZFP36, and TNFSF9 and analyzed their pre-mRNA and mRNA levels during lytic phase. Analysis of both steady-state and newly made RNAs revealed that these candidate ORF57-bound pre-mRNAs persisted for longer periods of time throughout infection than control RNAs, consistent with a role for ORF57 in pre-mRNA metabolism. In addition, exogenous expression of ORF57 was sufficient to increase the pre-mRNA levels and, in one case, the mRNA levels of the putative ORF57 targets. These results demonstrate that ORF57 interacts with specific host pre-mRNAs during lytic reactivation and alters their processing, likely by stabilizing pre-mRNAs. These data suggest that ORF57 is involved in modulating host gene expression in addition to KSHV gene expression during lytic reactivation.

Unsupervised learning of facial emotion decoding skills.

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Huelle, Jan O; Sack, Benjamin; Broer, Katja; Komlewa, Irina; Anders, Silke

2014-01-01

Research on the mechanisms underlying human facial emotion recognition has long focussed on genetically determined neural algorithms and often neglected the question of how these algorithms might be tuned by social learning. Here we show that facial emotion decoding skills can be significantly and sustainably improved by practice without an external teaching signal. Participants saw video clips of dynamic facial expressions of five different women and were asked to decide which of four possible emotions (anger, disgust, fear, and sadness) was shown in each clip. Although no external information about the correctness of the participant's response or the sender's true affective state was provided, participants showed a significant increase of facial emotion recognition accuracy both within and across two training sessions two days to several weeks apart. We discuss several similarities and differences between the unsupervised improvement of facial decoding skills observed in the current study, unsupervised perceptual learning of simple stimuli described in previous studies and practice effects often observed in cognitive tasks.

Correlation of mRNA Profiles, miRNA Profiles, and Functional Immune Response in Rainbow Trout (Oncorrhynkus Mykiss) During Infection With Viral Hemorrhagic Septicemia Virus (VHSV) and in Fish Vaccinated With an Anti-VHSV DNA Vaccine

DEFF Research Database (Denmark)

Bela-Ong, Dennis; Schyth, Brian Dall; Lorenzen, Niels

fish. Linking mRNA and miRNA profiles with phenotypic, genotypic, and immunological data will provide an integrated view of the mechanisms of resistance and the strong protective immune responses provided by vaccination. This information is important in designing effective strategies to mitigate......-mediated) responses. MRNA and miRNA profiles will be correlated and combined with in vitro work in cell culture to describe target relationships between miRNAs and mRNAs and the effect of this targeting in fish. Vaccinated fish will also be used for mRNA/miRNA profiling and in challenge studies alongside non-vaccinated...

RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration

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Jing Zhang

2018-01-01

Full Text Available Background With the continuous discovery of microRNA’s (miRNA association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA’s role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS analysis. Methods The package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs. Results By incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow. Conclusions With RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS. More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865.

SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function.

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Xiao-Peng Xiong

2015-08-01

Full Text Available microRNAs (miRNAs are a class of endogenous regulatory RNAs that play a key role in myriad biological processes. Upon transcription, primary miRNA transcripts are sequentially processed by Drosha and Dicer ribonucleases into ~22-24 nt miRNAs. Subsequently, miRNAs are incorporated into the RNA-induced silencing complexes (RISCs that contain Argonaute (AGO family proteins and guide RISC to target RNAs via complementary base pairing, leading to post-transcriptional gene silencing by a combination of translation inhibition and mRNA destabilization. Select pre-mRNA splicing factors have been implicated in small RNA-mediated gene silencing pathways in fission yeast, worms, flies and mammals, but the underlying molecular mechanisms are not well understood. Here, we show that SmD1, a core component of the Drosophila small nuclear ribonucleoprotein particle (snRNP implicated in splicing, is required for miRNA biogenesis and function. SmD1 interacts with both the microprocessor component Pasha and pri-miRNAs, and is indispensable for optimal miRNA biogenesis. Depletion of SmD1 impairs the assembly and function of the miRISC without significantly affecting the expression of major canonical miRNA pathway components. Moreover, SmD1 physically and functionally associates with components of the miRISC, including AGO1 and GW182. Notably, miRNA defects resulting from SmD1 silencing can be uncoupled from defects in pre-mRNA splicing, and the miRNA and splicing machineries are physically and functionally distinct entities. Finally, photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP analysis identifies numerous SmD1-binding events across the transcriptome and reveals direct SmD1-miRNA interactions. Our study suggests that SmD1 plays a direct role in miRNA-mediated gene silencing independently of its pre-mRNA splicing activity and indicates that the dual roles of splicing factors in post-transcriptional gene regulation may be

About miRNAs, miRNA seeds, target genes and target pathways.

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Kehl, Tim; Backes, Christina; Kern, Fabian; Fehlmann, Tobias; Ludwig, Nicole; Meese, Eckart; Lenhof, Hans-Peter; Keller, Andreas

2017-12-05

miRNAs are typically repressing gene expression by binding to the 3' UTR, leading to degradation of the mRNA. This process is dominated by the eight-base seed region of the miRNA. Further, miRNAs are known not only to target genes but also to target significant parts of pathways. A logical line of thoughts is: miRNAs with similar (seed) sequence target similar sets of genes and thus similar sets of pathways. By calculating similarity scores for all 3.25 million pairs of 2,550 human miRNAs, we found that this pattern frequently holds, while we also observed exceptions. Respective results were obtained for both, predicted target genes as well as experimentally validated targets. We note that miRNAs target gene set similarity follows a bimodal distribution, pointing at a set of 282 miRNAs that seems to target genes with very high specificity. Further, we discuss miRNAs with different (seed) sequences that nonetheless regulate similar gene sets or pathways. Most intriguingly, we found miRNA pairs that regulate different gene sets but similar pathways such as miR-6886-5p and miR-3529-5p. These are jointly targeting different parts of the MAPK signaling cascade. The main goal of this study is to provide a general overview on the results, to highlight a selection of relevant results on miRNAs, miRNA seeds, target genes and target pathways and to raise awareness for artifacts in respective comparisons. The full set of information that allows to infer detailed results on each miRNA has been included in miRPathDB, the miRNA target pathway database (https://mpd.bioinf.uni-sb.de).

Investigation of miRNA Biology by Bioinformatic Tools and Impact of miRNAs in Colorectal Cancer: Regulatory Relationship of c-Myc and p53 with miRNAs

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Yaguang Xi

2007-01-01

Full Text Available MicroRNAs (miRNAs are a class of small non-coding RNAs that mediate gene expression at the posttranscriptional and translational levels and have been demonstrated to be involved in diverse biological functions. Mounting evidence in recent years has shown that miRNAs play key roles in tumorigenesis due to abnormal expression of and mutations in miRNAs. High throughput miRNA expression profiling of several major tumor types has identified miRNAs associated with clinical diagnosis and prognosis of cancer treatment. Previously our group has discovered a novel regulatory relationship between tumor suppressor gene p53 with miRNAs expression and a number of miRNA promoters contain putative p53 binding sites. In addition, others have reported that c-myc can mediate a large number of miRNAs expression. In this review, we will emphasize algorithms to identify mRNA targets of miRNAs and the roles of miRNAs in colorectal cancer. In particular, we will discuss a novel regulatory relationship of miRNAs with tumor suppressor p53 and c-myc. miRNAs are becoming promising novel targets and biomarkers for future cancer therapeutic development and clinical molecular diagnosis.

Unsupervised learning of facial emotion decoding skills

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Jan Oliver Huelle

2014-02-01

Full Text Available Research on the mechanisms underlying human facial emotion recognition has long focussed on genetically determined neural algorithms and often neglected the question of how these algorithms might be tuned by social learning. Here we show that facial emotion decoding skills can be significantly and sustainably improved by practise without an external teaching signal. Participants saw video clips of dynamic facial expressions of five different women and were asked to decide which of four possible emotions (anger, disgust, fear and sadness was shown in each clip. Although no external information about the correctness of the participant’s response or the sender’s true affective state was provided, participants showed a significant increase of facial emotion recognition accuracy both within and across two training sessions two days to several weeks apart. We discuss several similarities and differences between the unsupervised improvement of facial decoding skills observed in the current study, unsupervised perceptual learning of simple stimuli described in previous studies and practise effects often observed in cognitive tasks.

ARMOUR – A Rice miRNA: mRNA Interaction Resource

OpenAIRE

Neeti Sanan-Mishra; Anita Tripathi; Kavita Goswami; Rohit N. Shukla; Madavan Vasudevan; Hitesh Goswami

2018-01-01

ARMOUR was developed as ARice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of...

Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon.

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Skaftnesmo, K O; Edvardsen, R B; Furmanek, T; Crespo, D; Andersson, E; Kleppe, L; Taranger, G L; Bogerd, J; Schulz, R W; Wargelius, A

2017-10-18

Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty negatively impacts animal welfare and growth. We hypothesize that certain miRNAs modulate mRNAs relevant for the initiation of puberty. To explore which miRNAs regulate mRNAs during initiation of puberty in salmon, we performed an integrated transcriptome analysis (miRNA and mRNA-seq) of salmon testis at three stages of development: an immature, long-term quiescent stage, a prepubertal stage just before, and a pubertal stage just after the onset of single cell proliferation activity in the testis. Differentially expressed miRNAs clustered into 5 distinct expression profiles related to the immature, prepubertal and pubertal salmon testis. Potential mRNA targets of these miRNAs were predicted with miRmap and filtered for mRNAs displaying negatively correlated expression patterns. In summary, this analysis revealed miRNAs previously known to be regulated in immature vertebrate testis (miR-101, miR-137, miR-92b, miR-18a, miR-20a), but also miRNAs first reported here as regulated in the testis (miR-new289, miR-30c, miR-724, miR-26b, miR-new271, miR-217, miR-216a, miR-135a, miR-new194 and the novel predicted n268). By KEGG enrichment analysis, progesterone signaling and cell cycle pathway genes were found regulated by these differentially expressed miRNAs. During the transition into puberty we found differential expression of miRNAs previously associated (let7a/b/c), or newly associated (miR-15c, miR-2184, miR-145 and the novel predicted n7a and b) with this stage. KEGG enrichment analysis revealed that mRNAs of the Wnt, Hedgehog and Apelin signaling pathways were potential regulated targets during the transition into puberty. Likewise, several regulated miRNAs in the pubertal stage had earlier been associated (miR-20a, miR-25, miR-181a, miR-202, let7c/d/a, miR-125b

Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

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Woo, Ho-Hyung; Baker, Terri; Laszlo, Csaba; Chambers, Setsuko K.

2013-01-01

CSF-1 mRNA 3′UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3′UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3′UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of

Hepatitis C virus RNA functionally sequesters miR-122

DEFF Research Database (Denmark)

Luna, Joseph M; Scheel, Troels K H; Danino, Tal

2015-01-01

Hepatitis C virus (HCV) uniquely requires the liver-specific microRNA-122 for replication, yet global effects on endogenous miRNA targets during infection are unexplored. Here, high-throughput sequencing and crosslinking immunoprecipitation (HITS-CLIP) experiments of human Argonaute (AGO) during...

Iterative Signal Processing for Mitigation of Analog-to-Digital Converter Clipping Distortion in Multiband OFDMA Receivers

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Markus Allén

2012-01-01

Full Text Available In modern wideband communication receivers, the large input-signal dynamics is a fundamental problem. Unintentional signal clipping occurs, if the receiver front-end with the analog-to-digital interface cannot respond to rapidly varying conditions. This paper discusses digital postprocessing compensation of such unintentional clipping in multiband OFDMA receivers. The proposed method iteratively mitigates the clipping distortion by exploiting the symbol decisions. The performance of the proposed method is illustrated with various computer simulations and also verified by concrete laboratory measurements with commercially available analog-to-digital hardware. It is shown that the clipping compensation algorithm implemented in a turbo decoding OFDM receiver is able to remove almost all the clipping distortion even under significant clipping in fading channel circumstances. That is to say, it is possible to nearly recover the receiver performance to the level, which would be achieved in the equivalent nonclipped situation.

Analysis of miRNA and mRNA Expression Profiles Highlights Alterations in Ionizing Radiation Response of Human Lymphocytes under Modeled Microgravity

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Casara, Silvia; Sales, Gabriele; Lanfranchi, Gerolamo; Celotti, Lucia; Mognato, Maddalena

2012-01-01

Background Ionizing radiation (IR) can be extremely harmful for human cells since an improper DNA-damage response (DDR) to IR can contribute to carcinogenesis initiation. Perturbations in DDR pathway can originate from alteration in the functionality of the microRNA-mediated gene regulation, being microRNAs (miRNAs) small noncoding RNA that act as post-transcriptional regulators of gene expression. In this study we gained insight into the role of miRNAs in the regulation of DDR to IR under microgravity, a condition of weightlessness experienced by astronauts during space missions, which could have a synergistic action on cells, increasing the risk of radiation exposure. Methodology/Principal Findings We analyzed miRNA expression profile of human peripheral blood lymphocytes (PBL) incubated for 4 and 24 h in normal gravity (1 g) and in modeled microgravity (MMG) during the repair time after irradiation with 0.2 and 2Gy of γ-rays. Our results show that MMG alters miRNA expression signature of irradiated PBL by decreasing the number of radio-responsive miRNAs. Moreover, let-7i*, miR-7, miR-7-1*, miR-27a, miR-144, miR-200a, miR-598, miR-650 are deregulated by the combined action of radiation and MMG. Integrated analyses of miRNA and mRNA expression profiles, carried out on PBL of the same donors, identified significant miRNA-mRNA anti-correlations of DDR pathway. Gene Ontology analysis reports that the biological category of “Response to DNA damage” is enriched when PBL are incubated in 1 g but not in MMG. Moreover, some anti-correlated genes of p53-pathway show a different expression level between 1 g and MMG. Functional validation assays using luciferase reporter constructs confirmed miRNA-mRNA interactions derived from target prediction analyses. Conclusions/Significance On the whole, by integrating the transcriptome and microRNome, we provide evidence that modeled microgravity can affects the DNA-damage response to IR in human PBL. PMID:22347458

Mirna biogenesis pathway is differentially regulated during adipose derived stromal/stem cell differentiation.

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Martin, E C; Qureshi, A T; Llamas, C B; Burow, M E; King, A G; Lee, O C; Dasa, V; Freitas, M A; Forsberg, J A; Elster, E A; Davis, T A; Gimble, J M

2018-02-07

Stromal/stem cell differentiation is controlled by a vast array of regulatory mechanisms. Included within these are methods of mRNA gene regulation that occur at the level of epigenetic, transcriptional, and/or posttranscriptional modifications. Current studies that evaluate the posttranscriptional regulation of mRNA demonstrate microRNAs (miRNAs) as key mediators of stem cell differentiation through the inhibition of mRNA translation. miRNA expression is enhanced during both adipogenic and osteogenic differentiation; however, the mechanism by which miRNA expression is altered during stem cell differentiation is less understood. Here we demonstrate for the first time that adipose-derived stromal/stem cells (ASCs) induced to an adipogenic or osteogenic lineage have differences in strand preference (-3p and -5p) for miRNAs originating from the same primary transcript. Furthermore, evaluation of miRNA expression in ASCs demonstrates alterations in both miRNA strand preference and 5'seed site heterogeneity. Additionally, we show that during stem cell differentiation there are alterations in expression of genes associated with the miRNA biogenesis pathway. Quantitative RT-PCR demonstrated changes in the Argonautes (AGO1-4), Drosha, and Dicer at intervals of ASC adipogenic and osteogenic differentiation compared to untreated ASCs. Specifically, we demonstrated altered expression of the AGOs occurring during both adipogenesis and osteogenesis, with osteogenesis increasing AGO1-4 expression and adipogenesis decreasing AGO1 gene and protein expression. These data demonstrate changes to components of the miRNA biogenesis pathway during stromal/stem cell differentiation. Identifying regulatory mechanisms for miRNA processing during ASC differentiation may lead to novel mechanisms for the manipulation of lineage differentiation of the ASC through the global regulation of miRNA as opposed to singular regulatory mechanisms.

Pilotless recovery of clipped OFDM signals by compressive sensing over reliable data carriers

KAUST Repository

Al-Safadi, Ebrahim B.

2012-06-01

In this paper we propose a novel method of clipping mitigation in OFDM using compressive sensing that completely avoids using reserved tones or channel-estimation pilots. The method builds on selecting the most reliable perturbations from the constellation lattice upon decoding at the receiver (in the frequency domain), and performs compressive sensing over these observations in order to completely recover the sparse nonlinear distortion in the time domain. As such, the method provides a practical solution to the problem of initial erroneous decoding decisions in iterative ML methods, and the ability to recover the distorted signal in one shot. © 2012 IEEE.

Pilotless recovery of clipped OFDM signals by compressive sensing over reliable data carriers

KAUST Repository

Al-Safadi, Ebrahim B.; Al-Naffouri, Tareq Y.

2012-01-01

In this paper we propose a novel method of clipping mitigation in OFDM using compressive sensing that completely avoids using reserved tones or channel-estimation pilots. The method builds on selecting the most reliable perturbations from the constellation lattice upon decoding at the receiver (in the frequency domain), and performs compressive sensing over these observations in order to completely recover the sparse nonlinear distortion in the time domain. As such, the method provides a practical solution to the problem of initial erroneous decoding decisions in iterative ML methods, and the ability to recover the distorted signal in one shot. © 2012 IEEE.

Isolation and Identification of miRNAs in Jatropha curcas

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Wang, Chun Ming; Liu, Peng; Sun, Fei; Li, Lei; Liu, Peng; Ye, Jian; Yue, Gen Hua

2012-01-01

MicroRNAs (miRNAs) are small noncoding RNAs that play crucial regulatory roles by targeting mRNAs for silencing. To identify miRNAs in Jatropha curcas L, a bioenergy crop, cDNA clones from two small RNA libraries of leaves and seeds were sequenced and analyzed using bioinformatic tools. Fifty-two putative miRNAs were found from the two libraries, among them six were identical to known miRNAs and 46 were novel. Differential expression patterns of 15 miRNAs in root, stem, leave, fruit and seed were detected using quantitative real-time PCR. Ten miRNAs were highly expressed in fruit or seed, implying that they may be involved in seed development or fatty acids synthesis in seed. Moreover, 28 targets of the isolated miRNAs were predicted from a jatropha cDNA library database. The miRNA target genes were predicted to encode a broad range of proteins. Sixteen targets had clear BLASTX hits to the Uniprot database and were associated with genes belonging to the three major gene ontology categories of biological process, cellular component, and molecular function. Four targets were identified for JcumiR004. By silencing JcumiR004 primary miRNA, expressions of the four target genes were up-regulated and oil composition were modulated significantly, indicating diverse functions of JcumiR004. PMID:22419887

Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.

Science.gov (United States)

Jagtap, Soham; Shivaprasad, Padubidri V

2014-12-02

Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved. We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors. Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show

Integrating microRNA and mRNA expression profiles in response to radiation-induced injury in rat lung

International Nuclear Information System (INIS)

Xie, Ling; Zhou, Jundong; Zhang, Shuyu; Chen, Qing; Lai, Rensheng; Ding, Weiqun; Song, ChuanJun; Meng, XingJun; Wu, Jinchang

2014-01-01

Exposure to radiation provokes cellular responses, which are likely regulated by gene expression networks. MicroRNAs are small non-coding RNAs, which regulate gene expression by promoting mRNA degradation or inhibiting protein translation. The expression patterns of both mRNA and miRNA during the radiation-induced lung injury (RILI) remain less characterized and the role of miRNAs in the regulation of this process has not been studied. The present study sought to evaluate miRNA and mRNA expression profiles in the rat lung after irradiation. Male Wistar rats were subjected to single dose irradiation with 20 Gy using 6 MV x-rays to the right lung. (A dose rate of 5 Gy/min was applied). Rats were sacrificed at 3, 12 and 26 weeks after irradiation, and morphological changes in the lung were examined by haematoxylin and eosin. The miRNA and mRNA expression profiles were evaluated by microarrays and followed by quantitative RT-PCR analysis. A cDNA microarray analysis found 2183 transcripts being up-regulated and 2917 transcripts down-regulated (P ≤ 0.05, ≥2.0 fold change) in the lung tissues after irradiation. Likewise, a miRNAs microarray analysis indicated 15 miRNA species being up-regulated and 8 down-regulated (P ≤ 0.05). Subsequent bioinformatics anal -yses of the differentially expressed mRNA and miRNAs revealed that alterations in mRNA expression following irradiation were negatively correlated with miRNAs expression. Our results provide evidence indicating that irradiation induces alterations of mRNA and miRNA expression in rat lung and that there is a negative correlation of mRNA and miRNA expression levels after irradiation. These findings significantly advance our understanding of the regulatory mechanisms underlying the pathophysiology of radiation-induced lung injury. In summary, RILI does not develop gradually in a linear process. In fact, different cell types interact via cytokines in a very complex network. Furthermore, this study suggests that

HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages.

Directory of Open Access Journals (Sweden)

Valentina Vongrad

Full Text Available MiRNAs and other small noncoding RNAs (sncRNAs are key players in post-transcriptional gene regulation. HIV-1 derived small noncoding RNAs (sncRNAs have been described in HIV-1 infected cells, but their biological functions still remain to be elucidated. Here, we approached the question whether viral sncRNAs may play a role in the RNA interference (RNAi pathway or whether viral mRNAs are targeted by cellular miRNAs in human monocyte derived macrophages (MDM.The incorporation of viral sncRNAs and/or their target RNAs into RNA-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP as well as high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP, which capture Argonaute2-bound miRNAs and their target RNAs. HIV-1 infected monocyte-derived macrophages (MDM were chosen as target cells, as they have previously been shown to express HIV-1 sncRNAs. In addition, we applied small RNA deep sequencing to study differential cellular miRNA expression in HIV-1 infected versus non-infected MDMs.PAR-CLIP and HITS-CLIP data demonstrated the absence of HIV-1 RNAs in Ago2-RISC, although the presence of a multitude of HIV-1 sncRNAs in HIV-1 infected MDMs was confirmed by small RNA sequencing. Small RNA sequencing revealed that 1.4% of all sncRNAs were of HIV-1 origin. However, neither HIV-1 derived sncRNAs nor putative HIV-1 target sequences incorporated into Ago2-RISC were identified suggesting that HIV-1 sncRNAs are not involved in the canonical RNAi pathway nor is HIV-1 targeted by this pathway in HIV-1 infected macrophages.

A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration

DEFF Research Database (Denmark)

Scheel, Troels K H; Luna, Joseph M; Liniger, Matthias

2016-01-01

, critically depended on the interaction of cellular miR-17 and let-7 with the viral 3' UTR. Unlike canonical miRNA interactions, miR-17 and let-7 binding enhanced pestivirus translation and RNA stability. miR-17 sequestration by pestiviruses conferred reduced AGO binding and functional de...... immunoprecipitation (CLIP) of the Argonaute (AGO) proteins to characterize strengths and specificities of miRNA interactions in the context of 15 different RNA virus infections, including several clinically relevant pathogens. Notably, replication of pestiviruses, a major threat to milk and meat industries...

Monitoring the Spatiotemporal Activities of miRNAs in Small Animal Models Using Molecular Imaging Modalities

Directory of Open Access Journals (Sweden)

Patrick Baril

2015-03-01

Full Text Available MicroRNAs (miRNAs are a class of small non-coding RNAs that regulate gene expression by binding mRNA targets via sequence complementary inducing translational repression and/or mRNA degradation. A current challenge in the field of miRNA biology is to understand the functionality of miRNAs under physiopathological conditions. Recent evidence indicates that miRNA expression is more complex than simple regulation at the transcriptional level. MiRNAs undergo complex post-transcriptional regulations such miRNA processing, editing, accumulation and re-cycling within P-bodies. They are dynamically regulated and have a well-orchestrated spatiotemporal localization pattern. Real-time and spatio-temporal analyses of miRNA expression are difficult to evaluate and often underestimated. Therefore, important information connecting miRNA expression and function can be lost. Conventional miRNA profiling methods such as Northern blot, real-time PCR, microarray, in situ hybridization and deep sequencing continue to contribute to our knowledge of miRNA biology. However, these methods can seldom shed light on the spatiotemporal organization and function of miRNAs in real-time. Non-invasive molecular imaging methods have the potential to address these issues and are thus attracting increasing attention. This paper reviews the state-of-the-art of methods used to detect miRNAs and discusses their contribution in the emerging field of miRNA biology and therapy.

Monitoring the spatiotemporal activities of miRNAs in small animal models using molecular imaging modalities.

Science.gov (United States)

Baril, Patrick; Ezzine, Safia; Pichon, Chantal

2015-03-04

MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by binding mRNA targets via sequence complementary inducing translational repression and/or mRNA degradation. A current challenge in the field of miRNA biology is to understand the functionality of miRNAs under physiopathological conditions. Recent evidence indicates that miRNA expression is more complex than simple regulation at the transcriptional level. MiRNAs undergo complex post-transcriptional regulations such miRNA processing, editing, accumulation and re-cycling within P-bodies. They are dynamically regulated and have a well-orchestrated spatiotemporal localization pattern. Real-time and spatio-temporal analyses of miRNA expression are difficult to evaluate and often underestimated. Therefore, important information connecting miRNA expression and function can be lost. Conventional miRNA profiling methods such as Northern blot, real-time PCR, microarray, in situ hybridization and deep sequencing continue to contribute to our knowledge of miRNA biology. However, these methods can seldom shed light on the spatiotemporal organization and function of miRNAs in real-time. Non-invasive molecular imaging methods have the potential to address these issues and are thus attracting increasing attention. This paper reviews the state-of-the-art of methods used to detect miRNAs and discusses their contribution in the emerging field of miRNA biology and therapy.

Roles of miRNAs in microcystin-LR-induced Sertoli cell toxicity

Energy Technology Data Exchange (ETDEWEB)

Zhou, Yuan [Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093 (China); Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093 (China); Wang, Hui [The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping SE-58185 (Sweden); Wang, Cong [Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093 (China); Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093 (China); Qiu, Xuefeng [Department of Urology, Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing 210008 (China); Benson, Mikael [The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping SE-58185 (Sweden); Yin, Xiaoqin [Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093 (China); Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093 (China); Xiang, Zou [Department of Microbiology and Immunology, Mucosal Immunobiology and Vaccine Research Center, Institute of Biomedicine, University of Gothenburg, Gothenburg (Sweden); Li, Dongmei, E-mail: lidm@nju.edu.cn [Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093 (China); Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093 (China); and others

2015-08-15

Microcystin (MC)-LR, a cyclic heptapeptide, is a potent reproductive system toxin. To understand the molecular mechanisms of MC-induced reproductive system cytotoxicity, we evaluated global changes of miRNA and mRNA expression in mouse Sertoli cells following MC-LR treatment. Our results revealed that the exposure to MC-LR resulted in an altered miRNA expression profile that might be responsible for the modulation of mRNA expression. Bio-functional analysis indicated that the altered genes were involved in specific cellular processes, including cell death and proliferation. Target gene analysis suggested that junction injury in Sertoli cells exposed to MC-LR might be mediated by miRNAs through the regulation of the Sertoli cell-Sertoli cell pathway. Collectively, these findings may enhance our understanding on the modes of action of MC-LR on mouse Sertoli cells as well as the molecular mechanisms underlying the toxicity of MC-LR on the male reproductive system. - Highlights: • miRNAs were altered in Sertoli cells exposed to MC-LR. • Alerted genes were involved in different cell functions including the cell morphology. • MC-LR adversely affected Sertoli cell junction formation through the regulating miRNAs.

Prediction of Host-Derived miRNAs with the Potential to Target PVY in Potato Plants

Science.gov (United States)

Iqbal, Muhammad S.; Hafeez, Muhammad N.; Wattoo, Javed I.; Ali, Arfan; Sharif, Muhammad N.; Rashid, Bushra; Tabassum, Bushra; Nasir, Idrees A.

2016-01-01

Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe. PVY reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in the PVY genome. The PVY genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:CI, NIa, NIb-Pro, HC-Pro, CP, and VPg. A total of 343 mature miRNAs were retrieved from the miRBase database and were examined for their target sequences in PVY genes using the minimum free energy (mfe), minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. The identified potato miRNAs against viral mRNA targets have antiviral activities, leading to translational inhibition by mRNA cleavage and/or mRNA blockage. We found 86 miRNAs targeting the PVY genome at 151 different sites. Moreover, only 36 miRNAs potentially targeted the PVY genome at 101 loci. The CI gene of the PVY genome was targeted by 32 miRNAs followed by the complementarity of 26, 19, 18, 16, and 13 miRNAs. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h, and miR5303d) that could target the CI, NIa, NIb-Pro, HC-Pro, CP, and VPg genes of PVY. The predicted miRNAs can be used for the development of PVY-resistant potato crops in the future. PMID:27683585

Dynamics of miRNA biogenesis and nuclear transport

Directory of Open Access Journals (Sweden)

Kotipalli Aneesh

2016-12-01

Full Text Available MicroRNAs (miRNAs are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS are transported back to the nucleus and some remain in the cytoplasm. The functional roles of these miRNAs are seen in both the nucleus and the cytoplasm. In the nucleus, miRNAs regulate gene expression by binding to the targeted promoter sequences and affect either the transcriptional gene silencing (TGS or transcriptional gene activation (TGA. In the cytoplasm, targeted mRNAs are translationally repressed or cleaved based on the complementarity between the two sequences at the seed region of miRNA and mRNA. The selective transport of mature miRNAs to the nucleus follows the classical nuclear import mechanism. The classical nuclear import mechanism is a highly regulated process, involving exportins and importins. The nuclear pore complex (NPC regulates all these transport events like a gate keeper. The half-life of miRNAs is rather low, so within a short time miRNAs perform their function. Temporal studies of miRNA biogenesis are, therefore, useful. We have carried out simulation studies for important miRNA biogenesis steps and also classical nuclear import mechanism using ordinary differential equation (ODE solver in the Octave software.

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.

Science.gov (United States)

Burroughs, A Maxwell; Ando, Yoshinari; de Hoon, Michiel J L; Tomaru, Yasuhiro; Nishibu, Takahiro; Ukekawa, Ryo; Funakoshi, Taku; Kurokawa, Tsutomu; Suzuki, Harukazu; Hayashizaki, Yoshihide; Daub, Carsten O

2010-10-01

Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after knockdown of nucleotidyltransferase enzymes. The PAPD4 nucleotidyltransferase adenylates a wide range of miRNA loci, but adenylation does not appear to affect miRNA stability on a genome-wide scale. Adenine addition appears to reduce effectiveness of miRNA targeting of mRNA transcripts while deep-sequencing of RNA bound to immunoprecipitated Argonaute (AGO) subfamily proteins EIF2C1-EIF2C3 revealed substantial reduction of adenine addition in miRNA associated with EIF2C2 and EIF2C3. Our findings show 3' addition events are widespread and conserved across animals, PAPD4 is a primary miRNA adenylating enzyme, and suggest a role for 3' adenine addition in modulating miRNA effectiveness, possibly through interfering with incorporation into the RNA-induced silencing complex (RISC), a regulatory role that would complement the role of miRNA uridylation in blocking DICER1 uptake.

Integrated microRNA and mRNA signatures associated with survival in triple negative breast cancer.

Science.gov (United States)

Cascione, Luciano; Gasparini, Pierluigi; Lovat, Francesca; Carasi, Stefania; Pulvirenti, Alfredo; Ferro, Alfredo; Alder, Hansjuerg; He, Gang; Vecchione, Andrea; Croce, Carlo M; Shapiro, Charles L; Huebner, Kay

2013-01-01

Triple negative breast cancer (TNBC) is a heterogeneous disease at the molecular, pathologic and clinical levels. To stratify TNBCs, we determined microRNA (miRNA) expression profiles, as well as expression profiles of a cancer-focused mRNA panel, in tumor, adjacent non-tumor (normal) and lymph node metastatic lesion (mets) tissues, from 173 women with TNBCs; we linked specific miRNA signatures to patient survival and used miRNA/mRNA anti-correlations to identify clinically and genetically different TNBC subclasses. We also assessed miRNA signatures as potential regulators of TNBC subclass-specific gene expression networks defined by expression of canonical signal pathways.Tissue specific miRNAs and mRNAs were identified for normal vs tumor vs mets comparisons. miRNA signatures correlated with prognosis were identified and predicted anti-correlated targets within the mRNA profile were defined. Two miRNA signatures (miR-16, 155, 125b, 374a and miR-16, 125b, 374a, 374b, 421, 655, 497) predictive of overall survival (P = 0.05) and distant-disease free survival (P = 0.009), respectively, were identified for patients 50 yrs of age or younger. By multivariate analysis the risk signatures were independent predictors for overall survival and distant-disease free survival. mRNA expression profiling, using the cancer-focused mRNA panel, resulted in clustering of TNBCs into 4 molecular subclasses with different expression signatures anti-correlated with the prognostic miRNAs. Our findings suggest that miRNAs play a key role in triple negative breast cancer through their ability to regulate fundamental pathways such as: cellular growth and proliferation, cellular movement and migration, Extra Cellular Matrix degradation. The results define miRNA expression signatures that characterize and contribute to the phenotypic diversity of TNBC and its metastasis.

DNA methyltransferase 1-targeting miRNA-148aof dairymilk: apotential bioactive modifier of thehumanepigenome

Directory of Open Access Journals (Sweden)

Bodo C. Melnik

2017-09-01

Full Text Available Background: The perception of milk has changed from a “simple food” to a more sophisticated bioactive functional signaling system that promotes mTORC1-driven postnatal anabolism, growth, and development of the newborn infant. Accumulating evidence supports the view that milk´s miRNAs significantly contribute to these processes. The most abundant miRNA of milk found in milk fat and milk exosomes is miRNA-148a, which targets DNA methyltransferase 1 (DNMT1, a pivotal epigenetic regulator that suppresses transcription. Furthermore, milk-derived miRNA-125b, miRNA-30d, and miRNA-25 target TP53, the guardian of the genome that interacts with DNMT1 and regulates metabolism, cell kinetics, and apoptosis. Thus, the question arose whether cow´s milk-derived miRNAs may modify epigenetic regulation of the human milk consumer. Methods: To understand the potential impact of dairy milk consumption on human epigenetics, we have analyzed all relevant research-based bioinformatics data related to milk, milk miRNAs, epigenetic regulation, and lactation performance with special attention to bovine miRNAs that modify gene expression of DNA methyltransferase 1 (DNMT1 and p53 (TP53, the two guardians of the mammalian genome. By means of translational research and comparative functional genomics, we investigated the potential impact of cow´s milk miRNAs on epigenetic regulation of human DNMT1, TP53, FOXP3, and FTO, which are critically involved in immunologic and metabolic programming respectively. miRNA sequences have been obtained from mirbase.org. miRNA-target site prediction has been performed using TargetScan release 7.0. Results: The most abundant miRNA of cow´s milk is miRNA-148a, which represents more than 10% of all miRNAs of cow´s milk, survives pasteurization and refrigerated storage. The seed sequence of human and bovine miRNA-148a-3p is identical. Furthermore, human and bovine DNMT1 mRNA share 88% identity. The miRNA-148a 7mer seed is conserved in

The effect of tRNA levels on decoding times of mRNA codons.

Science.gov (United States)

Dana, Alexandra; Tuller, Tamir

2014-08-01

The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (-0.38 to -0.66, all P values decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Computational tools for genome-wide miRNA prediction and study

KAUST Repository

Malas, T.B.

2012-11-02

MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targets and functions. However, miRNAs are very difficult to clone in the lab and this has hindered the identification of novel miRNAs. Next-generation sequencing coupled with new computational tools has recently evolved to help researchers efficiently identify large numbers of novel miRNAs. In this review, we describe recent miRNA prediction tools and discuss their priorities, advantages and disadvantages. Malas and Ravasi.

Computational tools for genome-wide miRNA prediction and study

KAUST Repository

Malas, T.B.; Ravasi, Timothy

2012-01-01

MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targets and functions. However, miRNAs are very difficult to clone in the lab and this has hindered the identification of novel miRNAs. Next-generation sequencing coupled with new computational tools has recently evolved to help researchers efficiently identify large numbers of novel miRNAs. In this review, we describe recent miRNA prediction tools and discuss their priorities, advantages and disadvantages. Malas and Ravasi.

Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers.

Science.gov (United States)

Sijen, Titia

2015-09-01

Human biological traces have the potential to present strong evidence for placing a suspect at a crime scene. In cases, the activity that led to deposition of an individual's cellular material is increasingly disputed, for which the identification of cell types could be crucial. This review aims to give an overview of the possibilities of the employment of mRNA, miRNA, DNA methylation and microbial markers for tissue identification in a forensic context. The biological background that renders these markers tissue-specificity is considered, as this can affect data interpretation. Furthermore, the forensic relevance of inferring certain cell types is discussed, as are the various methodologies that can be applied. Forensic stains can carry minute amounts of cell material that may be degraded or polluted and most likely cell material of multiple sources will be present. The interpretational challenges that are imposed by this compromised state will be discussed as well. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

MIRNA-DISTILLER: a stand-alone application to compile microRNA data from databases

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Jessica K. Rieger

2011-07-01

Full Text Available MicroRNAs (miRNA are small non-coding RNA molecules of ~22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3’-UTR of target gene transcripts. The target mRNA is then usually degraded or translation is inhibited, although thus resulting in posttranscriptional down regulation of gene expression at the mRNA and/or protein level. Due to the bioinformatic difficulties in predicting functional miRNA binding sites, several publically available databases have been developed that predict miRNA binding sites based on different algorithms. The parallel use of different databases is currently indispensable, but highly uncomfortable and time consuming, especially when working with numerous genes of interest. We have therefore developed a new stand-alone program, termed MIRNA-DISTILLER, which allows to compile miRNA data for given target genes from public databases. Currently implemented are TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available at http://www.ikp-stuttgart.de/content/language1/html/10415.asp

MIRNA-DISTILLER: A Stand-Alone Application to Compile microRNA Data from Databases.

Science.gov (United States)

Rieger, Jessica K; Bodan, Denis A; Zanger, Ulrich M

2011-01-01

MicroRNAs (miRNA) are small non-coding RNA molecules of ∼22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3'-untranslated region of target gene transcripts. The target mRNA is then usually degraded or translation is inhibited, although thus resulting in posttranscriptional down regulation of gene expression at the mRNA and/or protein level. Due to the bioinformatic difficulties in predicting functional miRNA binding sites, several publically available databases have been developed that predict miRNA binding sites based on different algorithms. The parallel use of different databases is currently indispensable, but highly uncomfortable and time consuming, especially when working with numerous genes of interest. We have therefore developed a new stand-alone program, termed MIRNA-DISTILLER, which allows to compile miRNA data for given target genes from public databases. Currently implemented are TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available at http://www.ikp-stuttgart.de/content/language1/html/10415.asp.

How Major Depressive Disorder affects the ability to decode multimodal dynamic emotional stimuli

Directory of Open Access Journals (Sweden)

FILOMENA SCIBELLI

2016-09-01

Full Text Available Most studies investigating the processing of emotions in depressed patients reported impairments in the decoding of negative emotions. However, these studies adopted static stimuli (mostly stereotypical facial expressions corresponding to basic emotions which do not reflect the way people experience emotions in everyday life. For this reason, this work proposes to investigate the decoding of emotional expressions in patients affected by Recurrent Major Depressive Disorder (RMDDs using dynamic audio/video stimuli. RMDDs’ performance is compared with the performance of patients with Adjustment Disorder with Depressed Mood (ADs and healthy (HCs subjects. The experiments involve 27 RMDDs (16 with acute depression - RMDD-A, and 11 in a compensation phase - RMDD-C, 16 ADs and 16 HCs. The ability to decode emotional expressions is assessed through an emotion recognition task based on short audio (without video, video (without audio and audio/video clips. The results show that AD patients are significantly less accurate than HCs in decoding fear, anger, happiness, surprise and sadness. RMDD-As with acute depression are significantly less accurate than HCs in decoding happiness, sadness and surprise. Finally, no significant differences were found between HCs and RMDD-Cs in a compensation phase. The different communication channels and the types of emotion play a significant role in limiting the decoding accuracy.

Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

NARCIS (Netherlands)

Farazi, Thalia A.; ten Hoeve, Jelle J.; Brown, Miguel; Mihailovic, Aleksandra; Horlings, Hugo M.; van de Vijver, Marc J.; Tuschl, Thomas; Wessels, Lodewyk F. A.

2014-01-01

Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to

Therapeutic modulation of miRNA for the treatment of proinflammatory lung diseases.

LENUS (Irish Health Repository)

Hassan, Tidi

2012-03-01

miRNAs are short, nonprotein coding RNAs that regulate target gene expression principally by causing translational repression and\\/or mRNA degradation. miRNAs are involved in most mammalian biological processes and have pivotal roles in controlling the expression of factors involved in basal and stimulus-induced signaling pathways. Considering their central role in the regulation of gene expression, miRNAs represent therapeutic drug targets. Here we describe how miRNAs are involved in the regulation of aspects of innate immunity and inflammation, what happens when this goes awry, such as in the chronic inflammatory lung diseases cystic fibrosis and asthma, and discuss the current state-of-the-art miRNA-targeted therapeutics.

Different miRNA signatures of oral and pharyngeal squamous cell carcinomas: a prospective translational study

DEFF Research Database (Denmark)

Lajer, C B; Nielsen, F C; Friis-Hansen, L

2011-01-01

MicroRNAs (miRNAs) are small non-coding RNAs, which regulate mRNA translation/decay, and may serve as biomarkers. We characterised the expression of miRNAs in clinically sampled oral and pharyngeal squamous cell carcinoma (OSCC and PSCC) and described the influence of human papilloma virus (HPV)....

A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness

Science.gov (United States)

Burroughs, A. Maxwell; Ando, Yoshinari; de Hoon, Michiel J.L.; Tomaru, Yasuhiro; Nishibu, Takahiro; Ukekawa, Ryo; Funakoshi, Taku; Kurokawa, Tsutomu; Suzuki, Harukazu; Hayashizaki, Yoshihide; Daub, Carsten O.

2010-01-01

Animal microRNA sequences are subject to 3′ nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3′ adenylation function, we deep-sequenced RNA after knockdown of nucleotidyltransferase enzymes. The PAPD4 nucleotidyltransferase adenylates a wide range of miRNA loci, but adenylation does not appear to affect miRNA stability on a genome-wide scale. Adenine addition appears to reduce effectiveness of miRNA targeting of mRNA transcripts while deep-sequencing of RNA bound to immunoprecipitated Argonaute (AGO) subfamily proteins EIF2C1–EIF2C3 revealed substantial reduction of adenine addition in miRNA associated with EIF2C2 and EIF2C3. Our findings show 3′ addition events are widespread and conserved across animals, PAPD4 is a primary miRNA adenylating enzyme, and suggest a role for 3′ adenine addition in modulating miRNA effectiveness, possibly through interfering with incorporation into the RNA-induced silencing complex (RISC), a regulatory role that would complement the role of miRNA uridylation in blocking DICER1 uptake. PMID:20719920

Prediction of host-derived miRNAs with the potential to target PVY in potato plants

Directory of Open Access Journals (Sweden)

Muhammad Shahzad Iqbal

2016-09-01

Full Text Available Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe PVY reduces the yield and quality of potato cultivars. During last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in PVY genome. PVY genome is about 9 thousand nucleotides approximately which transcribes 6 genes CI, NIa, NIb-Pro, HC-Pro, CP and VPg. A total of 343 mature miRNAs were retrieved from miRbase database and searched for their target sequences in PVY genes using minimum free energy (mfe, minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. Identified Potato miRNAs against viral mRNA targets have antiviral activities leading to either translational inhibition by mRNA cleavage/mRNA blockage or both. We have found 86 miRNAs targeting PVY genome at 151 different sites on PVY genome. Moreover, only 36 miRNA potentially targeted the PVY genome at 101 loci. CI gene of PVY genome was targeted by 32 miRNAs followed by complementarity by 26, 19, 18, 16 and 13 miRNAs respectively. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h and miR5303d could target CI, NIa, NIb-Pro, HC-Pro, CP and VPg genes of PVY. The predicted miRNAs can be used for development of PVY resistant potato crops in future.

Integrative Analysis of miRNA and mRNA Profiles in Response to Ethylene in Rose Petals during Flower Opening

Science.gov (United States)

Pei, Haixia; Ma, Nan; Chen, Jiwei; Zheng, Yi; Tian, Ji; Li, Jing; Zhang, Shuai; Fei, Zhangjun; Gao, Junping

2013-01-01

MicroRNAs play an important role in plant development and plant responses to various biotic and abiotic stimuli. As one of the most important ornamental crops, rose (Rosa hybrida) possesses several specific morphological and physiological features, including recurrent flowering, highly divergent flower shapes, colors and volatiles. Ethylene plays an important role in regulating petal cell expansion during rose flower opening. Here, we report the population and expression profiles of miRNAs in rose petals during flower opening and in response to ethylene based on high throughput sequencing. We identified a total of 33 conserved miRNAs, as well as 47 putative novel miRNAs were identified from rose petals. The conserved and novel targets to those miRNAs were predicted using the rose floral transcriptome database. Expression profiling revealed that expression of 28 known (84.8% of known miRNAs) and 39 novel (83.0% of novel miRNAs) miRNAs was substantially changed in rose petals during the earlier opening period. We also found that 28 known and 22 novel miRNAs showed expression changes in response to ethylene treatment. Furthermore, we performed integrative analysis of expression profiles of miRNAs and their targets. We found that ethylene-caused expression changes of five miRNAs (miR156, miR164, miR166, miR5139 and rhy-miRC1) were inversely correlated to those of their seven target genes. These results indicate that these miRNA/target modules might be regulated by ethylene and were involved in ethylene-regulated petal growth. PMID:23696879

Post-Vacuum-Assisted Stereotactic Core Biopsy Clip Displacement: A Comparison Between Commercially Available Clips and Surgical Clip.

Science.gov (United States)

Yen, Peggy; Dumas, Sandra; Albert, Arianne; Gordon, Paula

2018-02-01

The placement of localization clips following percutaneous biopsy is a standard practice for a variety of situations. Subsequent clip displacement creates challenges for imaging surveillance and surgical planning, and may cause confusion amongst radiologists and between surgeons and radiologists. Many causes have been attributed for this phenomenon including the commonly accepted "accordion effect." Herein, we investigate the performance of a low cost surgical clip system against 4 commercially available clips. We retrospectively reviewed 2112 patients who underwent stereotactic vacuum-assisted core biopsy followed by clip placement between January 2013 and June 2016. The primary performance parameter compared was displacement >10 mm following vacuum-assisted stereotactic core biopsy. Within the group of clips that had displaced, the magnitude of displacement was compared. There was a significant difference in displacement among the clip types (P < .0001) with significant pairwise comparisons between pediatric surgical clips and SecureMark (38% vs 28%; P = .001) and SenoMark (38% vs 27%; P = .0001) in the proportion displaced. The surgical clips showed a significant magnitude of displacement of approximately 25% greater average distance displaced. As a whole, the commercial clips performed better than the surgical clip after stereotactic vacuum-assisted core biopsy suggesting the surrounding outer component acts to anchor the central clip and minimizes clip displacement. The same should apply to tomosynthesis-guided biopsy. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Simultaneous visualization of the subfemtomolar expression of microRNA and microRNA target gene using HILO microscopy† †Electronic supplementary information (ESI) available: The LED device for the sample photobleaching, a schematic presentation of HILO microscopy, fluorescence spectra and hybridization curves of the molecular beacons, the linear correlation between the miRNA fluorescence intensity and the miRNA copy number, a validation of the miRNA adsorption and miRNA target gene expression via RT-qPCR, a validation of RT-qPCR using capillary electrophoresis, the reproducibility of RT-qPCR and Poisson distribution of the miRNA pipetting as well as a complete list of the oligonucleotides used in this study. See DOI: 10.1039/c7sc02701j Click here for additional data file.

Science.gov (United States)

Lin, Yi-Zhen; Ou, Da-Liang; Chang, Hsin-Yuan; Lin, Wei-Yu; Hsu, Chiun

2017-01-01

The family of microRNAs (miRNAs) not only plays an important role in gene regulation but is also useful for the diagnosis of diseases. A reliable method with high sensitivity may allow researchers to detect slight fluctuations in ultra-trace amounts of miRNA. In this study, we propose a sensitive imaging method for the direct probing of miR-10b (miR-10b-3p, also called miR-10b*) and its target (HOXD10 mRNA) in fixed cells based on the specific recognition of molecular beacons combined with highly inclined and laminated optical sheet (HILO) fluorescence microscopy. The designed dye-quencher-labelled molecular beacons offer excellent efficiencies of fluorescence resonance energy transfer that allow us to detect miRNA and the target mRNA simultaneously in hepatocellular carcinoma cells using HILO fluorescence microscopy. Not only can the basal trace amount of miRNA be observed in each individual cell, but the obtained images also indicate that this method is useful for monitoring the fluctuations in ultra-trace amounts of miRNA when the cells are transfected with a miRNA precursor or a miRNA inhibitor (anti-miR). Furthermore, a reasonable causal relation between the miR-10b and HOXD10 expression levels was observed in miR-10b* precursor-transfected cells and miR-10b* inhibitor-transfected cells. The trends of the miRNA alterations obtained using HILO microscopy completely matched the RT-qPCR data and showed remarkable reproducibility (the coefficient of variation [CV] = 0.86%) and sensitivity (<1.0 fM). This proposed imaging method appears to be useful for the simultaneous visualisation of ultra-trace amounts of miRNA and target mRNA and excludes the procedures for RNA extraction and amplification. Therefore, the visualisation of miRNA and the target mRNA should facilitate the exploration of the functions of ultra-trace amounts of miRNA in fixed cells in biological studies and may serve as a powerful tool for diagnoses based on circulating cancer cells. PMID:28989695

Identification of miRNAs associated with recurrence of stage II colorectal cancer

DEFF Research Database (Denmark)

Christensen, Lise Lotte; Tobiasen, Heidi; Schepeler, Troels

2011-01-01

Colorectal cancer (CRC) is one of the leading causes of cancer deaths. Twenty-five percent of the patients radically treated for a stage II CRC (no lymph node or distant metastasis) later develop recurrence and dies from the disease. MicroRNAs (miRNAs) are aberrantly expressed or mutated in human...... target prediction and transcript profiling. Initially, miRNA over-expression in HCT116 cells was followed by transcriptional profiling of transfected cells using GeneChip Human Exon 1.0 ST Arrays. Three in silico predicted miRNA targets showing differential mRNA expression upon miRNA up-regulation were...... cancers, and function either as tumour suppressors or oncogenes. Additionally, they also appear to have both diagnostic and prognostic significance. The aim of the present study was to identify miRNAs associated with recurrence of stage II CRC, followed up by an investigation of how these potential...

Sensing miRNA: Signal Amplification by Cognate RISC for Intracellular Detection of miRNA in Live Cells.

Science.gov (United States)

Kavishwar, Amol; Medarova, Zdravka

2016-01-01

The ability to detect miRNA expression in live cells would leave these cells available for further manipulation or culture. Here, we describe the design of a miRNA sensor oligonucleotide whose sequence mimics the target mRNA. The sensor has a fluorescent label on one end of the oligo and a quencher on the other. When inside the cell, the sensor is recognized by its cognate miRNA-RISC and gets cleaved, setting the fluorophore free from its quencher. This results in fluorescence "turn on." Since cleavage by the RISC complex is an enzymatic process, the described approach has a very high level of sensitivity (nM). The rate of nonspecific cleavage of the sensor is very slow permitting the collection of meaningful signal over a long period of time.

miRNAs in human subcutaneous adipose tissue: Effects of weight loss induced by hypocaloric diet and exercise.

Science.gov (United States)

Kristensen, Malene M; Davidsen, Peter K; Vigelsø, Andreas; Hansen, Christina N; Jensen, Lars J; Jessen, Niels; Bruun, Jens M; Dela, Flemming; Helge, Jørn W

2017-03-01

Obesity is central in the development of insulin resistance. However, the underlying mechanisms still need elucidation. Dysregulated microRNAs (miRNAs; post-transcriptional regulators) in adipose tissue may present an important link. The miRNA expression in subcutaneous adipose tissue from 19 individuals with severe obesity (10 women and 9 men) before and after a 15-week weight loss intervention was studied using genome-wide microarray analysis. The microarray results were validated with RT-qPCR, and pathway enrichment analysis of in silico predicted targets was performed to elucidate the biological consequences of the miRNA dysregulation. Lastly, the messenger RNA (mRNA) and/or protein expression of multiple predicted targets as well as several proteins involved in lipolysis were investigated. The intervention led to upregulation of miR-29a-3p and miR-29a-5p and downregulation of miR-20b-5p. The mRNA and protein expression of predicted targets was not significantly affected by the intervention. However, negative correlations between miR-20b-5p and the protein levels of its predicted target, acyl-CoA synthetase long-chain family member 1, were observed. Several other miRNA-target relationships correlated negatively, indicating possible miRNA regulation, including miR-29a-3p and lipoprotein lipase mRNA levels. Proteins involved in lipolysis were not affected by the intervention. Weight loss influenced several miRNAs, some of which were negatively correlated with predicted targets. These dysregulated miRNAs may affect adipocytokine signaling and forkhead box protein O signaling. © 2017 The Obesity Society.

DeepMirTar: a deep-learning approach for predicting human miRNA targets.

Science.gov (United States)

Wen, Ming; Cong, Peisheng; Zhang, Zhimin; Lu, Hongmei; Li, Tonghua

2018-06-01

MicroRNAs (miRNAs) are small noncoding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates. In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed, and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance. DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA. lith@tongji.edu.cn, hongmeilu@csu.edu.cn. Supplementary data are available at Bioinformatics online.

Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.

Directory of Open Access Journals (Sweden)

Gabriela Moura

Full Text Available BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.

Targeting miRNAs by polyphenols: Novel therapeutic strategy for cancer.

Science.gov (United States)

Pandima Devi, Kasi; Rajavel, Tamilselvam; Daglia, Maria; Nabavi, Seyed Fazel; Bishayee, Anupam; Nabavi, Seyed Mohammad

2017-10-01

In the recent years, polyphenols have gained significant attention in scientific community owing to their potential anticancer effects against a wide range of human malignancies. Epidemiological, clinical and preclinical studies have supported that daily intake of polyphenol-rich dietary fruits have a strong co-relationship in the prevention of different types of cancer. In addition to direct antioxidant mechanisms, they also regulate several therapeutically important oncogenic signaling and transcription factors. However, after the discovery of microRNA (miRNA), numerous studies have identified that polyphenols, including epigallocatechin-3-gallate, genistein, resveratrol and curcumin exert their anticancer effects by regulating different miRNAs which are implicated in all the stages of cancer. MiRNAs are short, non-coding endogenous RNA, which silence the gene functions by targeting messenger RNA (mRNA) through degradation or translation repression. However, cancer associated miRNAs has emerged only in recent years to support its applications in cancer therapy. Preclinical experiments have suggested that deregulation of single miRNA is sufficient for neoplastic transformation of cells. Indeed, the widespread deregulation of several miRNA profiles of tumor and healthy tissue samples revealed the involvement of many types of miRNA in the development of numerous cancers. Hence, targeting the miRNAs using polyphenols will be a novel and promising strategy in anticancer chemotherapy. Herein, we have critically reviewed the potential applications of polyphenols on various human miRNAs, especially which are involved in oncogenic and tumor suppressor pathways. Copyright © 2017 Elsevier Ltd. All rights reserved.

Differentially expressed miRNAs after GnRH treatment and their potential roles in FSH regulation in porcine anterior pituitary cell.

Directory of Open Access Journals (Sweden)

Rui-Song Ye

Full Text Available Hypothalamic gonadotropin-releasing hormone (GnRH is a major regulator of follicle-stimulating hormone (FSH secretion in gonadotrope cell in the anterior pituitary gland. microRNAs (miRNAs are small RNA molecules that control gene expression by imperfect binding to the 3'-untranslated region (3'-UTR of mRNA at the post-transcriptional level. It has been proven that miRNAs play an important role in hormone response and/or regulation. However, little is known about miRNAs in the regulation of FSH secretion. In this study, primary anterior pituitary cells were treated with 100 nM GnRH. The supernatant of pituitary cell was collected for FSH determination by enzyme-linked immunosorbent assay (ELISA at 3 hours and 6 hours post GnRH treatment respectively. Results revealed that GnRH significantly promoted FSH secretion at 3 h and 6 h post-treatment by 1.40-fold and 1.80-fold, respectively. FSHβ mRNA at 6 h post GnRH treatment significantly increased by 1.60-fold. At 6 hours, cells were collected for miRNA expression profile analysis using MiRCURY LNA Array and quantitative PCR (qPCR. Consequently, 21 up-regulated and 10 down-regulated miRNAs were identified, and qPCR verification of 10 randomly selected miRNAs showed a strong correlation with microarray results. Chromosome location analysis indicated that 8 miRNAs were mapped to chromosome 12 and 4 miRNAs to chromosome X. Target and pathway analysis showed that some miRNAs may be associated with GnRH regulation pathways. In addition, In-depth analysis indicated that 10 up-regulated and 3 down-regulated miRNAs probably target FSHβ mRNA 3'-UTR directly, including miR-361-3p, a highly conserved X-linked miRNA. Most importantly, functional experimental results showed that miR-361-3p was involved in FSH secretion regulation, and up-regulated miR-361-3p expression inhibited FSH secretion, while down-regulated miR-361-3p expression promoted FSH secretion in pig pituitary cell model. These differentially

Elsevier Trophoblast Research Award Lecture: origin, evolution and future of placenta miRNAs.

Science.gov (United States)

Morales-Prieto, D M; Ospina-Prieto, S; Schmidt, A; Chaiwangyen, W; Markert, U R

2014-02-01

MicroRNAs (miRNAs) regulate the expression of a large number of genes in plants and animals. Placental miRNAs appeared late in evolution and can be found only in mammals. Nevertheless, these miRNAs are constantly under evolutionary pressure. As a consequence, miRNA sequences and their mRNA targets may differ between species, and some miRNAs can only be found in humans. Their expression can be tissue- or cell-specific and can vary time-dependently. Human placenta tissue exhibits a specific miRNA expression pattern that dynamically changes during pregnancy and is reflected in the maternal plasma. Some placental miRNAs are involved in or associated with major pregnancy disorders, such as preeclampsia, intrauterine growth restriction or preterm delivery and, therefore, have a strong potential for usage as sensitive and specific biomarkers. In this review we summarize current knowledge on the origin of placental miRNAs, their expression in humans with special regard to trophoblast cells, interspecies differences, and their future as biomarkers. It can be concluded that animal models for human reproduction have a different panel of miRNAs and targets, and can only partly reflect or predict the situation in humans. Copyright © 2013. Published by Elsevier Ltd.

Exploring the miRNA regulatory network using evolutionary correlations.

Directory of Open Access Journals (Sweden)

Benedikt Obermayer

2014-10-01

Full Text Available Post-transcriptional regulation by miRNAs is a widespread and highly conserved phenomenon in metazoans, with several hundreds to thousands of conserved binding sites for each miRNA, and up to two thirds of all genes under miRNA regulation. At the same time, the effect of miRNA regulation on mRNA and protein levels is usually quite modest and associated phenotypes are often weak or subtle. This has given rise to the notion that the highly interconnected miRNA regulatory network exerts its function less through any individual link and more via collective effects that lead to a functional interdependence of network links. We present a Bayesian framework to quantify conservation of miRNA target sites using vertebrate whole-genome alignments. The increased statistical power of our phylogenetic model allows detection of evolutionary correlation in the conservation patterns of site pairs. Such correlations could result from collective functions in the regulatory network. For instance, co-conservation of target site pairs supports a selective benefit of combinatorial regulation by multiple miRNAs. We find that some miRNA families are under pronounced co-targeting constraints, indicating a high connectivity in the regulatory network, while others appear to function in a more isolated way. By analyzing coordinated targeting of different curated gene sets, we observe distinct evolutionary signatures for protein complexes and signaling pathways that could reflect differences in control strategies. Our method is easily scalable to analyze upcoming larger data sets, and readily adaptable to detect high-level selective constraints between other genomic loci. We thus provide a proof-of-principle method to understand regulatory networks from an evolutionary perspective.

Changes in apoptotic microRNA and mRNA expression profiling in Caenorhabditis elegans during the Shenzhou-8 mission

International Nuclear Information System (INIS)

Gao Ying; Li Shuai; Xu Dan; Wang Junjun; Sun Yeqing

2015-01-01

Radiation and microgravity exposure have been proven to induce abnormal apoptosis in microRNA (miRNA) and mRNA expression, but whether space conditions, including radiation and microgravity, activate miRNAs to regulate the apoptosis is undetermined. For that purpose, we investigated miRNome and mRNA expression in the ced-1 Caenorhabditis elegans mutant vs the wild-type, both of which underwent spaceflight, spaceflight 1g-centrifuge control and ground control conditions during the Shenzhou-8 mission. Results showed that no morphological changes in the worms were detected, but differential miRNA expression increased from 43 (ground control condition) to 57 and 91 in spaceflight and spaceflight control conditions, respectively. Microgravity altered miRNA expression profiling by decreasing the number and significance of differentially expressed miRNA compared with 1 g incubation during spaceflight. Alterations in the miRNAs were involved in alterations in apoptosis, neurogenesis larval development, ATP metabolism and GTPase-mediated signal transduction. Among these, 17 altered miRNAs potentially involved in apoptosis were screened and showed obviously different expression signatures between space conditions. By integrated analysis of miRNA and mRNA, miR-797 and miR-81 may be involved in apoptosis by targeting the genes ced-10 and both drp-1 and hsp-1, respectively. Compared with ground condition, space conditions regulated apoptosis though a different manner on transcription, by altering expression of seven core apoptotic genes in spaceflight condition, and eight in spaceflight control condition. Results indicate that, miRNA of Caenorhabditis elegans probably regulates apoptotic gene expression in response to space environmental stress, and shows different behavior under microgravity condition compared with 1 g condition in the presence of space radiation. (author)

In silico profiling of miRNAs and their target polymorphisms in ...

African Journals Online (AJOL)

C. George Priya Doss

2013-02-20

Feb 20, 2013 ... breast, and colorectal, and altered patterns of miRNA expres- sion may ... World Wide Web to predict miRNA-target mRNA sites; how- ever, it is ..... RB, SJST, and SKR were involved in design, acquisition of data, analysis and ...

microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein.

Science.gov (United States)

Pinder, Benjamin D; Smibert, Craig A

2013-01-01

Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.

miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif.

Science.gov (United States)

Goldie, Belinda J; Fitzsimmons, Chantel; Weidenhofer, Judith; Atkins, Joshua R; Wang, Dan O; Cairns, Murray J

2017-01-01

While the cytoplasmic function of microRNA (miRNA) as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons.

An integrated computational validation approach for potential novel miRNA prediction

Directory of Open Access Journals (Sweden)

Pooja Viswam

2017-12-01

Full Text Available MicroRNAs (miRNAs are short, non-coding RNAs between 17bp-24bp length that regulate gene expression by targeting mRNA molecules. The regulatory functions of miRNAs are known to be majorly associated with disease phenotypes such as cancer, cell signaling, cell division, growth and other metabolisms. Novel miRNAs are defined as sequences which does not have any similarity with the existing known sequences and void of any experimental evidences. In recent decades, the advent of next-generation sequencing allows us to capture the small RNA molecules form the cells and developing methods to estimate their expression levels. Several computational algorithms are available to predict the novel miRNAs from the deep sequencing data. In this work, we integrated three novel miRNA prediction programs miRDeep, miRanalyzer and miRPRo to compare and validate their prediction efficiency. The dicer cleavage sites, alignment density, seed conservation, minimum free energy, AU-GC percentage, secondary loop scores, false discovery rates and confidence scores will be considered for comparison and evaluation. Efficiency to identify isomiRs and base pair mismatches in a strand specific manner will also be considered for the computational validation. Further, the criteria and parameters for the identification of the best possible novel miRNA with minimal false positive rates were deduced.

Plant and Animal microRNAs (miRNAs) and Their Potential for Inter-kingdom Communication.

Science.gov (United States)

Zhao, Yuhai; Cong, Lin; Lukiw, Walter J

2018-01-01

microRNAs (miRNAs) comprise a class of ~18-25 nucleotide (nt) single-stranded non-coding RNAs (sncRNAs) that are the smallest known carriers of gene-encoded, post-transcriptional regulatory information in both plants and animals. There are many fundamental similarities between plant and animal miRNAs-the miRNAs of both kingdoms play essential roles in development, aging and disease, and the shaping of the transcriptome of many cell types. Both plant and animal miRNAs appear to predominantly exert their genetic and transcriptomic influences by regulating gene expression at the level of messenger RNA (mRNA) stability and/or translational inhibition. Certain miRNA species, such as miRNA-155, miRNA-168, and members of the miRNA-854 family may be expressed in both plants and animals, suggesting a common origin and functional selection of specific miRNAs over vast periods of evolution (for example, Arabidopsis thaliana-Homo sapiens divergence ~1.5 billion years). Although there is emerging evidence for cross-kingdom miRNA communication-that plant-enriched miRNAs may enter the diet and play physiological and/or pathophysiological roles in human health and disease-some research reports repudiate this possibility. This research paper highlights some recent, controversial, and remarkable findings in plant- and animal-based miRNA signaling research with emphasis on the intriguing possibility that dietary miRNAs and/or sncRNAs may have potential to contribute to both intra- and inter-kingdom signaling, and in doing so modulate molecular-genetic mechanisms associated with human health and disease.

MiR-200a is involved in rat epididymal development by targeting β-catenin mRNA

Institute of Scientific and Technical Information of China (English)

Xiaojiang Wu; Botao Zhao; Wei Li; Yue Chen; Ruqiang Liang; Lin Li; Youxin Jin; Kangcheng Ruan

2012-01-01

The expression of 350 microRNAs (miRNAs) in epididymis of rat from postnatal development to adult (from postnatal days 7-70) was profiled with home-made miRNA microarray.Among them,48 miRNAs changed significantly, in which the expression of miR-200a increased obviously with time,in a good agreement with that obtained from northern blot analysis.The real-time quantitative-polymerase chain reaction result indicated that temporal expression of rat β-catenin was exactly inversed to that of miR-200a during rat epididymal development,implying that miR-200a might also target β-catenin mRNA in rat epididymis as reported by Saydam et al.in humans.The bioinformatic analysis indicated that 3' untranslated region of rat β-catenin mRNA did contain a putative binding site for miR-200a.Meanwhile,it was found that the sequence of this binding site was different from that of human β-catenin mRNA with a deletion of two adjacent nucleotides (U and C).But the results of luciferase targeting assay in HEK 293T cells and the overexpression of miR-200a in rat NRK cells demonstrated that miR-200a did target rat β-catenin mRNA and cause the suppression of its expression.All these results show that miR-200a should be involved in rat epididymal development by targeting β-catenin mRNA of rat and suppressing its expression.

miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif

Directory of Open Access Journals (Sweden)

Belinda J. Goldie

2017-08-01

Full Text Available While the cytoplasmic function of microRNA (miRNA as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons.

Predicting human miRNA target genes using a novel evolutionary methodology

KAUST Repository

Aigli, Korfiati; Kleftogiannis, Dimitrios A.; Konstantinos, Theofilatos; Spiros, Likothanassis; Athanasios, Tsakalidis; Seferina, Mavroudi

2012-01-01

The discovery of miRNAs had great impacts on traditional biology. Typically, miRNAs have the potential to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. The experimental identification of their targets has many drawbacks including cost, time and low specificity and these are the reasons why many computational approaches have been developed so far. However, existing computational approaches do not include any advanced feature selection technique and they are facing problems concerning their classification performance and their interpretability. In the present paper, we propose a novel hybrid methodology which combines genetic algorithms and support vector machines in order to locate the optimal feature subset while achieving high classification performance. The proposed methodology was compared with two of the most promising existing methodologies in the problem of predicting human miRNA targets. Our approach outperforms existing methodologies in terms of classification performances while selecting a much smaller feature subset. © 2012 Springer-Verlag.

Predicting human miRNA target genes using a novel evolutionary methodology

KAUST Repository

Aigli, Korfiati

2012-01-01

The discovery of miRNAs had great impacts on traditional biology. Typically, miRNAs have the potential to bind to the 3\\'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. The experimental identification of their targets has many drawbacks including cost, time and low specificity and these are the reasons why many computational approaches have been developed so far. However, existing computational approaches do not include any advanced feature selection technique and they are facing problems concerning their classification performance and their interpretability. In the present paper, we propose a novel hybrid methodology which combines genetic algorithms and support vector machines in order to locate the optimal feature subset while achieving high classification performance. The proposed methodology was compared with two of the most promising existing methodologies in the problem of predicting human miRNA targets. Our approach outperforms existing methodologies in terms of classification performances while selecting a much smaller feature subset. © 2012 Springer-Verlag.

Imaging translation dynamics of single mRNA molecules in live cells

NARCIS (Netherlands)

Ruijtenberg, Suzan; Hoek, Tim A.; Yan, Xiaowei; Tanenbaum, Marvin E.

2018-01-01

mRNA translation is a key step in decoding the genetic information stored in DNA. Regulation of translation efficiency contributes to gene expression control and is therefore important for cell fate and function. Here, we describe a recently developed microscopy-based method that allows for

Genome wide predictions of miRNA regulation by transcription factors.

Science.gov (United States)

Ruffalo, Matthew; Bar-Joseph, Ziv

2016-09-01

Reconstructing regulatory networks from expression and interaction data is a major goal of systems biology. While much work has focused on trying to experimentally and computationally determine the set of transcription-factors (TFs) and microRNAs (miRNAs) that regulate genes in these networks, relatively little work has focused on inferring the regulation of miRNAs by TFs. Such regulation can play an important role in several biological processes including development and disease. The main challenge for predicting such interactions is the very small positive training set currently available. Another challenge is the fact that a large fraction of miRNAs are encoded within genes making it hard to determine the specific way in which they are regulated. To enable genome wide predictions of TF-miRNA interactions, we extended semi-supervised machine-learning approaches to integrate a large set of different types of data including sequence, expression, ChIP-seq and epigenetic data. As we show, the methods we develop achieve good performance on both a labeled test set, and when analyzing general co-expression networks. We next analyze mRNA and miRNA cancer expression data, demonstrating the advantage of using the predicted set of interactions for identifying more coherent and relevant modules, genes, and miRNAs. The complete set of predictions is available on the supporting website and can be used by any method that combines miRNAs, genes, and TFs. Code and full set of predictions are available from the supporting website: http://cs.cmu.edu/~mruffalo/tf-mirna/ zivbj@cs.cmu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

34A, miRNA-944, miRNA-101 and miRNA-218 in cervical cancer

African Journals Online (AJOL)

RNAs (21 - 24 nucleotides in length) that are critical for many important processes such as development, ... RNA extraction and reverse transcription. Total RNA was extracted from each of the experimental groups using ... used as an endogenous control to normalize the expression of miRNA-143, miRNA-34A, miRNA-.

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

Science.gov (United States)

Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka-Weng; Wang, Jinfan; Petrov, Alexey; Prabhakar, Arjun; Rechavi, Gideon; Dominissini, Dan; He, Chuan; Ehrenberg, Måns; Puglisi, Joseph D

2018-03-01

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

Disruption of Claudin-1 Expression by miRNA-182 Alters the Susceptibility to Viral Infectivity in HCV Cell Models

Directory of Open Access Journals (Sweden)

Sarah E. Riad

2018-03-01

Full Text Available HCV entry involves a complex interplay between viral and host molecules. During post-binding interactions, the viral E2 complexes with CD81 receptor for delivery to the tight junction proteins CLDN1 and OCLN, which aid in viral internalization. Targeting HCV entry receptors represents an appealing approach to inhibit viral infectivity. This study aimed at investigating the impact of targeting CLDN1 by microRNAs on HCV infectivity. miR-155 was previously shown to target the 3′UTR of CLDN1 mRNA. Therefore, miR-155 was used as a control in this study. In-silico analysis and luciferase reporter assay were utilized to identify potential targeting miRNAs. The impact of the identified miRNAs on CLDN1 mRNA and protein expression was examined by qRT-PCR, indirect immunofluorescence and western blotting, respectively. The role of the selected miRNAs on HCV infectivity was assessed by measuring the viral load following the ectopic expression of the selected miRNAs. miR-182 was identified in-silico and by experimental validation to target CLDN1. Both miR-155 and miR-182 inhibited CLDN1 mRNA and protein expression in infected Huh7 cells. Ectopic expression of miR-155 increased, while miR-182 reduced the viral load. In conclusion, despite repressing CLDN1, the impact of miR-155 and miR-182 on HCV infectivity is contradictory. Ectopic miR-182 expression is suggested as an upstream regulator of the entry factor CLDN1, harnessing HCV infection.

miRNA Regulation Network Analysis in Qianliening Capsule Treatment of Benign Prostatic Hyperplasia

Directory of Open Access Journals (Sweden)

Liya Liu

2015-01-01

Full Text Available Objective. The objective of this study was to evaluate the molecular mechanism by which Qianliening capsule (QC treats benign prostatic hyperplasia (BPH. Methods. Benign prostatic hyperplasia epithelial cell line BPH-1 was treated with 0, 1.25, 2.5, and 5 mg/mL QC for 48 h, respectively. Evaluation of cell viability and observation of morphologic changes of BPH-1 cell gene expression and miRNA expression profiles were analyzed. Real-time quantitative PCR was used to confirm changes in miRNA and gene expression. GO and KEGG pathway-based approaches were used to investigate biological functions and signaling pathways affected by differentially expressed mRNAs. Results. QC inhibited BPH-1 cell proliferation. Differential expression of 19 upregulated and 2 downregulated miRNAs was observed in QC-treated BPH-1 cells compared to untreated control cells. 107 upregulated and 71 downregulated genes were identified between the two groups. Significantly enriched signaling pathways based on deregulated mRNAs were mainly involved in regulation of cell proliferation, apoptosis, and so on. Additionally, miRNA-mRNA network analysis integrated these miRNAs and genes by outlining interactions of miRNA and related genes. Conclusion. The study was the first report of differentially expressed miRNA and mRNA in QC-treated BPH-1 cells.

A multiplexed miRNA and transgene expression platform for simultaneous repression and expression of protein coding sequences.

Science.gov (United States)

Seyhan, Attila A

2016-01-01

Knockdown of single or multiple gene targets by RNA interference (RNAi) is necessary to overcome escape mutants or isoform redundancy. It is also necessary to use multiple RNAi reagents to knockdown multiple targets. It is also desirable to express a transgene or positive regulatory elements and inhibit a target gene in a coordinated fashion. This study reports a flexible multiplexed RNAi and transgene platform using endogenous intronic primary microRNAs (pri-miRNAs) as a scaffold located in the green fluorescent protein (GFP) as a model for any functional transgene. The multiplexed intronic miRNA - GFP transgene platform was designed to co-express multiple small RNAs within the polycistronic cluster from a Pol II promoter at more moderate levels to reduce potential vector toxicity. The native intronic miRNAs are co-transcribed with a precursor GFP mRNA as a single transcript and presumably cleaved out of the precursor-(pre) mRNA by the RNA splicing machinery, spliceosome. The spliced intron with miRNA hairpins will be further processed into mature miRNAs or small interfering RNAs (siRNAs) capable of triggering RNAi effects, while the ligated exons become a mature messenger RNA for the translation of the functional GFP protein. Data show that this approach led to robust RNAi-mediated silencing of multiple Renilla Luciferase (R-Luc)-tagged target genes and coordinated expression of functional GFP from a single transcript in transiently transfected HeLa cells. The results demonstrated that this design facilitates the coordinated expression of all mature miRNAs either as individual miRNAs or as multiple miRNAs and the associated protein. The data suggest that, it is possible to simultaneously deliver multiple negative (miRNA or shRNA) and positive (transgene) regulatory elements. Because many cellular processes require simultaneous repression and activation of downstream pathways, this approach offers a platform technology to achieve that dual manipulation efficiently

The post-transcriptional operon

DEFF Research Database (Denmark)

Tenenbaum, Scott A.; Christiansen, Jan; Nielsen, Henrik

2011-01-01

model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness...... of the model in identifying new participants in cellular pathways as well as in deepening our understanding of cellular responses....

Effects of Ghrelin miRNA on Inflammation and Calcium Pathway in Pancreatic Acinar Cells of Acute Pancreatitis.

Science.gov (United States)

Tang, Xiping; Tang, Guodu; Liang, Zhihai; Qin, Mengbin; Fang, Chunyun; Zhang, Luyi

The study investigated the effects of endogenous targeted inhibition of ghrelin gene on inflammation and calcium pathway in an in vitro pancreatic acinar cell model of acute pancreatitis. Lentiviral expression vector against ghrelin gene was constructed and transfected into AR42J cells. The mRNA and protein expression of each gene were detected by reverse transcription polymerase chain reaction, Western blotting, or enzyme-linked immunosorbent assay. The concentration of intracellular calcium ([Ca]i) was determined by calcium fluorescence mark probe combined with laser scanning confocal microscopy. Compared with the control group, cerulein could upregulate mRNA and protein expression of inflammatory factors, calcium pathway, ghrelin, and [Ca]i. mRNA and protein expression of inflammatory factors increased significantly in cells transfected with ghrelin miRNA compared with the other groups. Intracellular calcium and expression of some calcium pathway proteins decreased significantly in cells transfected with ghrelin miRNA compared with the other groups. Targeted inhibition of ghrelin gene in pancreatic acinar cells of acute pancreatitis can upregulate the expression of the intracellular inflammatory factors and alleviate the intracellular calcium overload.

Delineating miRNA profile induced by chewing tobacco in oral keratinocytes

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Mohd Younis Bhat

2017-10-01

Full Text Available The major established etiologic risk factor for oral cancer is tobacco (chewed, smoked and snuffed forms. Chewing form of tobacco is predominantly used in India making it the leading cause of oral cancer. Despite being one of the leading causes of oral cancer, the molecular alterations induced by chewing tobacco remains largely unclear. Carcinogenic effect of chewing tobacco is through chronic and not acute exposure. To understand the molecular alterations induced by chewing tobacco, we developed a cell line model where non-neoplastic oral keratinocytes were chronically exposed to chewing tobacco for a period of 6 months. This resulted in increased cellular proliferation and invasive ability of normal oral keratinocytes. Using this cellular model we studied the differential expression of miRNAs associated with chewing tobacco and the altered signaling pathways through which the aberrantly expressed miRNAs affect tumorigenesis. miRNA sequencing  was carried out using Illumina HiSeq 2500 platform  which resulted in the identification of 427 annotated miRNAs of which 10 were significantly dysregulated (≥ 4 fold; p-value ≤ 0.05 in tobacco exposed cells compared to untreated parental cells. To study the altered signaling in oral keratinocytes chronically exposed to chewing tobacco, we employed quantitative proteomics to characterize the dysregulated proteins. Integration of miRNA sequencing data with proteomic data resulted in identification of 36 proven protein targets which (≥1.5 fold; p-value ≤ 0.05 showed expression correlation with the 10 significantly dysregulated miRNAs. Pathway analysis of the dysregulated targets revealed enrichment of interferon signaling and mRNA processing related pathways in the chewing tobacco exposed cells. In addition, we also identified 6 novel miRNA in oral keratinocytes chronically exposed to chewing tobacco extract. Our study provides a framework to understand the oncogenic transformation induced by

Video encoder/decoder for encoding/decoding motion compensated images

NARCIS (Netherlands)

1996-01-01

Video encoder and decoder, provided with a motion compensator for motion-compensated video coding or decoding in which a picture is coded or decoded in blocks in alternately horizontal and vertical steps. The motion compensator is provided with addressing means (160) and controlled multiplexers

Dicer and miRNA in relation to clinicopathological variables in colorectal cancer patients

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Sun Xiao-Feng

2011-08-01

Full Text Available Abstract Background Dicer is aberrantly expressed in several types of cancers. Applying real-time PCR, we detected the expression of Dicer mRNA in normal mucosa (n = 162, primary colorectal cancer (CRC (n = 162 and liver metastasis (n = 37, and analysed the relationship between Dicer expression and clinicopathological features. We also correlated the expression of Dicer mRNA to the miRNA expression of miR-141, miR-200a, miR-200b, mir-200c and miR-429 in liver metastases. Methods RT-PCR and qPCR were used to analyse the Dicer expression in normal mucosa, primary tumour and liver metastasis by using the High Capacity cDNA Reverse Transcription Kit and TaqMan™® Gene Expression assays for Dicer and GAPDH. RT-PCR and qPCR were used to detect miRNA expression in liver metastases by utilizing TaqMan® MicroRNA Reverse Transcription Kit and TaqMan® miRNA Assays. Statistical analyses were performed with STATISTICA. Results Dicer expression in rectal cancer (3.146 ± 0.953 was higher than in colon cancer (2.703 ± 1.204, P = 0.018. Furthermore the Dicer expression was increased in primary tumours (3.146 ± 0.952 in comparison to that in normal mucosa from rectal cancer patients (2.816 ± 1.009, P = 0.034 but this is not evident in colon cancer patients. Dicer expression in liver metastases was decreased in comparison to that of either normal mucosa or primary tumour in both colon and rectal cancers (P Conclusion Dicer is up-regulated in the early development of rectal cancers. An increased expression of Dicer mRNA in normal mucosa from CRC patients is significantly related to poor survival independently of gender, age, tumour site, stage and differentiation.

Novel meiotic miRNAs and indications for a role of phasiRNAs in meiosis

Science.gov (United States)

Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and miRNAs directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolate...

Fuzzy expert systems using CLIPS

Science.gov (United States)

Le, Thach C.

1994-01-01

This paper describes a CLIPS-based fuzzy expert system development environment called FCLIPS and illustrates its application to the simulated cart-pole balancing problem. FCLIPS is a straightforward extension of CLIPS without any alteration to the CLIPS internal structures. It makes use of the object-oriented and module features in CLIPS version 6.0 for the implementation of fuzzy logic concepts. Systems of varying degrees of mixed Boolean and fuzzy rules can be implemented in CLIPS. Design and implementation issues of FCLIPS will also be discussed.

A tale of two sequences: microRNA-target chimeric reads.

Science.gov (United States)

Broughton, James P; Pasquinelli, Amy E

2016-04-04

In animals, a functional interaction between a microRNA (miRNA) and its target RNA requires only partial base pairing. The limited number of base pair interactions required for miRNA targeting provides miRNAs with broad regulatory potential and also makes target prediction challenging. Computational approaches to target prediction have focused on identifying miRNA target sites based on known sequence features that are important for canonical targeting and may miss non-canonical targets. Current state-of-the-art experimental approaches, such as CLIP-seq (cross-linking immunoprecipitation with sequencing), PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP), and iCLIP (individual-nucleotide resolution CLIP), require inference of which miRNA is bound at each site. Recently, the development of methods to ligate miRNAs to their target RNAs during the preparation of sequencing libraries has provided a new tool for the identification of miRNA target sites. The chimeric, or hybrid, miRNA-target reads that are produced by these methods unambiguously identify the miRNA bound at a specific target site. The information provided by these chimeric reads has revealed extensive non-canonical interactions between miRNAs and their target mRNAs, and identified many novel interactions between miRNAs and noncoding RNAs.

On minimizing the maximum broadcast decoding delay for instantly decodable network coding

KAUST Repository

Douik, Ahmed S.

2014-09-01

In this paper, we consider the problem of minimizing the maximum broadcast decoding delay experienced by all the receivers of generalized instantly decodable network coding (IDNC). Unlike the sum decoding delay, the maximum decoding delay as a definition of delay for IDNC allows a more equitable distribution of the delays between the different receivers and thus a better Quality of Service (QoS). In order to solve this problem, we first derive the expressions for the probability distributions of maximum decoding delay increments. Given these expressions, we formulate the problem as a maximum weight clique problem in the IDNC graph. Although this problem is known to be NP-hard, we design a greedy algorithm to perform effective packet selection. Through extensive simulations, we compare the sum decoding delay and the max decoding delay experienced when applying the policies to minimize the sum decoding delay and our policy to reduce the max decoding delay. Simulations results show that our policy gives a good agreement among all the delay aspects in all situations and outperforms the sum decoding delay policy to effectively minimize the sum decoding delay when the channel conditions become harsher. They also show that our definition of delay significantly improve the number of served receivers when they are subject to strict delay constraints.

In Vivo Short-Term Topical Application of BAY 11-7082 Prevents the Acidic Bile–Induced mRNA and miRNA Oncogenic Phenotypes in Exposed Murine Hypopharyngeal Mucosa

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Clarence T. Sasaki

2018-04-01

Full Text Available PURPOSE: Bile-containing gastroesophageal reflux may promote cancer at extraesophageal sites. Acidic bile can accelerate NF-κB activation and molecular events, linked to premalignant changes in murine hypopharyngeal mucosa (HM. We hypothesize that short-term in vivo topical application of NF-κB inhibitor BAY 11-7082 can prevent acidic bile–induced early preneoplastic molecular events, suggesting its potential role in disease prevention. EXPERIMENTAL DESIGN: We topically exposed HM (C57Bl/6j wild-type to a mixture of bile acids at pH 3.0 with and without BAY 11-7082 3 times/day for 7 days. We used immunofluorescence, Western blotting, immunohistochemistry, quantitative polymerase chain reaction, and polymerase chain reaction microarrays to identify NF-κB activation and its associated oncogenic mRNA and miRNA phenotypes, in murine hypopharyngeal cells in vitro and in murine HM in vivo. RESULTS: Short-term exposure of HM to acidic bile is a potent stimulus accelerating the expression of NF-κB signaling (70 out of 84 genes and oncogenic molecules. Topical application of BAY 11-7082 sufficiently blocks the effect of acidic bile. BAY 11-7082 eliminates NF-κB activation in regenerating basal cells of acidic bile–treated HM and prevents overexpression of molecules central to head and neck cancer, including bcl-2, STAT3, EGFR, TNF-α, and WNT5A. NF-κB inhibitor reverses the upregulated “oncomirs” miR-155 and miR-192 and the downregulated “tumor suppressors” miR-451a and miR-375 phenotypes in HM affected by acidic bile. CONCLUSION: There is novel evidence that acidic bile–induced NF-κB–related oncogenic mRNA and miRNA phenotypes are generated after short-term 7-day mucosal exposure and that topical mucosal application of BAY 11-7082 can prevent the acidic bile–induced molecular alterations associated with unregulated cell growth and proliferation of hypopharyngeal cells.

On minimizing the maximum broadcast decoding delay for instantly decodable network coding

KAUST Repository

Douik, Ahmed S.; Sorour, Sameh; Alouini, Mohamed-Slim; Ai-Naffouri, Tareq Y.

2014-01-01

In this paper, we consider the problem of minimizing the maximum broadcast decoding delay experienced by all the receivers of generalized instantly decodable network coding (IDNC). Unlike the sum decoding delay, the maximum decoding delay as a

Racial Differences in Expression Levels of miRNA Machinery-Related Genes, Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid Carcinoma and Comparative Validation Using the Cancer Genome Atlas

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Jaegil Kim

2017-01-01

Full Text Available Aberrant regulation of microRNA (miRNA machinery components is associated with various human cancers, including papillary thyroid carcinoma (PTC, which is the most common type of thyroid cancer, and a higher prevalent female malignancy. The purpose of this study is to investigate racial differences in mRNA expression levels of four miRNA machinery components, Dicer, Drosha, DGCR8, and AGO2, and their correlations with clinicopathological characteristics. Forty PTC samples from female Asian Korean PTC patients were enrolled. Using qPCR, we examined mRNA expression levels of the components and next validated our results by comparison with results of female white American in the TCGA PTC project. Interestingly, mRNA expression levels of the selected factors were altered in the TCGA PTC samples. However, only Drosha showed a significantly lower expression level in Asian Korean PTC samples. Furthermore, the mRNA expression levels of the four components showed no association with clinicopathological characteristics in both groups. On the other hand, positive correlations were observed between altered mRNA expression levels of Dicer and Drosha and DGCR8 and Drosha in TCGA PTC samples. These findings collectively revealed that altered mRNA expression levels of miRNA machinery components might be responsible for racial differences in the carcinogenesis of PTC.

miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases

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Laczny Cedric

2012-02-01

Full Text Available Abstract Background Expression profiling provides new insights into regulatory and metabolic processes and in particular into pathogenic mechanisms associated with diseases. Besides genes, non-coding transcripts as microRNAs (miRNAs gained increasing relevance in the last decade. To understand the regulatory processes of miRNAs on genes, integrative computer-aided approaches are essential, especially in the light of complex human diseases as cancer. Results Here, we present miRTrail, an integrative tool that allows for performing comprehensive analyses of interactions of genes and miRNAs based on expression profiles. The integrated analysis of mRNA and miRNA data should generate more robust and reliable results on deregulated pathogenic processes and may also offer novel insights into the regulatory interactions between miRNAs and genes. Our web-server excels in carrying out gene sets analysis, analysis of miRNA sets as well as the combination of both in a systems biology approach. To this end, miRTrail integrates information on 20.000 genes, almost 1.000 miRNAs, and roughly 280.000 putative interactions, for Homo sapiens and accordingly for Mus musculus and Danio rerio. The well-established, classical Chi-squared test is one of the central techniques of our tool for the joint consideration of miRNAs and their targets. For interactively visualizing obtained results, it relies on the network analyzers and viewers BiNA or Cytoscape-web, also enabling direct access to relevant literature. We demonstrated the potential of miRTrail by applying our tool to mRNA and miRNA data of malignant melanoma. MiRTrail identified several deregulated miRNAs that target deregulated mRNAs including miRNAs hsa-miR-23b and hsa-miR-223, which target the highest numbers of deregulated mRNAs and regulate the pathway "basal cell carcinoma". In addition, both miRNAs target genes like PTCH1 and RASA1 that are involved in many oncogenic processes. Conclusions The application

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

Science.gov (United States)

Zhang, Zijun; Xing, Yi

2017-09-19

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Global miRNA expression analysis of serous and clear cell ovarian carcinomas identifies differentially expressed miRNAs including miR-200c-3p as a prognostic marker

International Nuclear Information System (INIS)

Vilming Elgaaen, Bente; Olstad, Ole Kristoffer; Haug, Kari Bente Foss; Brusletto, Berit; Sandvik, Leiv; Staff, Anne Cathrine; Gautvik, Kaare M; Davidson, Ben

2014-01-01

Improved insight into the molecular characteristics of the different ovarian cancer subgroups is needed for developing a more individualized and optimized treatment regimen. The aim of this study was to a) identify differentially expressed miRNAs in high-grade serous ovarian carcinoma (HGSC), clear cell ovarian carcinoma (CCC) and ovarian surface epithelium (OSE), b) evaluate selected miRNAs for association with clinical parameters including survival and c) map miRNA-mRNA interactions. Differences in miRNA expression between HGSC, CCC and OSE were analyzed by global miRNA expression profiling (Affymetrix GeneChip miRNA 2.0 Arrays, n = 12, 9 and 9, respectively), validated by RT-qPCR (n = 35, 19 and 9, respectively), and evaluated for associations with clinical parameters. For HGSC, differentially expressed miRNAs were linked to differentially expressed mRNAs identified previously. Differentially expressed miRNAs (n = 78) between HGSC, CCC and OSE were identified (FDR < 0.01%), of which 18 were validated (p < 0.01) using RT-qPCR in an extended cohort. Compared with OSE, miR-205-5p was the most overexpressed miRNA in HGSC. miR-200 family members and miR-182-5p were the most overexpressed in HGSC and CCC compared with OSE, whereas miR-383 was the most underexpressed. miR-205-5p and miR-200 members target epithelial-mesenchymal transition (EMT) regulators, apparently being important in tumor progression. miR-509-3-5p, miR-509-5p, miR-509-3p and miR-510 were among the strongest differentiators between HGSC and CCC, all being significantly overexpressed in CCC compared with HGSC. High miR-200c-3p expression was associated with poor progression-free (p = 0.031) and overall (p = 0.026) survival in HGSC patients. Interacting miRNA and mRNA targets, including those of a TP53-related pathway presented previously, were identified in HGSC. Several miRNAs differentially expressed between HGSC, CCC and OSE have been identified, suggesting a carcinogenetic role for these miRNAs

Seismic signals hard clipping overcoming

Science.gov (United States)

Olszowa, Paula; Sokolowski, Jakub

2018-01-01

In signal processing the clipping is understand as the phenomenon of limiting the signal beyond certain threshold. It is often related to overloading of a sensor. Two particular types of clipping are being recognized: soft and hard. Beyond the limiting value soft clipping reduces the signal real gain while the hard clipping stiffly sets the signal values at the limit. In both cases certain amount of signal information is lost. Obviously if one possess the model which describes the considered signal and the threshold value (which might be slightly more difficult to obtain in the soft clipping case), the attempt of restoring the signal can be made. Commonly it is assumed that the seismic signals take form of an impulse response of some specific system. This may lead to belief that the sine wave may be the most appropriate to fit in the clipping period. However, this should be tested. In this paper the possibility of overcoming the hard clipping in seismic signals originating from a geoseismic station belonging to an underground mine is considered. A set of raw signals will be hard-clipped manually and then couple different functions will be fitted and compared in terms of least squares. The results will be then analysed.

Concept of the central clip

DEFF Research Database (Denmark)

Alegria-Barrero, Eduardo; Chan, Pak Hei; Foin, Nicolas

2014-01-01

AIMS: Percutaneous edge-to-edge mitral valve repair with the MitraClip(®) was shown to be a safe and feasible alternative compared to conventional surgical mitral valve repair. We analyse the concept of the central clip and the predictors for the need of more than one MitraClip(®) in our high.......8±10.7 years (30 males, 13 females; mean logistic EuroSCORE 24.1±11, mean LVEF 47.5±18.5%; mean±SD) were treated. Median follow-up was 385 days (104-630; Q1-Q3). Device implantation success was 93%. All patients were treated following the central clip concept: 52.5% of MR was degenerative in aetiology and 47....... The presence of a restricted posterior mitral valve leaflet (PML) was inversely correlated with the need for more than one clip (p=0.02). A cut-off value of ≥7.5 mm for vena contracta predicted the need for a second clip (sensitivity 83%, specificity 90%, p=0.01). CONCLUSIONS: The central MitraClip(®) concept...

Genome-wide mRNA and miRNA expression data analysis to screen for markers involved in sarcomagenesis in human chondrosarcoma cell lines

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Biju Issac

2014-12-01

Full Text Available Genes and miRNAs involved in sarcomagenesis related pathways are unknown and therefore signaling events leading to mesenchymal cell transformation to sarcoma are poorly elucidated. Exiqon and Illumina microarray study on human chondrosarcoma JJ012 and chondrocytes C28 cell lines to compare and analyze the differentially expressed miRNAs and their gene targets was recently published in the Journal Tumor Biology in 2014. Here we describe in details the contents and quality controls for the miRNA and gene expression data associated with the study that is relevant to this dataset.

Decoding of interleaved Reed-Solomon codes using improved power decoding

DEFF Research Database (Denmark)

Puchinger, Sven; Rosenkilde ne Nielsen, Johan

2017-01-01

We propose a new partial decoding algorithm for m-interleaved Reed-Solomon (IRS) codes that can decode, with high probability, a random error of relative weight 1 − Rm/m+1 at all code rates R, in time polynomial in the code length n. For m > 2, this is an asymptotic improvement over the previous...... state-of-the-art for all rates, and the first improvement for R > 1/3 in the last 20 years. The method combines collaborative decoding of IRS codes with power decoding up to the Johnson radius....

Low-Power Bitstream-Residual Decoder for H.264/AVC Baseline Profile Decoding

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Xu Ke

2009-01-01

Full Text Available Abstract We present the design and VLSI implementation of a novel low-power bitstream-residual decoder for H.264/AVC baseline profile. It comprises a syntax parser, a parameter decoder, and an Inverse Quantization Inverse Transform (IQIT decoder. The syntax parser detects and decodes each incoming codeword in the bitstream under the control of a hierarchical Finite State Machine (FSM; the IQIT decoder performs inverse transform and quantization with pipelining and parallelism. Various power reduction techniques, such as data-driven based on statistic results, nonuniform partition, precomputation, guarded evaluation, hierarchical FSM decomposition, TAG method, zero-block skipping, and clock gating , are adopted and integrated throughout the bitstream-residual decoder. With innovative architecture, the proposed design is able to decode QCIF video sequences of 30 fps at a clock rate as low as 1.5 MHz. A prototype H.264/AVC baseline decoding chip utilizing the proposed decoder is fabricated in UMC 0.18  m 1P6M CMOS technology. The proposed design is measured under 1 V 1.8 V supply with 0.1 V step. It dissipates 76  W at 1 V and 253  W at 1.8 V.

Zcchc11 Uridylates Mature miRNAs to Enhance Neonatal IGF-1 Expression, Growth, and Survival

Science.gov (United States)

Kozlowski, Elyse; Matsuura, Kori Y.; Ferrari, Joseph D.; Morris, Samantha A.; Powers, John T.; Daley, George Q.; Quinton, Lee J.; Mizgerd, Joseph P.

2012-01-01

The Zcchc11 enzyme is implicated in microRNA (miRNA) regulation. It can uridylate let-7 precursors to decrease quantities of the mature miRNA in embryonic stem cell lines, suggested to mediate stem cell maintenance. It can uridylate mature miR-26 to relieve silencing activity without impacting miRNA content in cancer cell lines, suggested to mediate cytokine and growth factor expression. Broader roles of Zcchc11 in shaping or remodeling the miRNome or in directing biological or physiological processes remain entirely speculative. We generated Zcchc11-deficient mice to address these knowledge gaps. Zcchc11 deficiency had no impact on embryogenesis or fetal development, but it significantly decreased survival and growth immediately following birth, indicating a role for this enzyme in early postnatal fitness. Deep sequencing of small RNAs from neonatal livers revealed roles of this enzyme in miRNA sequence diversity. Zcchc11 deficiency diminished the lengths and terminal uridine frequencies for diverse mature miRNAs, but it had no influence on the quantities of any miRNAs. The expression of IGF-1, a liver-derived protein essential to early growth and survival, was enhanced by Zcchc11 expression in vitro, and miRNA silencing of IGF-1 was alleviated by uridylation events observed to be Zcchc11-dependent in the neonatal liver. In neonatal mice, Zcchc11 deficiency significantly decreased IGF-1 mRNA in the liver and IGF-1 protein in the blood. We conclude that the Zcchc11-mediated terminal uridylation of mature miRNAs is pervasive and physiologically significant, especially important in the neonatal period for fostering IGF-1 expression and enhancing postnatal growth and survival. We propose that the miRNA 3′ terminus is a regulatory node upon which multiple enzymes converge to direct silencing activity and tune gene expression. PMID:23209448

Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival.

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Matthew R Jones

Full Text Available The Zcchc11 enzyme is implicated in microRNA (miRNA regulation. It can uridylate let-7 precursors to decrease quantities of the mature miRNA in embryonic stem cell lines, suggested to mediate stem cell maintenance. It can uridylate mature miR-26 to relieve silencing activity without impacting miRNA content in cancer cell lines, suggested to mediate cytokine and growth factor expression. Broader roles of Zcchc11 in shaping or remodeling the miRNome or in directing biological or physiological processes remain entirely speculative. We generated Zcchc11-deficient mice to address these knowledge gaps. Zcchc11 deficiency had no impact on embryogenesis or fetal development, but it significantly decreased survival and growth immediately following birth, indicating a role for this enzyme in early postnatal fitness. Deep sequencing of small RNAs from neonatal livers revealed roles of this enzyme in miRNA sequence diversity. Zcchc11 deficiency diminished the lengths and terminal uridine frequencies for diverse mature miRNAs, but it had no influence on the quantities of any miRNAs. The expression of IGF-1, a liver-derived protein essential to early growth and survival, was enhanced by Zcchc11 expression in vitro, and miRNA silencing of IGF-1 was alleviated by uridylation events observed to be Zcchc11-dependent in the neonatal liver. In neonatal mice, Zcchc11 deficiency significantly decreased IGF-1 mRNA in the liver and IGF-1 protein in the blood. We conclude that the Zcchc11-mediated terminal uridylation of mature miRNAs is pervasive and physiologically significant, especially important in the neonatal period for fostering IGF-1 expression and enhancing postnatal growth and survival. We propose that the miRNA 3' terminus is a regulatory node upon which multiple enzymes converge to direct silencing activity and tune gene expression.

miRNAs in brain development

International Nuclear Information System (INIS)

Petri, Rebecca; Malmevik, Josephine; Fasching, Liana; Åkerblom, Malin; Jakobsson, Johan

2014-01-01

MicroRNAs (miRNAs) are small, non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. In the brain, a large number of miRNAs are expressed and there is a growing body of evidence demonstrating that miRNAs are essential for brain development and neuronal function. Conditional knockout studies of the core components in the miRNA biogenesis pathway, such as Dicer and DGCR8, have demonstrated a crucial role for miRNAs during the development of the central nervous system. Furthermore, mice deleted for specific miRNAs and miRNA-clusters demonstrate diverse functional roles for different miRNAs during the development of different brain structures. miRNAs have been proposed to regulate cellular functions such as differentiation, proliferation and fate-determination of neural progenitors. In this review we summarise the findings from recent studies that highlight the importance of miRNAs in brain development with a focus on the mouse model. We also discuss the technical limitations of current miRNA studies that still limit our understanding of this family of non-coding RNAs and propose the use of novel and refined technologies that are needed in order to fully determine the impact of specific miRNAs in brain development. - Highlights: • miRNAs are essential for brain development and neuronal function. • KO of Dicer is embryonically lethal. • Conditional Dicer KO results in defective proliferation or increased apoptosis. • KO of individual miRNAs or miRNA families is necessary to determine function

miRNA-720 controls stem cell phenotype, proliferation and differentiation of human dental pulp cells.

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Emilio Satoshi Hara

Full Text Available Dental pulp cells (DPCs are known to be enriched in stem/progenitor cells but not well characterized yet. Small non-coding microRNAs (miRNAs have been identified to control protein translation, mRNA stability and transcription, and have been reported to play important roles in stem cell biology, related to cell reprogramming, maintenance of stemness and regulation of cell differentiation. In order to characterize dental pulp stem/progenitor cells and its mechanism of differentiation, we herein sorted stem-cell-enriched side population (SP cells from human DPCs and periodontal ligament cells (PDLCs, and performed a locked nucleic acid (LNA-based miRNA array. As a result, miR-720 was highly expressed in the differentiated main population (MP cells compared to that in SP cells. In silico analysis and a reporter assay showed that miR-720 targets the stem cell marker NANOG, indicating that miR-720 could promote differentiation of dental pulp stem/progenitor cells by repressing NANOG. Indeed, gain-and loss-of-function analyses showed that miR-720 controls NANOG transcript and protein levels. Moreover, transfection of miR-720 significantly decreased the number of cells positive for the early stem cell marker SSEA-4. Concomitantly, mRNA levels of DNA methyltransferases (DNMTs, which are known to play crucial factors during stem cell differentiation, were also increased by miR-720 through unknown mechanism. Finally, miR-720 decreased DPC proliferation as determined by immunocytochemical analysis against ki-67, and promoted odontogenic differentiation as demonstrated by alizarin red staining, as well as alkaline phosphatase and osteopontin mRNA levels. Our findings identify miR-720 as a novel miRNA regulating the differentiation of DPCs.

Activity-associated miRNA are packaged in Map1b-enriched exosomes released from depolarized neurons.

Science.gov (United States)

Goldie, Belinda J; Dun, Matthew D; Lin, Minjie; Smith, Nathan D; Verrills, Nicole M; Dayas, Christopher V; Cairns, Murray J

2014-08-01

Rapid input-restricted change in gene expression is an important aspect of synaptic plasticity requiring complex mechanisms of post-transcriptional mRNA trafficking and regulation. Small non-coding miRNA are uniquely poised to support these functions by providing a nucleic-acid-based specificity component for universal-sequence-dependent RNA binding complexes. We investigated the subcellular distribution of these molecules in resting and potassium chloride depolarized human neuroblasts, and found both selective enrichment and depletion in neurites. Depolarization was associated with a neurite-restricted decrease in miRNA expression; a subset of these molecules was recovered from the depolarization medium in nuclease resistant extracellular exosomes. These vesicles were enriched with primate specific miRNA and the synaptic-plasticity-associated protein MAP1b. These findings further support a role for miRNA as neural plasticity regulators, as they are compartmentalized in neurons and undergo activity-associated redistribution or release into the extracellular matrix. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Thyroid hormone negatively regulates CDX2 and SOAT2 mRNA expression via induction of miRNA-181d in hepatic cells

Energy Technology Data Exchange (ETDEWEB)

Yap, Chui Sun; Sinha, Rohit Anthony [Cardiovascular and Metabolic Disorders, Duke-NUS Graduate Medical School, 8, College Road, Singapore 169857 (Singapore); Ota, Sho; Katsuki, Masahito [Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Seiryo-machi, Aoba-ku, Sendai 980-8575 (Japan); Yen, Paul Michael, E-mail: paul.yen@duke-nus.edu.sg [Cardiovascular and Metabolic Disorders, Duke-NUS Graduate Medical School, 8, College Road, Singapore 169857 (Singapore)

2013-11-01

Highlights: •Thyroid hormone induces miR-181d expression in human hepatic cells and mouse livers. •Thyroid hormone downregulates CDX2 and SOAT2 (or ACAT2) via miR-181d. •miR-181d reduces cholesterol output from human hepatic cells. -- Abstract: Thyroid hormones (THs) regulate transcription of many metabolic genes in the liver through its nuclear receptors (TRs). Although the molecular mechanisms for positive regulation of hepatic genes by TH are well understood, much less is known about TH-mediated negative regulation. Recently, several nuclear hormone receptors were shown to downregulate gene expression via miRNAs. To further examine the potential role of miRNAs in TH-mediated negative regulation, we used a miRNA microarray to identify miRNAs that were directly regulated by TH in a human hepatic cell line. In our screen, we discovered that miRNA-181d is a novel hepatic miRNA that was regulated by TH in hepatic cell culture and in vivo. Furthermore, we identified and characterized two novel TH-regulated target genes that were downstream of miR-181d signaling: caudal type homeobox 2 (CDX2) and sterol O-acyltransferase 2 (SOAT2 or ACAT2). CDX2, a known positive regulator of hepatocyte differentiation, was regulated by miR-181d and directly activated SOAT2 gene expression. Since SOAT2 is an enzyme that generates cholesteryl esters that are packaged into lipoproteins, our results suggest miR-181d plays a significant role in the negative regulation of key metabolic genes by TH in the liver.

Completion time reduction in instantly decodable network coding through decoding delay control

KAUST Repository

Douik, Ahmed S.; Sorour, Sameh; Alouini, Mohamed-Slim; Al-Naffouri, Tareq Y.

2014-01-01

For several years, the completion time and the decoding delay problems in Instantly Decodable Network Coding (IDNC) were considered separately and were thought to completely act against each other. Recently, some works aimed to balance the effects of these two important IDNC metrics but none of them studied a further optimization of one by controlling the other. In this paper, we study the effect of controlling the decoding delay to reduce the completion time below its currently best known solution. We first derive the decoding-delay-dependent expressions of the users' and their overall completion times. Although using such expressions to find the optimal overall completion time is NP-hard, we use a heuristic that minimizes the probability of increasing the maximum of these decoding-delay-dependent completion time expressions after each transmission through a layered control of their decoding delays. Simulation results show that this new algorithm achieves both a lower mean completion time and mean decoding delay compared to the best known heuristic for completion time reduction. The gap in performance becomes significant for harsh erasure scenarios.

Completion time reduction in instantly decodable network coding through decoding delay control

KAUST Repository

Douik, Ahmed S.

2014-12-01

For several years, the completion time and the decoding delay problems in Instantly Decodable Network Coding (IDNC) were considered separately and were thought to completely act against each other. Recently, some works aimed to balance the effects of these two important IDNC metrics but none of them studied a further optimization of one by controlling the other. In this paper, we study the effect of controlling the decoding delay to reduce the completion time below its currently best known solution. We first derive the decoding-delay-dependent expressions of the users\\' and their overall completion times. Although using such expressions to find the optimal overall completion time is NP-hard, we use a heuristic that minimizes the probability of increasing the maximum of these decoding-delay-dependent completion time expressions after each transmission through a layered control of their decoding delays. Simulation results show that this new algorithm achieves both a lower mean completion time and mean decoding delay compared to the best known heuristic for completion time reduction. The gap in performance becomes significant for harsh erasure scenarios.

A viral microRNA down-regulates multiple cell cycle genes through mRNA 5'UTRs.

Directory of Open Access Journals (Sweden)

Finn Grey

2010-06-01

Full Text Available Global gene expression data combined with bioinformatic analysis provides strong evidence that mammalian miRNAs mediate repression of gene expression primarily through binding sites within the 3' untranslated region (UTR. Using RNA induced silencing complex immunoprecipitation (RISC-IP techniques we have identified multiple cellular targets for a human cytomegalovirus (HCMV miRNA, miR-US25-1. Strikingly, this miRNA binds target sites primarily within 5'UTRs, mediating significant reduction in gene expression. Intriguingly, many of the genes targeted by miR-US25-1 are associated with cell cycle control, including cyclin E2, BRCC3, EID1, MAPRE2, and CD147, suggesting that miR-US25-1 is targeting genes within a related pathway. Deletion of miR-US25-1 from HCMV results in over expression of cyclin E2 in the context of viral infection. Our studies demonstrate that a viral miRNA mediates translational repression of multiple cellular genes by targeting mRNA 5'UTRs.

Integration analysis of microRNA and mRNA paired expression profiling identifies deregulated microRNA-transcription factor-gene regulatory networks in ovarian endometriosis.

Science.gov (United States)

Zhao, Luyang; Gu, Chenglei; Ye, Mingxia; Zhang, Zhe; Li, Li'an; Fan, Wensheng; Meng, Yuanguang

2018-01-22

The etiology and pathophysiology of endometriosis remain unclear. Accumulating evidence suggests that aberrant microRNA (miRNA) and transcription factor (TF) expression may be involved in the pathogenesis and development of endometriosis. This study therefore aims to survey the key miRNAs, TFs and genes and further understand the mechanism of endometriosis. Paired expression profiling of miRNA and mRNA in ectopic endometria compared with eutopic endometria were determined by high-throughput sequencing techniques in eight patients with ovarian endometriosis. Binary interactions and circuits among the miRNAs, TFs, and corresponding genes were identified by the Pearson correlation coefficients. miRNA-TF-gene regulatory networks were constructed using bioinformatic methods. Eleven selected miRNAs and TFs were validated by quantitative reverse transcription-polymerase chain reaction in 22 patients. Overall, 107 differentially expressed miRNAs and 6112 differentially expressed mRNAs were identified by comparing the sequencing of the ectopic endometrium group and the eutopic endometrium group. The miRNA-TF-gene regulatory network consists of 22 miRNAs, 12 TFs and 430 corresponding genes. Specifically, some key regulators from the miR-449 and miR-34b/c cluster, miR-200 family, miR-106a-363 cluster, miR-182/183, FOX family, GATA family, and E2F family as well as CEBPA, SOX9 and HNF4A were suggested to play vital regulatory roles in the pathogenesis of endometriosis. Integration analysis of the miRNA and mRNA expression profiles presents a unique insight into the regulatory network of this enigmatic disorder and possibly provides clues regarding replacement therapy for endometriosis.

Iterative List Decoding

DEFF Research Database (Denmark)

Justesen, Jørn; Høholdt, Tom; Hjaltason, Johan

2005-01-01

We analyze the relation between iterative decoding and the extended parity check matrix. By considering a modified version of bit flipping, which produces a list of decoded words, we derive several relations between decodable error patterns and the parameters of the code. By developing a tree...... of codewords at minimal distance from the received vector, we also obtain new information about the code....

Adaptive decoding of convolutional codes

Science.gov (United States)

Hueske, K.; Geldmacher, J.; Götze, J.

2007-06-01

Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

Mounting clips for panel installation

Science.gov (United States)

Cavieres, Andres; Al-Haddad, Tristan; Goodman, Joseph; Valdes, Francisco

2017-02-14

An exemplary mounting clip for removably attaching panels to a supporting structure comprises a base, spring locking clips, a lateral flange, a lever flange, and a spring bonding pad. The spring locking clips extend upwardly from the base. The lateral flange extends upwardly from a first side of the base. The lateral flange comprises a slot having an opening configured to receive at least a portion of one of the one or more panels. The lever flange extends outwardly from the lateral flange. The spring bonding flange extends downwardly from the lever flange. At least a portion of the first spring bonding flange comprises a serrated edge for gouging at least a portion of the one or more panels when the one or more panels are attached to the mounting clip to electrically and mechanically couple the one or more panels to the mounting clip.

A Decade of Global mRNA and miRNA Profiling of HPV-Positive Cell Lines and Clinical Specimens

DEFF Research Database (Denmark)

Kaczkowski, Bogumil; Morevati, Marya; Rossing, Maria

2012-01-01

For more than a decade, global gene expression profiling has been extensively used to elucidate the biology of human papillomaviruses (HPV) and their role in cervical- and head-and-neck cancers. Since 2008, the expression profiling of miRNAs has been reported in multiple HPV studies. Two major...... as the fragmented miRNA-mRNA target correlation evidence. Furthermore, we propose an approach for future research to include more comprehensive miRNA-mRNA target correlation analysis and to apply systems biology/gene networks methodology....... strategies have been employed in the gene and miRNA profiling studies: In the first approach, HPV positive tumors were compared to normal tissues or to HPV negative tumors. The second strategy relied on analysis of cell cultures transfected with single HPV oncogenes or with HPV genomes compared...

Integrated analysis of miRNAs and transcriptomes in Aedes albopictus midgut reveals the differential expression profiles of immune-related genes during dengue virus serotype-2 infection.

Science.gov (United States)

Liu, Yan-Xia; Li, Fen-Xiang; Liu, Zhuan-Zhuan; Jia, Zhi-Rong; Zhou, Yan-He; Zhang, Hao; Yan, Hui; Zhou, Xian-Qiang; Chen, Xiao-Guang

2016-06-01

Mosquito microRNAs (miRNAs) are involved in host-virus interaction, and have been reported to be altered by dengue virus (DENV) infection in Aedes albopictus (Diptera: Culicidae). However, little is known about the molecular mechanisms of Aedes albopictus midgut-the first organ to interact with DENV-involved in its resistance to DENV. Here we used high-throughput sequencing to characterize miRNA and messenger RNA (mRNA) expression patterns in Aedes albopictus midgut in response to dengue virus serotype 2. A total of three miRNAs and 777 mRNAs were identified to be differentially expressed upon DENV infection. For the mRNAs, we identified 198 immune-related genes and 31 of them were differentially expressed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses also showed that the differentially expressed immune-related genes were involved in immune response. Then the differential expression patterns of six immune-related genes and three miRNAs were confirmed by real-time reverse transcription polymerase chain reaction. Furthermore, seven known miRNA-mRNA interaction pairs were identified by aligning our two datasets. These analyses of miRNA and mRNA transcriptomes provide valuable information for uncovering the DENV response genes and provide a basis for future study of the resistance mechanisms in Aedes albopictus midgut. © 2016 Institute of Zoology, Chinese Academy of Sciences.

Decoding Xing-Ling codes

DEFF Research Database (Denmark)

Nielsen, Rasmus Refslund

2002-01-01

This paper describes an efficient decoding method for a recent construction of good linear codes as well as an extension to the construction. Furthermore, asymptotic properties and list decoding of the codes are discussed.......This paper describes an efficient decoding method for a recent construction of good linear codes as well as an extension to the construction. Furthermore, asymptotic properties and list decoding of the codes are discussed....

Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA–microRNA regulatory network in nasopharyngeal carcinoma model systems

Directory of Open Access Journals (Sweden)

Carol Ying-Ying Szeto

2014-01-01

Full Text Available Nasopharyngeal carcinoma (NPC is a prevalent malignancy in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein–Barr virus (EBV-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 were sequenced by Solexa technology. We found 2812 genes and 149 miRNAs (human and EBV to be differentially expressed in NP460, HK1, C666 and X666 with RNASeq; 533 miRNA–mRNA target pairs were inversely regulated in the three NPC cell lines compared to NP460. Integrated mRNA/miRNA expression profiling and pathway analysis show extracellular matrix organization, Beta-1 integrin cell surface interactions, and the PI3K/AKT, EGFR, ErbB, and Wnt pathways were potentially deregulated in NPC. Real-time quantitative PCR was performed on selected mRNA/miRNAs in order to validate their expression. Transcript sequence variants such as short insertions and deletions (INDEL, single nucleotide variant (SNV, and isomiRs were characterized in the NPC model systems. A novel TP53 transcript variant was identified in NP460, HK1, and C666. Detection of three previously reported novel EBV-encoded BART miRNAs and their isomiRs were also observed. Meta-analysis of a model system to a clinical system aids the choice of different cell lines in NPC studies. This comprehensive characterization of mRNA and miRNA transcriptomes in NPC cell lines and the xenograft provides insights on miRNA regulation of mRNA and valuable resources on transcript variation and regulation in NPC, which are potentially useful for mechanistic and preclinical studies.

Adaptive decoding of convolutional codes

Directory of Open Access Journals (Sweden)

K. Hueske

2007-06-01

Full Text Available Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

MiRNA-155 and miRNA-132 as potential diagnostic biomarkers for pulmonary tuberculosis: A preliminary study.

Science.gov (United States)

Zheng, Meng-Li; Zhou, Nai-Kang; Luo, Cheng-Hua

2016-11-01

In our study, we aimed to profile a panel microRNAs (miRNAs) as potential biomarkers for the early diagnosis of pulmonary tuberculosis (PTB) and to illuminate the molecular mechanisms in the development of PTB. Firstly, gene expression profile of E-GEOD-49951 was downloaded from ArrayExpress database, and quantile-adjusted conditional maximum likelihood method was utilized to identify statistical difference between miRNAs of Mycobacterium tuberculosis (MTB)-infected individuals and healthy subjects. Furthermore, in order to assess the performance of our methodology, random forest (RF) classification model was utilized to identify the top 10 miRNAs with better Area Under The Curve (AUC) using 10-fold cross-validation method. Additionally, Monte Carlo Cross-Validation was repeated 50 times to explore the best miRNAs. In order to learn more about the differentially-expressed miRNAs, the target genes of differentially-expressed miRNAs were retrieved from TargetScan database and Ingenuity Pathways Analysis (IPA) was used to screen out biological pathways where target genes were involved. After normalization, a total of 478 miRNAs with higher than 0.25-fold quantile average across all samples were required. Based on the differential expression analysis, 38 differentially expressed miRNAs were identified when the significance was set as false discovery rate (FDR) < 0.01. Among the top 10 differentially expressed miRNAs, miRNA-155 obtained a highest AUC value 0.976, showing a good performance between PTB and control groups. Similarly, miRNA-449a, miRNA-212 and miRNA-132 revealed also a good performance with AUC values 0.947, 0.931 and 0.930, respectively. Moreover, miRNA-155, miRNA-449a, miRNA-29b-1* and miRNA-132 appeared in 50, 49, 49 and 48 bootstraps. Thus, miRNA-155 and miRNA-132 might be important in the progression of PTB and thereby, might present potential signatures for diagnosis of PTB. Copyright © 2016 Elsevier Ltd. All rights reserved.

A defect in the CLIP1 gene (CLIP-170) can cause autosomal recessive intellectual disability.

Science.gov (United States)

Larti, Farzaneh; Kahrizi, Kimia; Musante, Luciana; Hu, Hao; Papari, Elahe; Fattahi, Zohreh; Bazazzadegan, Niloofar; Liu, Zhe; Banan, Mehdi; Garshasbi, Masoud; Wienker, Thomas F; Ropers, H Hilger; Galjart, Niels; Najmabadi, Hossein

2015-03-01

In the context of a comprehensive research project, investigating novel autosomal recessive intellectual disability (ARID) genes, linkage analysis based on autozygosity mapping helped identify an intellectual disability locus on Chr.12q24, in an Iranian family (LOD score = 3.7). Next-generation sequencing (NGS) following exon enrichment in this novel interval, detected a nonsense mutation (p.Q1010*) in the CLIP1 gene. CLIP1 encodes a member of microtubule (MT) plus-end tracking proteins, which specifically associates with the ends of growing MTs. These proteins regulate MT dynamic behavior and are important for MT-mediated transport over the length of axons and dendrites. As such, CLIP1 may have a role in neuronal development. We studied lymphoblastoid and skin fibroblast cell lines established from healthy and affected patients. RT-PCR and western blot analyses showed the absence of CLIP1 transcript and protein in lymphoblastoid cells derived from affected patients. Furthermore, immunofluorescence analyses showed MT plus-end staining only in fibroblasts containing the wild-type (and not the mutant) CLIP1 protein. Collectively, our data suggest that defects in CLIP1 may lead to ARID.

Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events.

Directory of Open Access Journals (Sweden)

Xianxin Li

Full Text Available Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. Further comparative analyses at the systems level revealed that significant aberrations of the cell adhesion process, p53 signaling, calcium signaling, the ECM-receptor and cell cycle pathways, the DNA repair and replication processes and the immune and inflammatory response processes were the common hallmarks of human cancers. Gene sets showing testicular cancer-specific deregulation patterns were mainly implicated in processes related to male reproductive function, and general disruptions of multiple metabolic pathways and processes related to cell migration were the characteristic molecular events for renal and bladder cancer, respectively. Furthermore, we also demonstrated that tumors with the same histological origins and genes with similar functions tended to group together in a clustering analysis. By assessing the correlation between the expression of each miRNA and its targets, we determined that deregulation of 'key' miRNAs may result in the global aberration of one or more pathways or processes as a whole.This systematic analysis deciphered the molecular phenotypes of three genitourinary cancers and investigated their variations at the miRNA level simultaneously. Our results provided a valuable source for future studies and highlighted some promising genes, miRNAs, pathways and processes that may be useful for diagnostic or

Authoring Data-Driven Videos with DataClips.

Science.gov (United States)

Amini, Fereshteh; Riche, Nathalie Henry; Lee, Bongshin; Monroy-Hernandez, Andres; Irani, Pourang

2017-01-01

Data videos, or short data-driven motion graphics, are an increasingly popular medium for storytelling. However, creating data videos is difficult as it involves pulling together a unique combination of skills. We introduce DataClips, an authoring tool aimed at lowering the barriers to crafting data videos. DataClips allows non-experts to assemble data-driven "clips" together to form longer sequences. We constructed the library of data clips by analyzing the composition of over 70 data videos produced by reputable sources such as The New York Times and The Guardian. We demonstrate that DataClips can reproduce over 90% of our data videos corpus. We also report on a qualitative study comparing the authoring process and outcome achieved by (1) non-experts using DataClips, and (2) experts using Adobe Illustrator and After Effects to create data-driven clips. Results indicated that non-experts are able to learn and use DataClips with a short training period. In the span of one hour, they were able to produce more videos than experts using a professional editing tool, and their clips were rated similarly by an independent audience.

Preserving Sharp Edges with Volume Clipping

NARCIS (Netherlands)

Termeer, M.A.; Oliván Bescós, J.; Telea, A.C.

2006-01-01

Volume clipping is a useful aid for exploring volumetric datasets. To maximize the effectiveness of this technique, the clipping geometry should be flexibly specified and the resulting images should not contain artifacts due to the clipping techniques. We present an improvement to an existing

Changes in miRNA expression profile of space-flown Caenorhabditis elegans during Shenzhou-8 mission

Science.gov (United States)

Xu, Dan; Gao, Ying; Huang, Lei; Sun, Yeqing

2014-04-01

Recent advances in the field of molecular biology have demonstrated that small non-coding microRNAs (miRNAs) have a broad effect on gene expression networks and play a key role in biological responses to environmental stressors. However, little is known about how space radiation exposure and altered gravity affect miRNA expression. The "International Space Biological Experiments" project was carried out in November 2011 by an international collaboration between China and Germany during the Shenzhou-8 (SZ-8) mission. To study the effects of spaceflight on Caenorhabditis elegans (C. elegans), we explored the expression profile miRNA changes in space-flown C. elegans. Dauer C. elegans larvae were taken by SZ-8 spacecraft and experienced the 16.5-day shuttle spaceflight. We performed miRNA microarray analysis, and the results showed that 23 miRNAs were altered in a complex space environment and different expression patterns were observed in the space synthetic and radiation environments. Most putative target genes of the altered miRNAs in the space synthetic environment were predicted to be involved in developmental processes instead of in the regulation of transcription, and the enrichment of these genes was due to space radiation. Furthermore, integration analysis of the miRNA and mRNA expression profiles confirmed that twelve genes were differently regulated by seven miRNAs. These genes may be involved in embryonic development, reproduction, transcription factor activity, oviposition in a space synthetic environment, positive regulation of growth and body morphogenesis in a space radiation environment. Specifically, we found that cel-miR-52, -55, and -56 of the miR-51 family were sensitive to space environmental stressors and could regulate biological behavioural responses and neprilysin activity through the different isoforms of T01C4.1 and F18A12.8. These findings suggest that C. elegans responded to spaceflight by altering the expression of miRNAs and some target

miRConnect: Identifying Effector Genes of miRNAs and miRNA Families in Cancer Cells

DEFF Research Database (Denmark)

Hua, Youjia; Duan, Shiwei; Murmann, Andrea E

2011-01-01

have generated custom data sets containing expression information of 54 miRNA families sharing the same seed match. We have developed a novel strategy for correlating miRNAs with individual genes based on a summed Pearson Correlation Coefficient (sPCC) that mimics an in silico titration experiment......micro(mi)RNAs are small non-coding RNAs that negatively regulate expression of most mRNAs. They are powerful regulators of various differentiation stages, and the expression of genes that either negatively or positively correlate with expressed miRNAs is expected to hold information....... By focusing on the genes that correlate with the expression of miRNAs without necessarily being direct targets of miRNAs, we have clustered miRNAs into different functional groups. This has resulted in the identification of three novel miRNAs that are linked to the epithelial-to-mesenchymal transition (EMT...

Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco.

Science.gov (United States)

Chen, Qiansi; Li, Meng; Zhang, Zhongchun; Tie, Weiwei; Chen, Xia; Jin, Lifeng; Zhai, Niu; Zheng, Qingxia; Zhang, Jianfeng; Wang, Ran; Xu, Guoyun; Zhang, Hui; Liu, Pingping; Zhou, Huina

2017-01-10

Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed miRNAs

Arctigenin Confers Neuroprotection Against Mechanical Trauma Injury in Human Neuroblastoma SH-SY5Y Cells by Regulating miRNA-16 and miRNA-199a Expression to Alleviate Inflammation.

Science.gov (United States)

Song, Jie; Li, Na; Xia, Yang; Gao, Zhong; Zou, Sa-Feng; Yan, Yu-Hui; Li, Shao-Heng; Wang, Yue; Meng, Ya-Kun; Yang, Jing-Xian; Kang, Ting-Guo

2016-09-01

Mechanical trauma injury is a severe insult to neural cells. Subsequent secondary injury involves the release of inflammatory factors that have dramatic consequences for undamaged cells, leading to normal cell death after the initial injury. The present study investigated the capacity for arctigenin (ARC) to prevent secondary effects and evaluated the mechanism underlying the action of microRNA (miRNA)-199a and miRNA-16 in a mechanical trauma injury (MTI) model using SH-SY5Y cells in vitro. SH-SY5Y cells are often applied to in vitro models of neuronal function and differentiation. Recently, miRNAs have been demonstrated to play a crucial role in NF-κB and cholinergic signaling, which can regulate inflammation. The cell model was established by scratch-induced injury of human SH-SY5Y cells, which mimics the characteristics of MTI. A cell counting kit-8 (CCK-8), terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL), and immunocytochemistry were used to measure cell viability. Enzyme-linked immunosorbent assay (ELISA) was used to evaluate the inflammatory cytokine and cholinesterase (CHE) content. The lactate dehydrogenase (LDH) content was measured to assess the degree of cell injury. The mRNA levels were measured by RT-PCR to analyze ARC's mechanism of action. miRNA inhibitors and mimics were used to inhibit and strengthen the expression of miRNAs. Protein expression was detected by western blotting analysis. ARC treatment reduced the TNF-α and IL-6 levels as well as the number of TUNEL+ apoptotic SH-SY5Y cells surrounding the scratch and increased the IL-10 level compared to the controls. ARC attenuated the increase of the cell damage degree and LDH content induced by scratching, indicating increased cell survival. Mechanistic studies showed that ARC upregulated the miRNA-16 and miRNA-199a levels to reduce upstream protein (IKKα and IKKβ) expression and inhibit NF-κB signaling pathway activity; moreover, the increased miRNA-199a suppresses

Decoding Facial Expressions: A New Test with Decoding Norms.

Science.gov (United States)

Leathers, Dale G.; Emigh, Ted H.

1980-01-01

Describes the development and testing of a new facial meaning sensitivity test designed to determine how specialized are the meanings that can be decoded from facial expressions. Demonstrates the use of the test to measure a receiver's current level of skill in decoding facial expressions. (JMF)

The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature.

Science.gov (United States)

Jung, Inuk; Kang, Hyejin; Kim, Jang Uk; Chang, Hyeonsook; Kim, Sun; Jung, Woosuk

2018-03-19

Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss. Despite of its importance as a traditional medicine, biological mechanisms of ginseng has not been well studied and even the genome sequence of ginseng is yet to be determined due to its complex genome structure. Thus, it is challenging to investigate the molecular biology mechanisms at the transcript level. To investigate how ginseng responds to the high ambient temperature environment, we performed high throughput RNA sequencing and implemented a bioinformatics pipeline for the integrated analysis of small-RNA and mRNA-seq data without a reference genome. By performing reverse transcriptase (RT) PCR and sanger sequencing of transcripts that were assembled using our pipeline, we validated that their sequences were expressed in our samples. Furthermore, to investigate the interaction between genes and non-coding small RNAs and their regulation status under the high ambient temperature, we identified potential gene regulatory miRNAs. As a result, 100,672 contigs with significant expression level were identified and 6 known, 214 conserved and 60 potential novel miRNAs were predicted to be expressed under the high ambient temperature. Collectively, we have found that development, flowering and temperature responsive genes were induced under high ambient temperature, whereas photosynthesis related genes were repressed. Functional miRNAs were down-regulated under the high ambient temperature. Among them are miR156 and miR396 that target flowering (SPL6

Forced Sequence Sequential Decoding

DEFF Research Database (Denmark)

Jensen, Ole Riis; Paaske, Erik

1998-01-01

We describe a new concatenated decoding scheme based on iterations between an inner sequentially decoded convolutional code of rate R=1/4 and memory M=23, and block interleaved outer Reed-Solomon (RS) codes with nonuniform profile. With this scheme decoding with good performance is possible as low...... as Eb/N0=0.6 dB, which is about 1.25 dB below the signal-to-noise ratio (SNR) that marks the cutoff rate for the full system. Accounting for about 0.45 dB due to the outer codes, sequential decoding takes place at about 1.7 dB below the SNR cutoff rate for the convolutional code. This is possible since...... the iteration process provides the sequential decoders with side information that allows a smaller average load and minimizes the probability of computational overflow. Analytical results for the probability that the first RS word is decoded after C computations are presented. These results are supported...

Identification of novel miRNAs and miRNA dependent developmental shifts of gene expression in Arabidopsis thaliana.

Directory of Open Access Journals (Sweden)

Shuhua Zhan

Full Text Available microRNAs (miRNAs are small, endogenous RNAs of 20 approximately 25 nucleotides, processed from stem-loop regions of longer RNA precursors. Plant miRNAs act as negative regulators of target mRNAs predominately by slicing target transcripts, and a number of miRNAs play important roles in development. We analyzed a number of published datasets from Arabidopsis thaliana to characterize novel miRNAs, novel miRNA targets, and miRNA-regulated developmental changes in gene expression. These data include microarray profiling data and small RNA (sRNA deep sequencing data derived from miRNA biogenesis/transport mutants, microarray profiling data of mRNAs in a developmental series, and computational predictions of conserved genomic stem-loop structures. Our conservative analyses identified five novel mature miRNAs and seven miRNA targets, including one novel target gene. Two complementary miRNAs that target distinct mRNAs were encoded by one gene. We found that genes targeted by known miRNAs, and genes up-regulated or down-regulated in miRNA mutant inflorescences, are highly expressed in the wild type inflorescence. In addition, transcripts upregulated within the mutant inflorescences were abundant in wild type leaves and shoot meristems and low in pollen and seed. Downregulated transcripts were abundant in wild type pollen and seed and low in shoot meristems, roots and leaves. Thus, disrupting miRNA function causes the inflorescence transcriptome to resemble the leaf and meristem and to differ from pollen and seed. Applications of our computational approach to other species and the use of more liberal criteria than reported here will further expand the number of identified miRNAs and miRNA targets. Our findings suggest that miRNAs have a global role in promoting vegetative to reproductive transitions in A. thaliana.

21 CFR 882.4215 - Clip rack.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Clip rack. 882.4215 Section 882.4215 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Surgical Devices § 882.4215 Clip rack. (a) Identification. A clip rack is a...

Dicer and miRNA in relation to clinicopathological variables in colorectal cancer patients

International Nuclear Information System (INIS)

Stratmann, Johannes; Wang, Chao-Jie; Gnosa, Sebastian; Wallin, Åsa; Hinselwood, David; Sun, Xiao-Feng; Zhang, Hong

2011-01-01

Dicer is aberrantly expressed in several types of cancers. Applying real-time PCR, we detected the expression of Dicer mRNA in normal mucosa (n = 162), primary colorectal cancer (CRC) (n = 162) and liver metastasis (n = 37), and analysed the relationship between Dicer expression and clinicopathological features. We also correlated the expression of Dicer mRNA to the miRNA expression of miR-141, miR-200a, miR-200b, mir-200c and miR-429 in liver metastases. RT-PCR and qPCR were used to analyse the Dicer expression in normal mucosa, primary tumour and liver metastasis by using the High Capacity cDNA Reverse Transcription Kit and TaqMan™ ® Gene Expression assays for Dicer and GAPDH. RT-PCR and qPCR were used to detect miRNA expression in liver metastases by utilizing TaqMan ® MicroRNA Reverse Transcription Kit and TaqMan ® miRNA Assays. Statistical analyses were performed with STATISTICA. Dicer expression in rectal cancer (3.146 ± 0.953) was higher than in colon cancer (2.703 ± 1.204, P = 0.018). Furthermore the Dicer expression was increased in primary tumours (3.146 ± 0.952) in comparison to that in normal mucosa from rectal cancer patients (2.816 ± 1.009, P = 0.034) but this is not evident in colon cancer patients. Dicer expression in liver metastases was decreased in comparison to that of either normal mucosa or primary tumour in both colon and rectal cancers (P < 0.05). Patients with a high Dicer expression in normal mucosa had a worse prognosis compared to those with a low Dicer expression, independently of gender, age, tumour site, stage and differentiation (P < 0.001, RR 3.682, 95% CI 1.749 - 7.750). In liver metastases, Dicer was positively related to miR-141 (R = 0.419, P = 0.015). Dicer is up-regulated in the early development of rectal cancers. An increased expression of Dicer mRNA in normal mucosa from CRC patients is significantly related to poor survival independently of gender, age, tumour site, stage and differentiation

Intelligent tutoring using HyperCLIPS

Science.gov (United States)

Hill, Randall W., Jr.; Pickering, Brad

1990-01-01

HyperCard is a popular hypertext-like system used for building user interfaces to databases and other applications, and CLIPS is a highly portable government-owned expert system shell. We developed HyperCLIPS in order to fill a gap in the U.S. Army's computer-based instruction tool set; it was conceived as a development environment for building adaptive practical exercises for subject-matter problem-solving, though it is not limited to this approach to tutoring. Once HyperCLIPS was developed, we set out to implement a practical exercise prototype using HyperCLIPS in order to demonstrate the following concepts: learning can be facilitated by doing; student performance evaluation can be done in real-time; and the problems in a practical exercise can be adapted to the individual student's knowledge.

Bioinformatics of cardiovascular miRNA biology.

Science.gov (United States)

Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

2015-12-01

MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

Content-based video retrieval by example video clip

Science.gov (United States)

Dimitrova, Nevenka; Abdel-Mottaleb, Mohamed

1997-01-01

This paper presents a novel approach for video retrieval from a large archive of MPEG or Motion JPEG compressed video clips. We introduce a retrieval algorithm that takes a video clip as a query and searches the database for clips with similar contents. Video clips are characterized by a sequence of representative frame signatures, which are constructed from DC coefficients and motion information (`DC+M' signatures). The similarity between two video clips is determined by using their respective signatures. This method facilitates retrieval of clips for the purpose of video editing, broadcast news retrieval, or copyright violation detection.

Forced Sequence Sequential Decoding

DEFF Research Database (Denmark)

Jensen, Ole Riis

In this thesis we describe a new concatenated decoding scheme based on iterations between an inner sequentially decoded convolutional code of rate R=1/4 and memory M=23, and block interleaved outer Reed-Solomon codes with non-uniform profile. With this scheme decoding with good performance...... is possible as low as Eb/No=0.6 dB, which is about 1.7 dB below the signal-to-noise ratio that marks the cut-off rate for the convolutional code. This is possible since the iteration process provides the sequential decoders with side information that allows a smaller average load and minimizes the probability...... of computational overflow. Analytical results for the probability that the first Reed-Solomon word is decoded after C computations are presented. This is supported by simulation results that are also extended to other parameters....

The First Report of miRNAs from a Thysanopteran Insect, Thrips palmi Karny Using High-Throughput Sequencing.

Directory of Open Access Journals (Sweden)

K B Rebijith

Full Text Available Thrips palmi Karny (Thysanoptera: Thripidae is the sole vector of Watermelon bud necrosis tospovirus, where the crop loss has been estimated to be around USD 50 million annually. Chemical insecticides are of limited use in the management of T. palmi due to the thigmokinetic behaviour and development of high levels of resistance to insecticides. There is an urgent need to find out an effective futuristic management strategy, where the small RNAs especially microRNAs hold great promise as a key player in the growth and development. miRNAs are a class of short non-coding RNAs involved in regulation of gene expression either by mRNA cleavage or by translational repression. We identified and characterized a total of 77 miRNAs from T. palmi using high-throughput deep sequencing. Functional classifications of the targets for these miRNAs revealed that majority of them are involved in the regulation of transcription and translation, nucleotide binding and signal transduction. We have also validated few of these miRNAs employing stem-loop RT-PCR, qRT-PCR and Northern blot. The present study not only provides an in-depth understanding of the biological and physiological roles of miRNAs in governing gene expression but may also lead as an invaluable tool for the management of thysanopteran insects in the future.

Cortical Response Similarities Predict which Audiovisual Clips Individuals Viewed, but Are Unrelated to Clip Preference.

Directory of Open Access Journals (Sweden)

David A Bridwell

Full Text Available Cortical responses to complex natural stimuli can be isolated by examining the relationship between neural measures obtained while multiple individuals view the same stimuli. These inter-subject correlation's (ISC's emerge from similarities in individual's cortical response to the shared audiovisual inputs, which may be related to their emergent cognitive and perceptual experience. Within the present study, our goal is to examine the utility of using ISC's for predicting which audiovisual clips individuals viewed, and to examine the relationship between neural responses to natural stimuli and subjective reports. The ability to predict which clips individuals viewed depends on the relationship of the EEG response across subjects and the nature in which this information is aggregated. We conceived of three approaches for aggregating responses, i.e. three assignment algorithms, which we evaluated in Experiment 1A. The aggregate correlations algorithm generated the highest assignment accuracy (70.83% chance = 33.33% and was selected as the assignment algorithm for the larger sample of individuals and clips within Experiment 1B. The overall assignment accuracy was 33.46% within Experiment 1B (chance = 06.25%, with accuracies ranging from 52.9% (Silver Linings Playbook to 11.75% (Seinfeld within individual clips. ISC's were significantly greater than zero for 15 out of 16 clips, and fluctuations within the delta frequency band (i.e. 0-4 Hz primarily contributed to response similarities across subjects. Interestingly, there was insufficient evidence to indicate that individuals with greater similarities in clip preference demonstrate greater similarities in cortical responses, suggesting a lack of association between ISC and clip preference. Overall these results demonstrate the utility of using ISC's for prediction, and further characterize the relationship between ISC magnitudes and subjective reports.

Cortical Response Similarities Predict which Audiovisual Clips Individuals Viewed, but Are Unrelated to Clip Preference.

Science.gov (United States)

Bridwell, David A; Roth, Cullen; Gupta, Cota Navin; Calhoun, Vince D

2015-01-01

Cortical responses to complex natural stimuli can be isolated by examining the relationship between neural measures obtained while multiple individuals view the same stimuli. These inter-subject correlation's (ISC's) emerge from similarities in individual's cortical response to the shared audiovisual inputs, which may be related to their emergent cognitive and perceptual experience. Within the present study, our goal is to examine the utility of using ISC's for predicting which audiovisual clips individuals viewed, and to examine the relationship between neural responses to natural stimuli and subjective reports. The ability to predict which clips individuals viewed depends on the relationship of the EEG response across subjects and the nature in which this information is aggregated. We conceived of three approaches for aggregating responses, i.e. three assignment algorithms, which we evaluated in Experiment 1A. The aggregate correlations algorithm generated the highest assignment accuracy (70.83% chance = 33.33%) and was selected as the assignment algorithm for the larger sample of individuals and clips within Experiment 1B. The overall assignment accuracy was 33.46% within Experiment 1B (chance = 06.25%), with accuracies ranging from 52.9% (Silver Linings Playbook) to 11.75% (Seinfeld) within individual clips. ISC's were significantly greater than zero for 15 out of 16 clips, and fluctuations within the delta frequency band (i.e. 0-4 Hz) primarily contributed to response similarities across subjects. Interestingly, there was insufficient evidence to indicate that individuals with greater similarities in clip preference demonstrate greater similarities in cortical responses, suggesting a lack of association between ISC and clip preference. Overall these results demonstrate the utility of using ISC's for prediction, and further characterize the relationship between ISC magnitudes and subjective reports.

On Decoding Interleaved Chinese Remainder Codes

DEFF Research Database (Denmark)

Li, Wenhui; Sidorenko, Vladimir; Nielsen, Johan Sebastian Rosenkilde

2013-01-01

We model the decoding of Interleaved Chinese Remainder codes as that of finding a short vector in a Z-lattice. Using the LLL algorithm, we obtain an efficient decoding algorithm, correcting errors beyond the unique decoding bound and having nearly linear complexity. The algorithm can fail...... with a probability dependent on the number of errors, and we give an upper bound for this. Simulation results indicate that the bound is close to the truth. We apply the proposed decoding algorithm for decoding a single CR code using the idea of “Power” decoding, suggested for Reed-Solomon codes. A combination...... of these two methods can be used to decode low-rate Interleaved Chinese Remainder codes....

A novel vascular clip design for the reliable induction of 2-kidney, 1-clip hypertension in the rat

OpenAIRE

Chelko, Stephen P.; Schmiedt, Chad W.; Lewis, Tristan H.; Lewis, Stephen J.; Robertson, Tom P.

2011-01-01

The 2-kidney, 1-clip (2K1C) model has provided many insights into the pathogenesis of renovascular hypertension. However, studies using the 2K1C model often report low success rates of hypertension, with typical success rates of just 40–60%. We hypothesized that these low success rates are due to fundamental design flaws in the clips traditionally used in 2K1C models. Specifically, the gap widths of traditional silver clips may not be maintained during investigator handling and these clips ma...

CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.

Science.gov (United States)

Shah, Ankeeta; Qian, Yingzhi; Weyn-Vanhentenryck, Sebastien M; Zhang, Chaolin

2017-02-15

UV cross-linking and immunoprecipitation (CLIP), followed by high-throughput sequencing, is a powerful biochemical assay that maps in vivo protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package. The software is implemented in Perl. The source code and detailed documentation are available at http://zhanglab.c2b2.columbia.edu/index.php/CTK . cz2294@columbia.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

KAUST Repository

Kleftogiannis, Dimitrios A.; Korfiati, Aigli; Theofilatos, Konstantinos A.; Likothanassis, Spiridon D.; Tsakalidis, Athanasios K.; Mavroudi, Seferina P.

2013-01-01

Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. © 2013 Elsevier Inc.

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

KAUST Repository

Kleftogiannis, Dimitrios A.

2013-06-01

Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3\\'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. © 2013 Elsevier Inc.

42 CFR 495.344 - Approval of the State Medicaid HIT plan, the HIT PAPD and update, the HIT IAPD and update, and...

Science.gov (United States)

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Approval of the State Medicaid HIT plan, the HIT PAPD and update, the HIT IAPD and update, and the annual HIT IAPD. 495.344 Section 495.344 Public... Requirements Specific to the Medicaid Program § 495.344 Approval of the State Medicaid HIT plan, the HIT PAPD...

Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.

Science.gov (United States)

Chen, Muyan; Storey, Kenneth B

2014-02-01

The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing its metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. We identified 279 sea cucumber miRNAs, including 15 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA; after at least 15 days of continuous torpor) were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 30 differentially expressed miRNAs ([RPM (reads per million) >10, |FC| (|fold change|)≥1, FDR (false discovery rate)<0.01]) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-124, miR-124-3p, miR-79, miR-9 and miR-2010 were significantly over-expressed during deep aestivation compared with non-aestivation animals, suggesting that these miRNAs may play important roles in metabolic rate suppression during aestivation. High-throughput sequencing data and microarray data have been submitted to the GEO database with accession number: 16902695. Copyright © 2014 Elsevier B.V. All rights reserved.

Generation of miRNA sponge constructs

NARCIS (Netherlands)

Kluiver, Joost; Slezak-Prochazka, Izabella; Smigielska-Czepiel, Katarzyna; Halsema, Nancy; Kroesen, Bart-Jan; van den Berg, Anke

2012-01-01

MicroRNA (miRNA) sponges are RNA molecules with repeated miRNA antisense sequences that can sequester miRNAs from their endogenous targets and thus serve as a decoy. Stably expressed miRNA sponges are especially valuable for long-term loss-of-function studies and can be used in vitro and in vivo. We

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.

Science.gov (United States)

Paraskevopoulou, Maria D; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A G

2013-07-01

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.

Modified Clipped LMS Algorithm

Directory of Open Access Journals (Sweden)

Lotfizad Mojtaba

2005-01-01

Full Text Available Abstract A new algorithm is proposed for updating the weights of an adaptive filter. The proposed algorithm is a modification of an existing method, namely, the clipped LMS, and uses a three-level quantization ( scheme that involves the threshold clipping of the input signals in the filter weight update formula. Mathematical analysis shows the convergence of the filter weights to the optimum Wiener filter weights. Also, it can be proved that the proposed modified clipped LMS (MCLMS algorithm has better tracking than the LMS algorithm. In addition, this algorithm has reduced computational complexity relative to the unmodified one. By using a suitable threshold, it is possible to increase the tracking capability of the MCLMS algorithm compared to the LMS algorithm, but this causes slower convergence. Computer simulations confirm the mathematical analysis presented.

List Decoding of Algebraic Codes

DEFF Research Database (Denmark)

Nielsen, Johan Sebastian Rosenkilde

We investigate three paradigms for polynomial-time decoding of Reed–Solomon codes beyond half the minimum distance: the Guruswami–Sudan algorithm, Power decoding and the Wu algorithm. The main results concern shaping the computational core of all three methods to a problem solvable by module...... Hermitian codes using Guruswami–Sudan or Power decoding faster than previously known, and we show how to Wu list decode binary Goppa codes....... to solve such using module minimisation, or using our new Demand–Driven algorithm which is also based on module minimisation. The decoding paradigms are all derived and analysed in a self-contained manner, often in new ways or examined in greater depth than previously. Among a number of new results, we...

Decoding Delay Controlled Completion Time Reduction in Instantly Decodable Network Coding

KAUST Repository

Douik, Ahmed

2016-06-27

For several years, the completion time and the decoding delay problems in Instantly Decodable Network Coding (IDNC) were considered separately and were thought to act completely against each other. Recently, some works aimed to balance the effects of these two important IDNC metrics but none of them studied a further optimization of one by controlling the other. This paper investigates the effect of controlling the decoding delay to reduce the completion time below its currently best-known solution in both perfect and imperfect feedback with persistent erasure channels. To solve the problem, the decodingdelay- dependent expressions of the users’ and overall completion times are derived in the complete feedback scenario. Although using such expressions to find the optimal overall completion time is NP-hard, the paper proposes two novel heuristics that minimizes the probability of increasing the maximum of these decoding-delay-dependent completion time expressions after each transmission through a layered control of their decoding delays. Afterward, the paper extends the study to the imperfect feedback scenario in which uncertainties at the sender affects its ability to anticipate accurately the decoding delay increase at each user. The paper formulates the problem in such environment and derives the expression of the minimum increase in the completion time. Simulation results show the performance of the proposed solutions and suggest that both heuristics achieves a lower mean completion time as compared to the best-known heuristics for the completion time reduction in perfect and imperfect feedback. The gap in performance becomes more significant as the erasure of the channel increases.

Decoding Delay Controlled Completion Time Reduction in Instantly Decodable Network Coding

KAUST Repository

Douik, Ahmed S.; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim

2016-01-01

For several years, the completion time and the decoding delay problems in Instantly Decodable Network Coding (IDNC) were considered separately and were thought to act completely against each other. Recently, some works aimed to balance the effects of these two important IDNC metrics but none of them studied a further optimization of one by controlling the other. This paper investigates the effect of controlling the decoding delay to reduce the completion time below its currently best-known solution in both perfect and imperfect feedback with persistent erasure channels. To solve the problem, the decodingdelay- dependent expressions of the users’ and overall completion times are derived in the complete feedback scenario. Although using such expressions to find the optimal overall completion time is NP-hard, the paper proposes two novel heuristics that minimizes the probability of increasing the maximum of these decoding-delay-dependent completion time expressions after each transmission through a layered control of their decoding delays. Afterward, the paper extends the study to the imperfect feedback scenario in which uncertainties at the sender affects its ability to anticipate accurately the decoding delay increase at each user. The paper formulates the problem in such environment and derives the expression of the minimum increase in the completion time. Simulation results show the performance of the proposed solutions and suggest that both heuristics achieves a lower mean completion time as compared to the best-known heuristics for the completion time reduction in perfect and imperfect feedback. The gap in performance becomes more significant as the erasure of the channel increases.

Improved decoding for a concatenated coding system

DEFF Research Database (Denmark)

Paaske, Erik

1990-01-01

The concatenated coding system recommended by CCSDS (Consultative Committee for Space Data Systems) uses an outer (255,233) Reed-Solomon (RS) code based on 8-b symbols, followed by the block interleaver and an inner rate 1/2 convolutional code with memory 6. Viterbi decoding is assumed. Two new...... decoding procedures based on repeated decoding trials and exchange of information between the two decoders and the deinterleaver are proposed. In the first one, where the improvement is 0.3-0.4 dB, only the RS decoder performs repeated trials. In the second one, where the improvement is 0.5-0.6 dB, both...... decoders perform repeated decoding trials and decoding information is exchanged between them...

IMP3 RNP safe houses prevent miRNA-directed HMGA2 mRNA decay in cancer and development

DEFF Research Database (Denmark)

Jønson, Lars; Christiansen, Jan; Hansen, Thomas van Overeem

2014-01-01

by let-7, and let-7 antagomiRs make HMGA2 refractory to IMP3. Removal of let-7 target sites eliminates IMP3-dependent stabilization, and IMP3-containing bodies are depleted of Ago1-4 and miRNAs. The relationship between Hmga2 mRNA and IMPs also exists in the developing limb bud, where IMP1-deficient...... that IMP3 RNPs may function as cytoplasmic safe houses and prevent miRNA-directed mRNA decay of oncogenes during tumor progression....

MiRNA Biogenesis and Intersecting Pathways

DEFF Research Database (Denmark)

Ben Chaabane, Samir

MicroRNAs (miRNAs) are small non-coding RNAs that function as guide molecules in RNA silencing. Plant miRNAs are critical for plant growth, development and stress response, and are processed in Arabidopsis from primary miRNA transcripts (pri-miRNAs) by the endonuclease activity of the DICER-LIKE1...... questions need to be addressed to establish a valid link, we provide encouraging evidence of the involvement of chromatin remodeling factors FAS1 and FAS2 in miRNA biogenesis. Together, we have expanded our understanding of the intersections between miRNA biogenesis and other pathways....

Sepsis from dropped clips at laparoscopic cholecystectomy

International Nuclear Information System (INIS)

Hussain, Sarwat

2001-01-01

We report seven patients in whom five dropped surgical clips and two gallstones were visualized in the peritoneal cavity, on radiological studies. In two, subphrenic abscesses and empyemas developed as a result of dropped clips into the peritoneal cavity during or following laparoscopic cholecystectomy. In one of these two, a clip was removed surgically from the site of an abscess. In two other patients dropped gallstones, and in three, dropped clips led to no complications. These were seen incidentally on studies done for other indications. Abdominal abscess secondary to dropped gallstones is a well-recognized complication of laparoscopic cholecystectomy (LC). We conclude that even though dropped surgical clips usually do not cause problems, they should be considered as a risk additional to other well-known causes of post-LC abdominal sepsis

You never think about my feelings: interpersonal dominance as a predictor of emotion decoding accuracy.

Science.gov (United States)

Moeller, Sara K; Lee, Elizabeth A Ewing; Robinson, Michael D

2011-08-01

Dominance and submission constitute fundamentally different social interaction strategies that may be enacted most effectively to the extent that the emotions of others are relatively ignored (dominance) versus noticed (submission). On the basis of such considerations, we hypothesized a systematic relationship between chronic tendencies toward high versus low levels of interpersonal dominance and emotion decoding accuracy in objective tasks. In two studies (total N = 232), interpersonally dominant individuals exhibited poorer levels of emotion recognition in response to audio and video clips (Study 1) and facial expressions of emotion (Study 2). The results provide a novel perspective on interpersonal dominance, suggest its strategic nature (Study 2), and are discussed in relation to Fiske's (1993) social-cognitive theory of power. 2011 APA, all rights reserved

Integrated microRNA and gene expression profiling reveals the crucial miRNAs in curcumin anti-lung cancer cell invasion.

Science.gov (United States)

Zhan, Jian-Wei; Jiao, De-Min; Wang, Yi; Song, Jia; Wu, Jin-Hong; Wu, Li-Jun; Chen, Qing-Yong; Ma, Sheng-Lin

2017-09-01

Curcumin (diferuloylmethane) has chemopreventive and therapeutic properties against many types of tumors, both in vitro and in vivo. Previous reports have shown that curcumin exhibits anti-invasive activities, but the mechanisms remain largely unclear. In this study, both microRNA (miRNA) and messenger RNA (mRNA) expression profiles were used to characterize the anti-metastasis mechanisms of curcumin in human non-small cell lung cancer A549 cell line. Microarray analysis revealed that 36 miRNAs were differentially expressed between the curcumin-treated and control groups. miR-330-5p exhibited maximum upregulation, while miR-25-5p exhibited maximum downregulation in the curcumin treatment group. mRNA expression profiles and functional analysis indicated that 226 differentially expressed mRNAs belonged to different functional categories. Significant pathway analysis showed that mitogen-activated protein kinase, transforming growth factor-β, and Wnt signaling pathways were significantly downregulated. At the same time, axon guidance, glioma, and ErbB tyrosine kinase receptor signaling pathways were significantly upregulated. We constructed a miRNA gene network that contributed to the curcumin inhibition of metastasis in lung cancer cells. let-7a-3p, miR-1262, miR-499a-5p, miR-1276, miR-331-5p, and miR-330-5p were identified as key microRNA regulators in the network. Finally, using miR-330-5p as an example, we confirmed the role of miR-330-5p in mediating the anti-migration effect of curcumin, suggesting the importance of miRNAs in the regulation of curcumin biological activity. Our findings provide new insights into the anti-metastasis mechanism of curcumin in lung cancer. © 2017 The Authors. Thoracic Cancer published by China Lung Oncology Group and John Wiley & Sons Australia, Ltd.

Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity.

Science.gov (United States)

Wyman, Stacia K; Knouf, Emily C; Parkin, Rachael K; Fritz, Brian R; Lin, Daniel W; Dennis, Lucas M; Krouse, Michael A; Webster, Philippa J; Tewari, Muneesh

2011-09-01

Modification of microRNA sequences by the 3' addition of nucleotides to generate so-called "isomiRs" adds to the complexity of miRNA function, with recent reports showing that 3' modifications can influence miRNA stability and efficiency of target repression. Here, we show that the 3' modification of miRNAs is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications result predominantly from adenylation and uridylation and are seen across tissue types, disease states, and developmental stages. To quantitatively profile 3' nucleotide additions, we developed and validated a novel assay based on NanoString Technologies' nCounter platform. For certain miRNAs, the frequency of modification was altered by processes such as cell differentiation, indicating that 3' modification is a biologically regulated process. To investigate the mechanism of 3' nucleotide additions, we used RNA interference to screen a panel of eight candidate miRNA nucleotidyl transferases for 3' miRNA modification activity in human cells. Multiple enzymes, including MTPAP, PAPD4, PAPD5, ZCCHC6, ZCCHC11, and TUT1, were found to govern 3' nucleotide addition to miRNAs in a miRNA-specific manner. Three of these enzymes-MTPAP, ZCCHC6, and TUT1-have not previously been known to modify miRNAs. Collectively, our results indicate that 3' modification observed in next-generation small RNA sequencing data is a biologically relevant process, and identify enzymatic mechanisms that may lead to new approaches for modulating miRNA activity in vivo.

Integrated Analysis of Dysregulated ncRNA and mRNA Expression Profiles in Humans Exposed to Carbon Nanotubes.

Directory of Open Access Journals (Sweden)

Anna A Shvedova

Full Text Available As the application of carbon nanotubes (CNT in consumer products continues to rise, studies have expanded to determine the associated risks of exposure on human and environmental health. In particular, several lines of evidence indicate that exposure to multi-walled carbon nanotubes (MWCNT could pose a carcinogenic risk similar to asbestos fibers. However, to date the potential markers of MWCNT exposure are not yet explored in humans.In the present study, global mRNA and ncRNA expression profiles in the blood of exposed workers, having direct contact with MWCNT aerosol for at least 6 months (n = 8, were compared with expression profiles of non-exposed (n = 7 workers (e.g., professional and/or technical staff from the same manufacturing facility.Significant changes in the ncRNA and mRNA expression profiles were observed between exposed and non-exposed worker groups. An integrative analysis of ncRNA-mRNA correlations was performed to identify target genes, functional relationships, and regulatory networks in MWCNT-exposed workers. The coordinated changes in ncRNA and mRNA expression profiles revealed a set of miRNAs and their target genes with roles in cell cycle regulation/progression/control, apoptosis and proliferation. Further, the identified pathways and signaling networks also revealed MWCNT potential to trigger pulmonary and cardiovascular effects as well as carcinogenic outcomes in humans, similar to those previously described in rodents exposed to MWCNTs.This study is the first to investigate aberrant changes in mRNA and ncRNA expression profiles in the blood of humans exposed to MWCNT. The significant changes in several miRNAs and mRNAs expression as well as their regulatory networks are important for getting molecular insights into the MWCNT-induced toxicity and pathogenesis in humans. Further large-scale prospective studies are necessary to validate the potential applicability of such changes in mRNAs and miRNAs as prognostic markers

CLIPS - C LANGUAGE INTEGRATED PRODUCTION SYSTEM (MACINTOSH VERSION)

Science.gov (United States)

Culbert, C.

1994-01-01

The C Language Integrated Production System, CLIPS, is a shell for developing expert systems. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. The primary design goals for CLIPS are portability, efficiency, and functionality. For these reasons, the program is written in C. CLIPS meets or outperforms most micro- and minicomputer based artificial intelligence tools. CLIPS is a forward chaining rule-based language. The program contains an inference engine and a language syntax that provide a framework for the construction of an expert system. It also includes tools for debugging an application. CLIPS is based on the Rete algorithm, which enables very efficient pattern matching. The collection of conditions and actions to be taken if the conditions are met is constructed into a rule network. As facts are asserted either prior to or during a session, CLIPS pattern-matches the number of fields. Wildcards and variables are supported for both single and multiple fields. CLIPS syntax allows the inclusion of externally defined functions (outside functions which are written in a language other than CLIPS). CLIPS itself can be embedded in a program such that the expert system is available as a simple subroutine call. Advanced features found in CLIPS version 4.3 include an integrated microEMACS editor, the ability to generate C source code from a CLIPS rule base to produce a dedicated executable, binary load and save capabilities for CLIPS rule bases, and the utility program CRSV (Cross-Reference, Style, and Verification) designed to facilitate the development and maintenance of large rule bases. Five machine versions are available. Each machine version includes the source and the executable for that machine. The UNIX version includes the source and binaries for IBM RS/6000, Sun3 series, and Sun4 series computers. The UNIX, DEC VAX, and DEC RISC Workstation versions are line oriented. The PC version and the Macintosh

Methylation of miRNA genes and oncogenesis.

Science.gov (United States)

Loginov, V I; Rykov, S V; Fridman, M V; Braga, E A

2015-02-01

Interaction between microRNA (miRNA) and messenger RNA of target genes at the posttranscriptional level provides fine-tuned dynamic regulation of cell signaling pathways. Each miRNA can be involved in regulating hundreds of protein-coding genes, and, conversely, a number of different miRNAs usually target a structural gene. Epigenetic gene inactivation associated with methylation of promoter CpG-islands is common to both protein-coding genes and miRNA genes. Here, data on functions of miRNAs in development of tumor-cell phenotype are reviewed. Genomic organization of promoter CpG-islands of the miRNA genes located in inter- and intragenic areas is discussed. The literature and our own results on frequency of CpG-island methylation in miRNA genes from tumors are summarized, and data regarding a link between such modification and changed activity of miRNA genes and, consequently, protein-coding target genes are presented. Moreover, the impact of miRNA gene methylation on key oncogenetic processes as well as affected signaling pathways is discussed.

Microvesicles derived from adult human bone marrow and tissue specific mesenchymal stem cells shuttle selected pattern of miRNAs.

Directory of Open Access Journals (Sweden)

Federica Collino

Full Text Available BACKGROUND: Cell-derived microvesicles (MVs have been described as a new mechanism of cell-to-cell communication. MVs after internalization within target cells may deliver genetic information. Human bone marrow derived mesenchymal stem cells (MSCs and liver resident stem cells (HLSCs were shown to release MVs shuttling functional mRNAs. The aim of the present study was to evaluate whether MVs derived from MSCs and HLSCs contained selected micro-RNAs (miRNAs. METHODOLOGY/PRINCIPAL FINDINGS: MVs were isolated from MSCs and HLSCs. The presence in MVs of selected ribonucleoproteins involved in the traffic and stabilization of RNA was evaluated. We observed that MVs contained TIA, TIAR and HuR multifunctional proteins expressed in nuclei and stress granules, Stau1 and 2 implicated in the transport and stability of mRNA and Ago2 involved in miRNA transport and processing. RNA extracted from MVs and cells of origin was profiled for 365 known human mature miRNAs by real time PCR. Hierarchical clustering and similarity analysis of miRNAs showed 41 co-expressed miRNAs in MVs and cells. Some miRNAs were accumulated within MVs and absent in the cells after MV release; others were retained within the cells and not secreted in MVs. Gene ontology analysis of predicted and validated targets showed that the high expressed miRNAs in cells and MVs could be involved in multi-organ development, cell survival and differentiation. Few selected miRNAs shuttled by MVs were also associated with the immune system regulation. The highly expressed miRNAs in MVs were transferred to target cells after MV incorporation. CONCLUSIONS: This study demonstrated that MVs contained ribonucleoproteins involved in the intracellular traffic of RNA and selected pattern of miRNAs, suggesting a dynamic regulation of RNA compartmentalization in MVs. The observation that MV-highly expressed miRNAs were transferred to target cells, rises the possibility that the biological effect of stem

Identification of age- and disease-related alterations in circulating miRNAs in a mouse model of Alzheimer's disease

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Sylvia eGarza-Manero

2015-02-01

Full Text Available Alzheimer's disease (AD is a neurodegenerative disorder characterized clinically by the progressive decline of memory and cognition. Histopathologically, two main hallmarks have been identified in AD: amyloid-β peptide extracellular neuritic plaques and neurofibrillary tangles formed by posttranslational modified tau protein. A definitive diagnosis can only be achieved after the post mortem verification of the histological mentioned alterations. Therefore the development of biomarkers that allow an early diagnosis and/or predict disease progression is imperative. The prospect of a blood-based biomarker is possible with the finding of circulating microRNAs (miRNAs, a class of small non-coding RNAs of 22-25 nucleotides length that regulate mRNA translation rate. miRNAs travel through blood and recent studies performed in potential AD cases suggest the possibility of finding pathology-associated differences in circulating miRNA levels that may serve to assist in early diagnosis of the disease. However, these studies analyzed samples at a single time-point, limiting the use of miRNAs as biomarkers in AD progression. In this study we evaluated miRNA levels in plasma samples at different time-points of the evolution of an AD-like pathology in a transgenic mouse model of the disease (3xTg-AD. We performed multiplex qRT-PCR and compared the plasmatic levels of 84 miRNAs previously associated to central nervous system development and disease. No significant differences were detected between WT and transgenic young mice. However, age-related significant changes in miRNA abundance were observed for both WT and transgenic mice, and some of these were specific for the 3xTg-AD. In agreement, variations in the levels of particular miRNAs were identified between WT and transgenic old mice thus suggesting that the age-dependent evolution of the AD-like pathology, rather than the presence and expression of the transgenes, modifies the circulating miRNA levels in

Characterization of novel precursor miRNAs using next generation sequencing and prediction of miRNA targets in Atlantic halibut.

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Teshome Tilahun Bizuayehu

Full Text Available BACKGROUND: microRNAs (miRNAs are implicated in regulation of many cellular processes. miRNAs are processed to their mature functional form in a step-wise manner by multiple proteins and cofactors in the nucleus and cytoplasm. Many miRNAs are conserved across vertebrates. Mature miRNAs have recently been characterized in Atlantic halibut (Hippoglossus hippoglossus L.. The aim of this study was to identify and characterize precursor miRNA (pre-miRNAs and miRNA targets in this non-model flatfish. Discovery of miRNA precursor forms and targets in non-model organisms is difficult because of limited source information available. Therefore, we have developed a methodology to overcome this limitation. METHODS: Genomic DNA and small transcriptome of Atlantic halibut were sequenced using Roche 454 pyrosequencing and SOLiD next generation sequencing (NGS, respectively. Identified pre- miRNAs were further validated with reverse-transcription PCR. miRNA targets were identified using miRanda and RNAhybrid target prediction tools using sequences from public databases. Some of miRNA targets were also identified using RACE-PCR. miRNA binding sites were validated with luciferase assay using the RTS34st cell line. RESULTS: We obtained more than 1.3 M and 92 M sequence reads from 454 genomic DNA sequencing and SOLiD small RNA sequencing, respectively. We identified 34 known and 9 novel pre-miRNAs. We predicted a number of miRNA target genes involved in various biological pathways. miR-24 binding to kisspeptin 1 receptor-2 (kiss1-r2 was confirmed using luciferase assay. CONCLUSION: This study demonstrates that identification of conserved and novel pre-miRNAs in a non-model vertebrate lacking substantial genomic resources can be performed by combining different next generation sequencing technologies. Our results indicate a wide conservation of miRNA precursors and involvement of miRNA in multiple regulatory pathways, and provide resources for further research on miRNA

Evaluation of the miRNA-146a and miRNA-155 Expression Levels in Patients with Oral Lichen Planus.

Science.gov (United States)

Ahmadi-Motamayel, Fatemeh; Bayat, Zeynab; Hajilooi, Mehrdad; Shahryar-Hesami, Soroosh; Mahdavinezhad, Ali; Samie, Lida; Solgi, Ghasem

2017-12-01

Oral Lichen Planus (OLP) is a chronic autoimmune disease that could be considered as a potential premalignant status. To evaluate the miRNA-146a and miRNA-155 expression levels in patients with oral Lichen planus lesions compared to healthy subjects with normal oral mucosa. Forty patients with oral lichen planus and 18 healthy age and gender-matched controls were recruited in this case-control study. Oral lichen planus was diagnosed clinically and pathologically. The expression levels of two miRNAs in peripheral blood samples were determined using commercial TaqMan MicroRNA Assays. Relative quantification of gene expression was calculated by the 2-ΔΔct method. The expression levels of miRNA-146a and miRNA-155 in patients with oral Lichen planus were significantly higher than those of healthy controls. Also, a direct but insignificant correlation was found between miRNA-155 and miRNA-146a expression levels among the patient group. Our findings indicate that miRNA-146a and miRNA-155 could be potential biomarkers for the immunopathogenesis of oral lichen planus.

A novel vascular clip design for the reliable induction of 2-kidney, 1-clip hypertension in the rat.

Science.gov (United States)

Chelko, Stephen P; Schmiedt, Chad W; Lewis, Tristan H; Lewis, Stephen J; Robertson, Tom P

2012-02-01

The 2-kidney, 1-clip (2K1C) model has provided many insights into the pathogenesis of renovascular hypertension. However, studies using the 2K1C model often report low success rates of hypertension, with typical success rates of just 40-60%. We hypothesized that these low success rates are due to fundamental design flaws in the clips traditionally used in 2K1C models. Specifically, the gap widths of traditional silver clips may not be maintained during investigator handling and these clips may also be easily dislodged from the renal artery following placement. Therefore, we designed and tested a novel vascular clip possessing design features to maintain both gap width and position around the renal artery. In this initial study, application of these new clips to the left renal artery produced reliable and consistent levels of hypertension in rats. Nine-day application of clips with gap widths of 0.27, 0.25, and 0.23 mm elicited higher mean arterial blood pressures of 112 ± 4, 121 ± 6, and 135 ± 7 mmHg, respectively (n = 8 for each group), than those of sham-operated controls (95 ± 2 mmHg, n = 8). Moreover, 8 out of 8 rats in each of the 0.23 and 0.25 mm 2K1C groups were hypertensive, whereas 7 out of 8 rats in the 0.27 mm 2K1C group were hypertensive. Plasma renin concentrations were also increased in all 2K1C groups compared with sham-operated controls. In summary, this novel clip design may help eliminate the large degree of unreliability commonly encountered with the 2K1C model.

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

Science.gov (United States)

2017-01-01

Post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression. It is mainly performed by RNA binding proteins and microRNAs, which target RNAs and typically affect their stability. Recent efforts from the scientific community have aimed at understanding post-transcriptional regulation at a global scale by using high-throughput sequencing techniques such as cross-linking and immunoprecipitation (CLIP), which facilitates identification of binding sites of these regulatory factors. However, the diversity in the experimental procedures and bioinformatics analyses has hindered the integration of multiple datasets and thus limited the development of an integrated view of post-transcriptional regulation. In this work, we have performed a comprehensive analysis of 107 CLIP datasets from 49 different RBPs in HEK293 cells to shed light on the complex interactions that govern post-transcriptional regulation. By developing a more stringent CLIP analysis pipeline we have discovered the existence of conserved regulatory AU-rich regions in the 3’UTRs where miRNAs and RBPs that regulate several processes such as polyadenylation or mRNA stability bind. Analogous to promoters, many factors have binding sites overlapping or in close proximity in these hotspots and hence the regulation of the mRNA may depend on their relative concentrations. This hypothesis is supported by RBP knockdown experiments that alter the relative concentration of RBPs in the cell. Upon AGO2 knockdown (KD), transcripts containing “free” target sites show increased expression levels compared to those containing target sites in hotspots, which suggests that target sites within hotspots are less available for miRNAs to bind. Interestingly, these hotspots appear enriched in genes with regulatory functions such as DNA binding and RNA binding. Taken together, our results suggest that hotspots are functional regulatory elements that define an extra layer

77 FR 32639 - HIT Standards Committee and HIT Policy Committee; Call for Nominations

Science.gov (United States)

2012-06-01

... DEPARTMENT OF HEALTH AND HUMAN SERVICES HIT Standards Committee and HIT Policy Committee; Call for... Health Information Technology Policy Committee (HITPC). Name of Committees: HIT Standards Committee and HIT Policy Committee. General Function of the Committees: The HITSC is charged to provide...

Anesthesia management for MitraClip device implantation

Directory of Open Access Journals (Sweden)

Harikrishnan Kothandan

2014-01-01

Full Text Available Aims and Objectives: Percutaneous MitraClip implantation has been demonstrated as an alternative procedure in high-risk patients with symptomatic severe mitral regurgitation (MR who are not suitable (or denied mitral valve repair/replacement due to excessive co morbidity. The MitraClip implantation was performed under general anesthesia and with 3-dimensional transesophageal echocardiography (TEE and fluoroscopic guidance. Materials and Methods: Peri-operative patient data were extracted from the electronic and paper medical records of 21 patients who underwent MitraClip implantations. Results: Four MitraClip implantation were performed in the catheterization laboratory; remaining 17 were performed in the hybrid operating theatre. In 2 patients, procedure was aborted, in one due to migration of the Chiari network into the left atrium and in second one, the leaflets and chords of the mitral valve torn during clipping resulting in consideration for open surgery. In the remaining 19 patients, MitraClip was implanted and the patients showed acute reduction of severe MR to mild-moderate MR. All the patients had invasive blood pressure monitoring and the initial six patients had central venous catheterization prior to the procedure. Intravenous heparin was administered after the guiding catheter was introduced through the inter-atrial septum and activated clotting time was maintained beyond 250 s throughout the procedure. Protamine was administered at the end of the procedure. All the patients were monitored in the intensive care unit after the procedure. Conclusions: Percutaneous MitraClip implantation is a feasible alternative in high-risk patients with symptomatic severe MR. Anesthesia management requirements are similar to open surgical mitral valve repair or replacement. TEE plays a vital role during the MitraClip implantation.

Hit Parade

DEFF Research Database (Denmark)

Backe, Hans-Joachim

2017-01-01

Daniel Cermak-Sassenrath, Max Alexander Wrighton, Hans-Joachim Backe. Hit Parade. Installation. Kulturnatten 2017, ITU, Copenhagen, DK, Oct 13, 2017.......Daniel Cermak-Sassenrath, Max Alexander Wrighton, Hans-Joachim Backe. Hit Parade. Installation. Kulturnatten 2017, ITU, Copenhagen, DK, Oct 13, 2017....

Hit Parade

DEFF Research Database (Denmark)

Cermak, Daniel; Wrighton, Max Alexander; Backe, Hans-Joachim

2016-01-01

Daniel Cermak-Sassenrath, Max Alexander Wrighton, Hans-Joachim Backe. Hit Parade. Installation. Demo Night, ITU, Copenhagen, DK, Oct 5, 2016.......Daniel Cermak-Sassenrath, Max Alexander Wrighton, Hans-Joachim Backe. Hit Parade. Installation. Demo Night, ITU, Copenhagen, DK, Oct 5, 2016....

NIMROD Simulations of the HIT-SI and HIT-SI3 Devices

Science.gov (United States)

Morgan, Kyle; Jarboe, Tom; Hossack, Aaron; Chandra, Rian; Everson, Chris

2017-10-01

The Helicity Injected Torus with Steady Inductive helicity injection (HIT-SI) experiment uses a set of inductively driven helicity injectors to apply non-axisymmetric current drive on the edge of the plasma, driving an axisymmetric spheromak equilibrium in a central confinement volume. Significant improvements have been made to extended MHD modeling of HIT-SI, with both the resolution of disagreement at high injector frequencies in HIT-SI in addition to successes with the new upgraded HIT-SI3 device. Previous numerical studies of HIT-SI, using a zero-beta eMHD model, focused on operations with a drive frequency of 14.5 kHz, and found reduced agreement with both the magnetic profile and current amplification at higher frequencies (30-70 kHz). HIT-SI3 has three helicity injectors which are able to operate with different mode structures of perturbations through the different relative temporal phasing of the injectors. Simulations that allow for pressure gradients have been performed in the parameter regimes of both devices using the NIMROD code and show improved agreement with experimental results, most notably capturing the observed Shafranov-shift due to increased beta observed at higher finj in HIT-SI and the variety of toroidal perturbation spectra available in HIT-SI3. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences under Award Number DE-FG02- 96ER54361.

P2X7 mRNA expression in non-small cell lung cancer: MicroRNA regulation and prognostic value

OpenAIRE

BOLDRINI, LAURA; GIORDANO, MIRELLA; ALÌ, GRETA; MELFI, FRANCA; ROMANO, GAETANO; LUCCHI, MARCO; FONTANINI, GABRIELLA

2014-01-01

The human P2X7 receptor is significant and exhibits several functions in neoplasia. At present, little is known with regard to its regulation. P2X7 expression may be regulated post-transcriptionally and putative microRNA (miRNA) binding sites are considered to be involved. The aim of this study was to determine whether miRNAs (miR-21, let-7 g and miR-205) regulate P2X7 mRNA stability. In addition, the impact of P2X7 expression in patients with non-small cell lung cancer (NSCLC) was investigat...

Fast decoders for qudit topological codes

International Nuclear Information System (INIS)

Anwar, Hussain; Brown, Benjamin J; Campbell, Earl T; Browne, Dan E

2014-01-01

Qudit toric codes are a natural higher-dimensional generalization of the well-studied qubit toric code. However, standard methods for error correction of the qubit toric code are not applicable to them. Novel decoders are needed. In this paper we introduce two renormalization group decoders for qudit codes and analyse their error correction thresholds and efficiency. The first decoder is a generalization of a ‘hard-decisions’ decoder due to Bravyi and Haah (arXiv:1112.3252). We modify this decoder to overcome a percolation effect which limits its threshold performance for many-level quantum systems. The second decoder is a generalization of a ‘soft-decisions’ decoder due to Poulin and Duclos-Cianci (2010 Phys. Rev. Lett. 104 050504), with a small cell size to optimize the efficiency of implementation in the high dimensional case. In each case, we estimate thresholds for the uncorrelated bit-flip error model and provide a comparative analysis of the performance of both these approaches to error correction of qudit toric codes. (paper)

Targeting oncomiRNAs and mimicking tumor suppressor miRNAs: New trends in the development of miRNA therapeutic strategies in oncology (Review)

Science.gov (United States)

GAMBARI, ROBERTO; BROGNARA, ELEONORA; SPANDIDOS, DEMETRIOS A.; FABBRI, ENRICA

2016-01-01

MicroRNA (miRNA or miR) therapeutics in cancer are based on targeting or mimicking miRNAs involved in cancer onset, progression, angiogenesis, epithelial-mesenchymal transition and metastasis. Several studies conclusively have demonstrated that miRNAs are deeply involved in tumor onset and progression, either behaving as tumor-promoting miRNAs (oncomiRNAs and metastamiRNAs) or as tumor suppressor miRNAs. This review focuses on the most promising examples potentially leading to the development of anticancer, miRNA-based therapeutic protocols. The inhibition of miRNA activity can be readily achieved by the use of miRNA inhibitors and oligomers, including RNA, DNA and DNA analogues (miRNA antisense therapy), small molecule inhibitors, miRNA sponges or through miRNA masking. On the contrary, the enhancement of miRNA function (miRNA replacement therapy) can be achieved by the use of modified miRNA mimetics, such as plasmid or lentiviral vectors carrying miRNA sequences. Combination strategies have been recently developed based on the observation that i) the combined administration of different antagomiR molecules induces greater antitumor effects and ii) some anti-miR molecules can sensitize drug-resistant tumor cell lines to therapeutic drugs. In this review, we discuss two additional issues: i) the combination of miRNA replacement therapy with drug administration and ii) the combination of antagomiR and miRNA replacement therapy. One of the solid results emerging from different independent studies is that miRNA replacement therapy can enhance the antitumor effects of the antitumor drugs. The second important conclusion of the reviewed studies is that the combination of anti-miRNA and miRNA replacement strategies may lead to excellent results, in terms of antitumor effects. PMID:27175518

Low-power priority Address-Encoder and Reset-Decoder data-driven readout for Monolithic Active Pixel Sensors for tracker system

International Nuclear Information System (INIS)

Yang, P.; Aglieri, G.; Cavicchioli, C.; Chalmet, P.L.; Chanlek, N.; Collu, A.; Gao, C.; Hillemanns, H.; Junique, A.; Kofarago, M.; Keil, M.; Kugathasan, T.; Kim, D.; Kim, J.; Lattuca, A.; Marin Tobon, C.A.; Marras, D.; Mager, M.; Martinengo, P.; Mazza, G.

2015-01-01

Active Pixel Sensors used in High Energy Particle Physics require low power consumption to reduce the detector material budget, low integration time to reduce the possibilities of pile-up and fast readout to improve the detector data capability. To satisfy these requirements, a novel Address-Encoder and Reset-Decoder (AERD) asynchronous circuit for a fast readout of a pixel matrix has been developed. The AERD data-driven readout architecture operates the address encoding and reset decoding based on an arbitration tree, and allows us to readout only the hit pixels. Compared to the traditional readout structure of the rolling shutter scheme in Monolithic Active Pixel Sensors (MAPS), AERD can achieve a low readout time and a low power consumption especially for low hit occupancies. The readout is controlled at the chip periphery with a signal synchronous with the clock, allows a good digital and analogue signal separation in the matrix and a reduction of the power consumption. The AERD circuit has been implemented in the TowerJazz 180 nm CMOS Imaging Sensor (CIS) process with full complementary CMOS logic in the pixel. It works at 10 MHz with a matrix height of 15 mm. The energy consumed to read out one pixel is around 72 pJ. A scheme to boost the readout speed to 40 MHz is also discussed. The sensor chip equipped with AERD has been produced and characterised. Test results including electrical beam measurement are presented

Low-power priority Address-Encoder and Reset-Decoder data-driven readout for Monolithic Active Pixel Sensors for tracker system

Energy Technology Data Exchange (ETDEWEB)

Yang, P., E-mail: yangping0710@126.com [Central China Normal University, Wuhan (China); Aglieri, G.; Cavicchioli, C. [CERN, 1210 Geneva 23 (Switzerland); Chalmet, P.L. [MIND, Archamps (France); Chanlek, N. [Suranaree University of Technology, Nakhon Ratchasima (Thailand); Collu, A. [University of Cagliari, Cagliari (Italy); INFN (Italy); Gao, C. [Central China Normal University, Wuhan (China); Hillemanns, H.; Junique, A. [CERN, 1210 Geneva 23 (Switzerland); Kofarago, M. [CERN, 1210 Geneva 23 (Switzerland); University of Utrecht, Utrecht (Netherlands); Keil, M.; Kugathasan, T. [CERN, 1210 Geneva 23 (Switzerland); Kim, D. [Dongguk and Yonsei University, Seoul (Korea, Republic of); Kim, J. [Pusan National University, Busan (Korea, Republic of); Lattuca, A. [University of Torino, Torino (Italy); INFN (Italy); Marin Tobon, C.A. [CERN, 1210 Geneva 23 (Switzerland); Marras, D. [University of Cagliari, Cagliari (Italy); INFN (Italy); Mager, M.; Martinengo, P. [CERN, 1210 Geneva 23 (Switzerland); Mazza, G. [University of Torino, Torino (Italy); INFN (Italy); and others

2015-06-11

Active Pixel Sensors used in High Energy Particle Physics require low power consumption to reduce the detector material budget, low integration time to reduce the possibilities of pile-up and fast readout to improve the detector data capability. To satisfy these requirements, a novel Address-Encoder and Reset-Decoder (AERD) asynchronous circuit for a fast readout of a pixel matrix has been developed. The AERD data-driven readout architecture operates the address encoding and reset decoding based on an arbitration tree, and allows us to readout only the hit pixels. Compared to the traditional readout structure of the rolling shutter scheme in Monolithic Active Pixel Sensors (MAPS), AERD can achieve a low readout time and a low power consumption especially for low hit occupancies. The readout is controlled at the chip periphery with a signal synchronous with the clock, allows a good digital and analogue signal separation in the matrix and a reduction of the power consumption. The AERD circuit has been implemented in the TowerJazz 180 nm CMOS Imaging Sensor (CIS) process with full complementary CMOS logic in the pixel. It works at 10 MHz with a matrix height of 15 mm. The energy consumed to read out one pixel is around 72 pJ. A scheme to boost the readout speed to 40 MHz is also discussed. The sensor chip equipped with AERD has been produced and characterised. Test results including electrical beam measurement are presented.

Low-power priority Address-Encoder and Reset-Decoder data-driven readout for Monolithic Active Pixel Sensors for tracker system

Science.gov (United States)

Yang, P.; Aglieri, G.; Cavicchioli, C.; Chalmet, P. L.; Chanlek, N.; Collu, A.; Gao, C.; Hillemanns, H.; Junique, A.; Kofarago, M.; Keil, M.; Kugathasan, T.; Kim, D.; Kim, J.; Lattuca, A.; Marin Tobon, C. A.; Marras, D.; Mager, M.; Martinengo, P.; Mazza, G.; Mugnier, H.; Musa, L.; Puggioni, C.; Rousset, J.; Reidt, F.; Riedler, P.; Snoeys, W.; Siddhanta, S.; Usai, G.; van Hoorne, J. W.; Yi, J.

2015-06-01

Active Pixel Sensors used in High Energy Particle Physics require low power consumption to reduce the detector material budget, low integration time to reduce the possibilities of pile-up and fast readout to improve the detector data capability. To satisfy these requirements, a novel Address-Encoder and Reset-Decoder (AERD) asynchronous circuit for a fast readout of a pixel matrix has been developed. The AERD data-driven readout architecture operates the address encoding and reset decoding based on an arbitration tree, and allows us to readout only the hit pixels. Compared to the traditional readout structure of the rolling shutter scheme in Monolithic Active Pixel Sensors (MAPS), AERD can achieve a low readout time and a low power consumption especially for low hit occupancies. The readout is controlled at the chip periphery with a signal synchronous with the clock, allows a good digital and analogue signal separation in the matrix and a reduction of the power consumption. The AERD circuit has been implemented in the TowerJazz 180 nm CMOS Imaging Sensor (CIS) process with full complementary CMOS logic in the pixel. It works at 10 MHz with a matrix height of 15 mm. The energy consumed to read out one pixel is around 72 pJ. A scheme to boost the readout speed to 40 MHz is also discussed. The sensor chip equipped with AERD has been produced and characterised. Test results including electrical beam measurement are presented.

MiRNA-548ah, a Potential Molecule Associated with Transition from Immune Tolerance to Immune Activation of Chronic Hepatitis B

Directory of Open Access Journals (Sweden)

Tong-Jing Xing

2014-08-01

Full Text Available Objective: The present study aims to identify the differently expressed microRNA (miRNA molecules and target genes of miRNA in the immune tolerance (IT and immune activation (IA stages of chronic hepatitis B (CHB. Methods: miRNA expression profiles of peripheral blood mononuclear cells (PBMCs at the IT and IA stages of CHB were screened using miRNA microarrays and authenticated using a quantitative real-time polymerase chain reaction (RT-PCR. Gene ontology (GO and the Kyoto encyclopedia of genes and genomes (KEGG were used to analyze the significant functions and pathways of possible target genes of miRNAs. Assays of the gain and loss of function of the miRNAs were performed to verify the target genes in THP-1 cell lines. The luciferase reporter test was used on 293T cells as direct targets. Results: Significantly upregulated miR-548 and miR-4804 were observed in the miRNA microarrays and confirmed by RT-PCR in PBMCs at the IT and IA stages of CHB. GO and KEGG analysis revealed that MiR-548 and miR-4804 could be involved in numerous signaling pathways and protein binding activity. IFNγR1 was predicted as a target gene and validated as the direct gene of MiR-548. Significant negative correlation was found between the miR-548ah and mRNA levels of IFN-γR1 in CHB patients. Conclusions: The abnormal expression profiles of miRNA in PBMCs could be closely associated with immune activation of chronic HBV infection. miR-548, by targeting IFN-γR1, may represent a mechanism that can facilitate viral pathogenesis and help determine new therapeutic molecular targets.

Recurrence of ICA-PCoA aneurysms after neck clipping.

Science.gov (United States)

Sakaki, T; Takeshima, T; Tominaga, M; Hashimoto, H; Kawaguchi, S

1994-01-01

Between 1975 and 1992, 2211 patients underwent aneurysmal neck clipping at the Nara Medical University clinic and associated hospitals. The aneurysm in 931 of these patients was situated at the junction of the internal carotid artery (ICA) and posterior communicating artery (PCoA). Seven patients were readmitted 4 to 17 years after the first surgery because of regrowth and rupture of an ICA-PCoA aneurysmal sac that had arisen from the residual neck. On angiograms obtained following aneurysmal neck clipping, a large primitive type of PCoA was demonstrated in six patients and a small PCoA in one. A small residual aneurysm was confirmed in only two patients and angiographically complete neck clipping in five. Recurrent ICA-PCoA aneurysms were separated into two types based on the position of the old clip in relation to the new growth. Type 1 aneurysms regrow from the entire neck and balloon eccentrically. In this type, it is possible to apply the clip at the neck as in conventional clipping for a ruptured aneurysm. Type 2 includes aneurysms in which the proximal portion of a previous clip is situated at the corner of the ICA and aneurysmal neck and the distal portion on the enlarged dome of the aneurysm, because the sac is regrowing from a portion of the residual neck. In this type of aneurysm, a Sugita fenestrated clip can occlude the residual neck, overriding the old clip. Classifying these aneurysms into two groups is very useful from a surgical point of view because it is possible to apply a new clip without removing the old clip, which was found to be adherent to surrounding tissue.

Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes. Part 3; The Map and Related Decoding Algirithms

Science.gov (United States)

Lin, Shu; Fossorier, Marc

1998-01-01

In a coded communication system with equiprobable signaling, MLD minimizes the word error probability and delivers the most likely codeword associated with the corresponding received sequence. This decoding has two drawbacks. First, minimization of the word error probability is not equivalent to minimization of the bit error probability. Therefore, MLD becomes suboptimum with respect to the bit error probability. Second, MLD delivers a hard-decision estimate of the received sequence, so that information is lost between the input and output of the ML decoder. This information is important in coded schemes where the decoded sequence is further processed, such as concatenated coding schemes, multi-stage and iterative decoding schemes. In this chapter, we first present a decoding algorithm which both minimizes bit error probability, and provides the corresponding soft information at the output of the decoder. This algorithm is referred to as the MAP (maximum aposteriori probability) decoding algorithm.

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems.

Directory of Open Access Journals (Sweden)

Abdimajid Osman

Full Text Available Platelet concentrates (PCs are prepared at blood banks for transfusion to patients in certain clinical conditions associated with a low platelet count. To prevent transfusion-transmitted infections via PCs, different pathogen reduction (PR systems have been developed that inactivate the nucleic acids of contaminating pathogens by chemical cross-linking, a mechanism that may also affect platelets' nucleic acids. We previously reported that treatment of stored platelets with the PR system Intercept significantly reduced the level of half of the microRNAs that were monitored, induced platelet activation and compromised the platelet response to physiological agonists. Using genome-wide differential expression (DE RNA sequencing (RNA-Seq, we now report that Intercept markedly perturbs the mRNA transcriptome of human platelets and alters the expression level of >800 mRNAs (P<0.05 compared to other PR systems and control platelets. Of these, 400 genes were deregulated with DE corresponding to fold changes (FC ≥ 2. At the p-value < 0.001, as many as 147 genes were deregulated by ≥ 2-fold in Intercept-treated platelets, compared to none in the other groups. Finally, integrated analysis combining expression data for microRNA (miRNA and mRNA, and involving prediction of miRNA-mRNA interactions, disclosed several positive and inverse correlations between miRNAs and mRNAs in stored platelets. In conclusion, this study demonstrates that Intercept markedly deregulates the platelet mRNA transcriptome, concomitant with reduced levels of mRNA-regulatory miRNAs. These findings should enlighten authorities worldwide when considering the implementation of PR systems, that target nucleic acids and are not specific to pathogens, for the management of blood products.

Epigenetic architecture and miRNA: reciprocal regulators

DEFF Research Database (Denmark)

Wiklund, Erik D; Kjems, Jørgen; Clark, Susan J

2010-01-01

Deregulation of epigenetic and microRNA (miRNA) pathways are emerging as key events in carcinogenesis. miRNA genes can be epigenetically regulated and miRNAs can themselves repress key enzymes that drive epigenetic remodeling. Epigenetic and miRNA functions are thus tightly interconnected......RNAs) are considered especially promising in clinical applications, and their biogenesis and function is a subject of active research. In this review, the current status of epigenetic miRNA regulation is summarized and future therapeutic prospects in the field are discussed with a focus on cancer....

Hit Parade

DEFF Research Database (Denmark)

Cermak, Daniel; Wrighton, Max Alexander; Backe, Hans-Joachim

2016-01-01

Daniel Cermak-Sassenrath, Max Alexander Wrighton, Hans-Joachim Backe. Hit Parade. Installation. Kulturnatten 2016, Danish Science Ministry, Copenhagen, DK, Oct 14, 2016.......Daniel Cermak-Sassenrath, Max Alexander Wrighton, Hans-Joachim Backe. Hit Parade. Installation. Kulturnatten 2016, Danish Science Ministry, Copenhagen, DK, Oct 14, 2016....

Journal of Clipped Words in Reader's Digest Magazine

OpenAIRE

Simanjuntak, Lestari

2012-01-01

This study deals with Clipped Words in the “Laughter, the Best Medicine” of Reader's Digest. The objectives of the study are to find out the types of clipped words which are used in the “Laughter, the Best Medicine” of Reader's Digest, to find out sthe dominantly used in the whole story and to reason the dominant clipped word use in the text. The study use descriptive qualitative method. The data were collected from seventeen selected Reader's Digest which contains the clipped word by applie...

Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

OpenAIRE

Wyman, Stacia K.; Knouf, Emily C.; Parkin, Rachael K.; Fritz, Brian R.; Lin, Daniel W.; Dennis, Lucas M.; Krouse, Michael A.; Webster, Philippa J.; Tewari, Muneesh

2011-01-01

Modification of microRNA sequences by the 3′ addition of nucleotides to generate so-called “isomiRs” adds to the complexity of miRNA function, with recent reports showing that 3′ modifications can influence miRNA stability and efficiency of target repression. Here, we show that the 3′ modification of miRNAs is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications resul...

21 CFR 868.6225 - Nose clip.

Science.gov (United States)

2010-04-01

... ANESTHESIOLOGY DEVICES Miscellaneous § 868.6225 Nose clip. (a) Identification. A nose clip is a device intended to close a patient's external nares (nostrils) during diagnostic or therapeutic procedures. (b... from the current good manufacturing practice requirements of the quality system regulation in part 820...

Toric Codes, Multiplicative Structure and Decoding

DEFF Research Database (Denmark)

Hansen, Johan Peder

2017-01-01

Long linear codes constructed from toric varieties over finite fields, their multiplicative structure and decoding. The main theme is the inherent multiplicative structure on toric codes. The multiplicative structure allows for \\emph{decoding}, resembling the decoding of Reed-Solomon codes and al...

Fast decoding algorithms for geometric coded apertures

International Nuclear Information System (INIS)

Byard, Kevin

2015-01-01

Fast decoding algorithms are described for the class of coded aperture designs known as geometric coded apertures which were introduced by Gourlay and Stephen. When compared to the direct decoding method, the algorithms significantly reduce the number of calculations required when performing the decoding for these apertures and hence speed up the decoding process. Experimental tests confirm the efficacy of these fast algorithms, demonstrating a speed up of approximately two to three orders of magnitude over direct decoding.

Exploration of miRNA families for hypotheses generation.

KAUST Repository

Kamanu, T.K.

2013-10-15

Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. Exploratory tools to enhance investigation of characteristics of miRNA families and the functions of family-specific miRNA genes are lacking. We have developed, miRNAVISA, a user-friendly web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. This study illustrates hypothesis generation using miRNAVISA in seven species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.

FPGA implementation of low complexity LDPC iterative decoder

Science.gov (United States)

Verma, Shivani; Sharma, Sanjay

2016-07-01

Low-density parity-check (LDPC) codes, proposed by Gallager, emerged as a class of codes which can yield very good performance on the additive white Gaussian noise channel as well as on the binary symmetric channel. LDPC codes have gained lots of importance due to their capacity achieving property and excellent performance in the noisy channel. Belief propagation (BP) algorithm and its approximations, most notably min-sum, are popular iterative decoding algorithms used for LDPC and turbo codes. The trade-off between the hardware complexity and the decoding throughput is a critical factor in the implementation of the practical decoder. This article presents introduction to LDPC codes and its various decoding algorithms followed by realisation of LDPC decoder by using simplified message passing algorithm and partially parallel decoder architecture. Simplified message passing algorithm has been proposed for trade-off between low decoding complexity and decoder performance. It greatly reduces the routing and check node complexity of the decoder. Partially parallel decoder architecture possesses high speed and reduced complexity. The improved design of the decoder possesses a maximum symbol throughput of 92.95 Mbps and a maximum of 18 decoding iterations. The article presents implementation of 9216 bits, rate-1/2, (3, 6) LDPC decoder on Xilinx XC3D3400A device from Spartan-3A DSP family.

21 CFR 886.1410 - Ophthalmic trial lens clip.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Ophthalmic trial lens clip. 886.1410 Section 886...) MEDICAL DEVICES OPHTHALMIC DEVICES Diagnostic Devices § 886.1410 Ophthalmic trial lens clip. (a) Identification. An ophthalmic trial lens clip is a device intended to hold prisms, spheres, cylinders, or...

Serum miRNA disregulation during transport-related stress in turkey (Meleagris gallopavo

Directory of Open Access Journals (Sweden)

Andreia Tomás Marques

2015-07-01

Full Text Available MicroRNAs (miRNAs are small 21-25 nucleotide regulatory non-coding RNAs that modulate gene expression in eukaryotic organisms. miRNAs are complementary to the 3′-untranslated regions of mRNA and act as post-transcriptional regulators of gene expression, exhibiting remarkable stability in extracellular fluids such as blood. Turkey (Meleagris gallopavo farming is a species economically relevant but the lack of efficient protocols for the evaluation of commercial turkeys prevents to measure the impact of industry practices on birds productivity and welfare. In order to identify potential molecular biomarkers for monitoring stress in turkey’s handling, we investigated by TaqMan qPCR the abundance of five circulating miRNA, namely miR-22, miR-155, miR-181a, miR-204 and miR-365, previously demonstrated to be involved in stress in chicken due to feed deprivation. Road transportation related procedures were selected as stressful model for this study. The serum of twenty healthy animals was collected before and after 2h transportation. Our results demonstrated that miR-22, miR-155 and miR-365 are statistically more expressed after road transportation. Receiver-operator characteristics (ROC analysis was used to estimate the diagnostic value of these miRNAs to evaluate the stress in animals. The serum level of miR-22, miR-155 and miR-365 can discriminate stressed from non-stressed animals with an AUC=0.763, 0.710 and 0.704, respectively, and the average expression of their combination has the same specificity (AUC=0.745. miR-22, miR-155 and miR-365 are stress-specific markers and can be considered as suitable biomarkers to identify turkeys stressed by road transportation.

Bounded-Angle Iterative Decoding of LDPC Codes

Science.gov (United States)

Dolinar, Samuel; Andrews, Kenneth; Pollara, Fabrizio; Divsalar, Dariush

2009-01-01

Bounded-angle iterative decoding is a modified version of conventional iterative decoding, conceived as a means of reducing undetected-error rates for short low-density parity-check (LDPC) codes. For a given code, bounded-angle iterative decoding can be implemented by means of a simple modification of the decoder algorithm, without redesigning the code. Bounded-angle iterative decoding is based on a representation of received words and code words as vectors in an n-dimensional Euclidean space (where n is an integer).

Concatenated coding system with iterated sequential inner decoding

DEFF Research Database (Denmark)

Jensen, Ole Riis; Paaske, Erik

1995-01-01

We describe a concatenated coding system with iterated sequential inner decoding. The system uses convolutional codes of very long constraint length and operates on iterations between an inner Fano decoder and an outer Reed-Solomon decoder......We describe a concatenated coding system with iterated sequential inner decoding. The system uses convolutional codes of very long constraint length and operates on iterations between an inner Fano decoder and an outer Reed-Solomon decoder...

miRNAs in Normal and Malignant Hematopoiesis

Directory of Open Access Journals (Sweden)

Ryutaro Kotaki

2017-07-01

Full Text Available Lineage specification is primarily regulated at the transcriptional level and lineage-specific transcription factors determine cell fates. MicroRNAs (miRNAs are 18–24 nucleotide-long non-coding RNAs that post-transcriptionally decrease the translation of target mRNAs and are essential for many cellular functions. miRNAs also regulate lineage specification during hematopoiesis. This review highlights the roles of miRNAs in B-cell development and malignancies, and discusses how miRNA expression profiles correlate with disease prognoses and phenotypes. We also discuss the potential for miRNAs as therapeutic targets and diagnostic tools for B-cell malignancies.

Biocompatibility of Plastic Clip in Neurocranium - Experimental Study on Dogs.

Science.gov (United States)

Delibegovic, Samir; Dizdarevic, Kemal; Cickusic, Elmir; Katica, Muhamed; Obhodjas, Muamer; Ocus, Muhamed

2016-01-01

A potential advantage of the use of the plastic clips in neurosurgery is their property of causing fewer artifacts than titanium clips as assessed by computed tomography and magnetic resonance scans. The biocompatibility of plastic clips was demonstrated in the peritoneal cavity, but their behavior in the neurocranium is not known. Twelve aggressive stray dogs designated for euthanasia were taken for this experimental study. The animals were divided into two groups. In all cases, after anesthesia, a craniotomy was performed, and after opening the dura, a proximal part titanium clip was placed on the isolated superficial Sylvian vein (a permanent Yasargil FT 746 T clip at a 90° angle, while a plastic Hem-o-lok clip ML was placed on another part of the vein). The first group of animals was sacrificed on the 7 th postoperative day and the second group on the 60 th postoperative day. Samples of tissue around the clips were taken for a histopathological evaluation. The plastic clip caused a more intensive tissue reaction than the titanium clip on the 7 th postoperative day, but there was no statistical difference. Even on the 60 th postoperative day there was no significant difference in tissue reaction between the titanium and plastic clips. These preliminary results confirm the possibility for the use of plastic clips in neurosurgery. Before their use in human neurosurgery, further studies are needed to investigate the long-term effects of the presence of plastic clips in the neurocranium, as well as studies of the aneurysmal model.

CLIPS - C LANGUAGE INTEGRATED PRODUCTION SYSTEM (IBM PC VERSION)

Science.gov (United States)

Riley, G.

1994-01-01

The C Language Integrated Production System, CLIPS, is a shell for developing expert systems. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. The primary design goals for CLIPS are portability, efficiency, and functionality. For these reasons, the program is written in C. CLIPS meets or outperforms most micro- and minicomputer based artificial intelligence tools. CLIPS is a forward chaining rule-based language. The program contains an inference engine and a language syntax that provide a framework for the construction of an expert system. It also includes tools for debugging an application. CLIPS is based on the Rete algorithm, which enables very efficient pattern matching. The collection of conditions and actions to be taken if the conditions are met is constructed into a rule network. As facts are asserted either prior to or during a session, CLIPS pattern-matches the number of fields. Wildcards and variables are supported for both single and multiple fields. CLIPS syntax allows the inclusion of externally defined functions (outside functions which are written in a language other than CLIPS). CLIPS itself can be embedded in a program such that the expert system is available as a simple subroutine call. Advanced features found in CLIPS version 4.3 include an integrated microEMACS editor, the ability to generate C source code from a CLIPS rule base to produce a dedicated executable, binary load and save capabilities for CLIPS rule bases, and the utility program CRSV (Cross-Reference, Style, and Verification) designed to facilitate the development and maintenance of large rule bases. Five machine versions are available. Each machine version includes the source and the executable for that machine. The UNIX version includes the source and binaries for IBM RS/6000, Sun3 series, and Sun4 series computers. The UNIX, DEC VAX, and DEC RISC Workstation versions are line oriented. The PC version and the Macintosh

Post-hit dynamics of price limit hits in the Chinese stock markets

Science.gov (United States)

Wu, Ting; Wang, Yue; Li, Ming-Xia

2017-01-01

Price limit trading rules are useful to cool off traders short-term trading mania on individual stocks. The price dynamics approaching the limit boards are known as the magnet effect. However, the price dynamics after opening price limit hits are not well investigated. Here, we provide a detailed analysis on the price dynamics after the hits of up-limit or down-limit is open based on all A-share stocks traded in the Chinese stock markets. A "W" shape is found in the expected return, which reveals high probability of a continuous price limit hit on the following day. We also find that price dynamics after opening limit hits are dependent on the market trends. The time span of continuously hitting the price limit is found to an influence factor of the expected profit after the limit hit is open. Our analysis provides a better understanding of the price dynamics around the limit boards and contributes potential practical values for investors.

Mounting clips for panel installation

Science.gov (United States)

Cavieres, Andres; Al-Haddad, Tristan; Goodman, Joseph

2017-07-11

A photovoltaic panel mounting clip comprising a base, central indexing tabs, flanges, lateral indexing tabs, and vertical indexing tabs. The mounting clip removably attaches one or more panels to a beam or the like structure, both mechanically and electrically. It provides secure locking of the panels in all directions, while providing guidance in all directions for accurate installation of the panels to the beam or the like structure.

Soft-decision decoding of RS codes

DEFF Research Database (Denmark)

Justesen, Jørn

2005-01-01

By introducing a few simplifying assumptions we derive a simple condition for successful decoding using the Koetter-Vardy algorithm for soft-decision decoding of RS codes. We show that the algorithm has a significant advantage over hard decision decoding when the code rate is low, when two or more...

Towards Clinical Applications of Blood-Borne miRNA Signatures: The Influence of the Anticoagulant EDTA on miRNA Abundance.

Directory of Open Access Journals (Sweden)

Petra Leidinger

Full Text Available Circulating microRNAs (miRNAs from blood are increasingly recognized as biomarker candidates for human diseases. Clinical routine settings frequently include blood sampling in tubes with EDTA as anticoagulant without considering the influence of phlebotomy on the overall miRNA expression pattern. We collected blood samples from six healthy individuals each in an EDTA blood collection tube. Subsequently, the blood was transferred into PAXgeneTM tubes at three different time points, i.e. directly (0 min, 10 min, and 2 h after phlebotomy. As control blood was also directly collected in PAXgeneTM blood RNA tubes that contain a reagent to directly lyse blood cells and stabilize their content. For all six blood donors at the four conditions (24 samples we analyzed the abundance of 1,205 miRNAs by human Agilent miRNA V16 microarrays.While we found generally a homogenous pattern of the miRNA abundance in all 24 samples, the duration of the EDTA treatment appears to influence the miRNA abundance of specific miRNAs. The most significant changes are observed after longer EDTA exposition. Overall, the impact of the different blood sample conditions on the miRNA pattern was substantially lower than intra-individual variations. While samples belonging to one of the six individuals mostly cluster together, there was no comparable clustering for any of the four tested blood sampling conditions. The most affected miRNA was miR-769-3p that was not detected in any of the six PAXgene blood samples, but in all EDTA 2h samples. Accordingly, hsa-miR-769-3p was also the only miRNA that showed a significantly different abundance between the 4 blood sample conditions by an ANOVA analysis (Benjamini-Hochberg adjusted p-value of 0.003. Validation by qRT-PCR confirmed this finding.The pattern of blood-borne miRNA abundance is rather homogenous between the four tested blood sample conditions of six blood donors. There was a clustering between the miRNA profiles that belong

IL-4 Up-Regulates MiR-21 and the MiRNAs Hosted in the CLCN5 Gene in Chronic Lymphocytic Leukemia.

Directory of Open Access Journals (Sweden)

Natalia Ruiz-Lafuente

Full Text Available Interleukin 4 (IL-4 induces B-cell differentiation and survival of chronic lymphocytic leukemia (CLL cells. MicroRNAs (miRNAs regulate mRNA and protein expression, and several miRNAs, deregulated in CLL, might play roles as oncogenes or tumor suppressors. We have studied the miRNA profile of CLL, and its response to IL-4, by oligonucleotide microarrays, resulting in the detection of a set of 129 mature miRNAs consistently expressed in CLL, which included 41 differentially expressed compared to normal B cells (NBC, and 6 significantly underexpressed in ZAP-70 positive patients. IL-4 stimulation brought about up-regulation of the 5p and 3p mature variants of the miR-21 gene, which maps immediately downstream to the VMP1 gene, and of the mature forms generated from the miR-362 (3p and 5p, miR-500a (3p, miR-502 (3p, and miR-532 (3p and 5p genes, which map within the third intron of the CLCN5 gene. Both genes are in turn regulated by IL-4, suggesting that these miRNAs were regulated by IL-4 as passengers from their carrier genes. Their levels of up-regulation by IL-4 significantly correlated with cytoprotection. MiR-21 has been reported to be leukemogenic, associated to bad prognosis in CLL, and the miRNA more frequently overexpressed in human cancer. Up-regulation by IL-4 of miR-21 and the miRNAs hosted in the CLCN5 locus may contribute to evasion of apoptosis of CLL cells. These findings indicate that the IL-4 pathway and the miRNAs induced by IL-4 are promising targets for the development of novel therapies in CLL.

Decoding small surface codes with feedforward neural networks

Science.gov (United States)

Varsamopoulos, Savvas; Criger, Ben; Bertels, Koen

2018-01-01

Surface codes reach high error thresholds when decoded with known algorithms, but the decoding time will likely exceed the available time budget, especially for near-term implementations. To decrease the decoding time, we reduce the decoding problem to a classification problem that a feedforward neural network can solve. We investigate quantum error correction and fault tolerance at small code distances using neural network-based decoders, demonstrating that the neural network can generalize to inputs that were not provided during training and that they can reach similar or better decoding performance compared to previous algorithms. We conclude by discussing the time required by a feedforward neural network decoder in hardware.

Chinese Language Video Clips. [CD-ROM].

Science.gov (United States)

Fleming, Stephen; Hipley, David; Ning, Cynthia

This compact disc includes video clips covering six topics for the learner of Chinese: personal information, commercial transactions, travel and leisure, health and sports, food and school. Filmed on location in Beijing, these naturalistic video clips consist mainly of unrehearsed interviews of ordinary people. The learner is lead through a series…

The Roles of Two miRNAs in Regulating the Immune Response of Sea Cucumber.

Science.gov (United States)

Zhang, Pengjuan; Li, Chenghua; Zhang, Ran; Zhang, Weiwei; Jin, Chunhua; Wang, Lingling; Song, Linsheng

2015-12-01

MicroRNAs (miRNAs) have emerged as key regulators in many pathological processes by suppressing the transcriptional and post-transcriptional expression of target genes. MiR-2008 was previously found to be significantly up-regulated in diseased sea cucumber Apostichopus japonicus by high-through sequencing, whereas the reads of miR-137, a well-documented tumor repressor, displayed no significant change. In the present study, we found that miR-137 expression was slightly attenuated and miR-2008 was significantly enhanced after Vibrio splendidus infection or Lipopolysaccharides application. Further target screening and dual-luciferase reporter assay revealed that the two important miRNAs shared a common target gene of betaine-homocysteine S-methyltransferase (AjBHMT), which exhibited noncorrelated messenger RNA and protein expression patterns after bacterial challenge. In order to fully understand their regulatory mechanisms, we conducted the functional experiments in vitro and in vivo. The overexpression of miR-137 in sea cucumber or primary coelomocytes significantly decreased, whereas the inhibition of miR-137 increased the mRNA and protein expression levels of AjBHMT. In contrast, miR-2008 overexpression and inhibition showed no effect on AjBHMT mRNA levels, but the concentration of AjBHMT protein displayed significant changes both in vitro and in vivo. Consistently, the homocysteine (Hcy) contents were also accordingly altered in the aberrant expression analysis of both miRNAs, consistent with the results of the AjBHMT silencing assay in vitro and in vivo. More importantly, small interfering RNA mediated AjBHMT knockdown and Hcy exposure analyses both significantly increased reactive oxygen species (ROS) production and decreased the number of surviving invasive pathogen in sea cucumber coelomocytes. Taken together, these findings confirmed the differential roles of sea cucumber miR-137 and miR-2008 in regulating the common target AjBHMT to promote ROS production

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

LENUS (Irish Health Repository)

Bray, Isabella

2009-01-01

MiRNAs regulate gene expression at a post-transcriptional level and their dysregulation can play major roles in the pathogenesis of many different forms of cancer, including neuroblastoma, an often fatal paediatric cancer originating from precursor cells of the sympathetic nervous system. We have analyzed a set of neuroblastoma (n = 145) that is broadly representative of the genetic subtypes of this disease for miRNA expression (430 loci by stem-loop RT qPCR) and for DNA copy number alterations (array CGH) to assess miRNA involvement in disease pathogenesis. The tumors were stratified and then randomly split into a training set (n = 96) and a validation set (n = 49) for data analysis. Thirty-seven miRNAs were significantly over- or under-expressed in MYCN amplified tumors relative to MYCN single copy tumors, indicating a potential role for the MYCN transcription factor in either the direct or indirect dysregulation of these loci. In addition, we also determined that there was a highly significant correlation between miRNA expression levels and DNA copy number, indicating a role for large-scale genomic imbalances in the dysregulation of miRNA expression. In order to directly assess whether miRNA expression was predictive of clinical outcome, we used the Random Forest classifier to identify miRNAs that were most significantly associated with poor overall patient survival and developed a 15 miRNA signature that was predictive of overall survival with 72.7% sensitivity and 86.5% specificity in the validation set of tumors. We conclude that there is widespread dysregulation of miRNA expression in neuroblastoma tumors caused by both over-expression of the MYCN transcription factor and by large-scale chromosomal imbalances. MiRNA expression patterns are also predicative of clinical outcome, highlighting the potential for miRNA mediated diagnostics and therapeutics.

Eyewitness Identification Reforms: Are Suggestiveness-Induced Hits and Guesses True Hits?

Science.gov (United States)

Wells, Gary L; Steblay, Nancy K; Dysart, Jennifer E

2012-05-01

Research-based reforms for collecting eyewitness identification evidence (e.g., unbiased pre-lineup instructions, double-blind administration) have been proposed by psychologists and adopted in increasing numbers of jurisdictions across the United States. It is well known that reducing rates of mistaken identifications can also reduce accurate identification rates (hits). But the reforms are largely designed to reduce the suggestiveness of the procedures they are meant to replace. Accordingly, we argue that it is misleading to label any hits obtained because of suggestive procedures as "hits" and then saddle reforms with the charge that they reduce the rate of these illegitimate hits. Eyewitness identification evidence should be based solely on the independent memory of the witness, not aided by biased instructions, cues from lineup administrators, or the use of lineup fillers who make the suspect stand out. Failure to call out these hits as being illegitimate can give solace to those who are motivated to preserve the status quo. © The Author(s) 2012.

Genome-wide identification and functional annotation of miRNAs in anti-inflammatory plant and their cross-kingdom regulation in Homo sapiens.

Science.gov (United States)

Sharma, Ankita; Sahu, Sarika; Kumari, Pooja; Gopi, Soundhara Rajan; Malhotra, Rajesh; Biswas, Sagarika

2017-05-01

MicroRNAs (miRNAs) are newly discovered non-coding small (~17-24 nucleotide) RNAs that regulate gene expression of its target mRNA at the post-transcriptional levels. In this study, total 12,593 ESTs of Curcuma longa were taken from database of expressed sequence tags (dbEST) and clustered into 2821 contigs using EGassembler web server. Precursor miRNAs (pre-miRNAs) were predicted from these contigs that folded into stem-loop structure using MFold server. Thirty-four mature C. longa miRNAs (clo-miRNAs) were identified from pre-miRNAs having targets involved in various important functions of plant such as self-defence, growth and development, alkaloid metabolic pathway and ethylene signalling process. Sequence analysis of identified clo-miRNAs indicated that 56% miRNAs belong to ORF and 44% belong to non-ORF region. clo-mir-5 and clo-mir-6 were established as the conserved miRNAs, whereas clo-mir-20 was predicted to be the most stable miRNA. Phylogenetic analysis carried out by molecular evolutionary genetics analysis (MEGA) software indicated close evolutionary relationship of clo-mir-5075 with osa-MIR5075. Further, identified clo-miRNAs were checked for their cross-kingdom regulatory potential. clo-mir-14 was found to regulate various gene transcripts in humans that has been further investigated for its biostability in foetal bovine serum (FBS). The results indicated higher degree of stability of clo-mir-14 (48 h) in FBS. Thus, contribution of this miRNA to the cellular immune response during the inflamed condition of rheumatoid arthritis and adequate stability may make it a good choice for the therapeutic agent in near future.

Video coding for decoding power-constrained embedded devices

Science.gov (United States)

Lu, Ligang; Sheinin, Vadim

2004-01-01

Low power dissipation and fast processing time are crucial requirements for embedded multimedia devices. This paper presents a technique in video coding to decrease the power consumption at a standard video decoder. Coupled with a small dedicated video internal memory cache on a decoder, the technique can substantially decrease the amount of data traffic to the external memory at the decoder. A decrease in data traffic to the external memory at decoder will result in multiple benefits: faster real-time processing and power savings. The encoder, given prior knowledge of the decoder"s dedicated video internal memory cache management scheme, regulates its choice of motion compensated predictors to reduce the decoder"s external memory accesses. This technique can be used in any standard or proprietary encoder scheme to generate a compliant output bit stream decodable by standard CPU-based and dedicated hardware-based decoders for power savings with the best quality-power cost trade off. Our simulation results show that with a relatively small amount of dedicated video internal memory cache, the technique may decrease the traffic between CPU and external memory over 50%.

Time-sequential changes of differentially expressed miRNAs during the process of anterior lumbar interbody fusion using equine bone protein extract, rhBMP-2 and autograft

Science.gov (United States)

Chen, Da-Fu; Zhou, Zhi-Yu; Dai, Xue-Jun; Gao, Man-Man; Huang, Bao-Ding; Liang, Tang-Zhao; Shi, Rui; Zou, Li-Jin; Li, Hai-Sheng; Bünger, Cody; Tian, Wei; Zou, Xue-Nong

2014-03-01

The precise mechanism of bone regeneration in different bone graft substitutes has been well studied in recent researches. However, miRNAs regulation of the bone formation has been always mysterious. We developed the anterior lumbar interbody fusion (ALIF) model in pigs using equine bone protein extract (BPE), recombinant human bone morphogenetic protein-2 (rhBMP-2) on an absorbable collagen sponge (ACS), and autograft as bone graft substitute, respectively. The miRNA and gene expression profiles of different bone graft materials were examined using microarray technology and data analysis, including self-organizing maps, KEGG pathway and Biological process GO analyses. We then jointly analyzed miRNA and mRNA profiles of the bone fusion tissue at different time points respectively. Results showed that miRNAs, including let-7, miR-129, miR-21, miR-133, miR-140, miR-146, miR-184, and miR-224, were involved in the regulation of the immune and inflammation response, which provided suitable inflammatory microenvironment for bone formation. At late stage, several miRNAs directly regulate SMAD4, Estrogen receptor 1 and 5-hydroxytryptamine (serotonin) receptor 2C for bone formation. It can be concluded that miRNAs play important roles in balancing the inflammation and bone formation.

A novel parallel pipeline structure of VP9 decoder

Science.gov (United States)

Qin, Huabiao; Chen, Wu; Yi, Sijun; Tan, Yunfei; Yi, Huan

2018-04-01

To improve the efficiency of VP9 decoder, a novel parallel pipeline structure of VP9 decoder is presented in this paper. According to the decoding workflow, VP9 decoder can be divided into sub-modules which include entropy decoding, inverse quantization, inverse transform, intra prediction, inter prediction, deblocking and pixel adaptive compensation. By analyzing the computing time of each module, hotspot modules are located and the causes of low efficiency of VP9 decoder can be found. Then, a novel pipeline decoder structure is designed by using mixed parallel decoding methods of data division and function division. The experimental results show that this structure can greatly improve the decoding efficiency of VP9.

SYMBOL LEVEL DECODING FOR DUO-BINARY TURBO CODES

Directory of Open Access Journals (Sweden)

Yogesh Beeharry

2017-05-01

Full Text Available This paper investigates the performance of three different symbol level decoding algorithms for Duo-Binary Turbo codes. Explicit details of the computations involved in the three decoding techniques, and a computational complexity analysis are given. Simulation results with different couple lengths, code-rates, and QPSK modulation reveal that the symbol level decoding with bit-level information outperforms the symbol level decoding by 0.1 dB on average in the error floor region. Moreover, a complexity analysis reveals that symbol level decoding with bit-level information reduces the decoding complexity by 19.6 % in terms of the total number of computations required for each half-iteration as compared to symbol level decoding.

NP-hardness of decoding quantum error-correction codes

Science.gov (United States)

Hsieh, Min-Hsiu; Le Gall, François

2011-05-01

Although the theory of quantum error correction is intimately related to classical coding theory and, in particular, one can construct quantum error-correction codes (QECCs) from classical codes with the dual-containing property, this does not necessarily imply that the computational complexity of decoding QECCs is the same as their classical counterparts. Instead, decoding QECCs can be very much different from decoding classical codes due to the degeneracy property. Intuitively, one expects degeneracy would simplify the decoding since two different errors might not and need not be distinguished in order to correct them. However, we show that general quantum decoding problem is NP-hard regardless of the quantum codes being degenerate or nondegenerate. This finding implies that no considerably fast decoding algorithm exists for the general quantum decoding problems and suggests the existence of a quantum cryptosystem based on the hardness of decoding QECCs.

NP-hardness of decoding quantum error-correction codes

International Nuclear Information System (INIS)

Hsieh, Min-Hsiu; Le Gall, Francois

2011-01-01

Although the theory of quantum error correction is intimately related to classical coding theory and, in particular, one can construct quantum error-correction codes (QECCs) from classical codes with the dual-containing property, this does not necessarily imply that the computational complexity of decoding QECCs is the same as their classical counterparts. Instead, decoding QECCs can be very much different from decoding classical codes due to the degeneracy property. Intuitively, one expects degeneracy would simplify the decoding since two different errors might not and need not be distinguished in order to correct them. However, we show that general quantum decoding problem is NP-hard regardless of the quantum codes being degenerate or nondegenerate. This finding implies that no considerably fast decoding algorithm exists for the general quantum decoding problems and suggests the existence of a quantum cryptosystem based on the hardness of decoding QECCs.

Evaluation framework for K-best sphere decoders

KAUST Repository

Shen, Chungan; Eltawil, Ahmed M.; Salama, Khaled N.

2010-01-01

or receive antennas. Tree-searching type decoder structures such as Sphere decoder and K-best decoder present an interesting trade-off between complexity and performance. Many algorithmic developments and VLSI implementations have been reported in literature

PF4-HIT antibody (KKO) complexes activate broad innate immune and inflammatory responses.

Science.gov (United States)

Haile, Lydia A; Rao, Roshni; Polumuri, Swamy K; Arepally, Gowthami M; Keire, David A; Verthelyi, Daniela; Sommers, Cynthia D

2017-11-01

Heparin-induced thrombocytopenia (HIT) is an immune-mediated complication of heparin anticoagulation therapy resulting in thrombocytopenia frequently accompanied by thrombosis. Current evidence suggests that HIT is associated with antibodies developed in response to multi-molecular complexes formed by platelet factor 4 (PF4) bound to heparin or cell surface glycosaminoglycans. These antibody complexes activate platelets and monocytes typically through FcγRIIA receptors increasing the production of PF4, inflammatory mediators, tissue factor and thrombin. The influence of underlying events in HIT including complex-induced pro-inflammatory cell activation and structural determinants leading to local inflammatory responses are not fully understood. The stoichiometry and complex component requirements were determined by incubating fresh peripheral blood mononuclear cells (PBMC) with different concentrations of unfractionated heparin (H), low molecular weight heparin (LMWH), PF4- and anti-PF4-H complex antibodies (KKO). Cytokine mRNA or protein were measured by qRT-PCR or Meso Scale Discovery technology, respectively. Gene expression profile analysis for 594 genes was performed using Nanostring technology and analyzed using Ingenuity Pathway Analysis software. The data show that antibodies magnify immune responses induced in PBMCs by PF4 alone or in complex with heparin or LMWH. We propose that following induction of HIT antibodies by heparin-PF4 complexes, binding of the antibodies to PF4 is sufficient to induce a local pro-inflammatory response which may play a role in the progression of HIT. In vitro assays using PBMCs may be useful in characterizing local inflammatory and innate immune responses induced by HIT antibodies in the presence of PF4 and different sources of heparins. The findings and conclusions in this article are solely the responsibility of the authors and are not being formally disseminated by the Food and Drug Administration. Thus, they should not be

Development of an artifact-free aneurysm clip

Directory of Open Access Journals (Sweden)

Brack Alexander

2016-09-01

Full Text Available For the treatment of intracranial aneurysms with aneurysm clips, usually a follow-up inspection in MRI is required. To avoid any artifacts, which can make a proper diagnosis difficult, a new approach for the manufacturing of an aneurysm clip entirely made from fiber-reinforced plastics has been developed. In this paper the concept for the design of the clip, the development of a new manufacturing technology for the fiber-reinforced components as well as first results from the examination of the components in phantom MRI testing is shown.

Viruses and miRNAs: More Friends than Foes.

Science.gov (United States)

Bruscella, Patrice; Bottini, Silvia; Baudesson, Camille; Pawlotsky, Jean-Michel; Feray, Cyrille; Trabucchi, Michele

2017-01-01

There is evidence that eukaryotic miRNAs (hereafter called host miRNAs) play a role in the replication and propagation of viruses. Expression or targeting of host miRNAs can be involved in cellular antiviral responses. Most times host miRNAs play a role in viral life-cycles and promote infection through complex regulatory pathways. miRNAs can also be encoded by a viral genome and be expressed in the host cell. Viral miRNAs can share common sequences with host miRNAs or have totally different sequences. They can regulate a variety of biological processes involved in viral infection, including apoptosis, evasion of the immune response, or modulation of viral life-cycle phases. Overall, virus/miRNA pathway interaction is defined by a plethora of complex mechanisms, though not yet fully understood. This article review summarizes recent advances and novel biological concepts related to the understanding of miRNA expression, control and function during viral infections. The article also discusses potential therapeutic applications of this particular host-pathogen interaction.

Exosomal miRNAs as biomarkers for prostate cancer

Directory of Open Access Journals (Sweden)

Nina Pettersen Hessvik

2013-03-01

Full Text Available miRNAs are small non-coding RNAs that finely regulate gene expression in cells. Alterations in miRNA expression have been associated with development of cancer, and miRNAs are now being investigated as biomarkers for cancer as well as other diseases. Recently, miRNAs have been found outside cells in body fluids. Extracellular miRNAs exist in different forms - associated with Ago2 proteins, loaded into extracellular vesicles (exosomes, microvesicles or apoptotic bodies or into high density lipoprotein particles. These extracellular miRNAs are probably products of distinct cellular processes, and might therefore play different roles. However, their functions in vivo are currently unknown. In spite of this, they are considered as promising, noninvasive diagnostic and prognostic tools. Prostate cancer is the most common cancer in men in the Western world, but the currently used biomarker (prostate specific antigen has low specificity. Therefore, novel biomarkers are highly needed. In this review we will discuss possible biological functions of extracellular miRNAs, as well as the potential use of miRNAs from extracellular vesicles as biomarkers for prostate cancer.

Digital video clips for improved pedagogy and illustration of scientific research — with illustrative video clips on atomic spectrometry

Science.gov (United States)

Michel, Robert G.; Cavallari, Jennifer M.; Znamenskaia, Elena; Yang, Karl X.; Sun, Tao; Bent, Gary

1999-12-01

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), a section of Spectrochimica Acta Part B (SAB). The hardcopy text is accompanied by an electronic archive, stored on the CD-ROM accompanying this issue. The archive contains video clips. The main article discusses the scientific aspects of the subject and explains the purpose of the video files. Short, 15-30 s, digital video clips are easily controllable at the computer keyboard, which gives a speaker the ability to show fine details through the use of slow motion. Also, they are easily accessed from the computer hard drive for rapid extemporaneous presentation. In addition, they are easily transferred to the Internet for dissemination. From a pedagogical point of view, the act of making a video clip by a student allows for development of powers of observation, while the availability of the technology to make digital video clips gives a teacher the flexibility to demonstrate scientific concepts that would otherwise have to be done as 'live' demonstrations, with all the likely attendant misadventures. Our experience with digital video clips has been through their use in computer-based presentations by undergraduate and graduate students in analytical chemistry classes, and by high school and middle school teachers and their students in a variety of science and non-science classes. In physics teaching laboratories, we have used the hardware to capture digital video clips of dynamic processes, such as projectiles and pendulums, for later mathematical analysis.

Neural Decoder for Topological Codes

Science.gov (United States)

Torlai, Giacomo; Melko, Roger G.

2017-07-01

We present an algorithm for error correction in topological codes that exploits modern machine learning techniques. Our decoder is constructed from a stochastic neural network called a Boltzmann machine, of the type extensively used in deep learning. We provide a general prescription for the training of the network and a decoding strategy that is applicable to a wide variety of stabilizer codes with very little specialization. We demonstrate the neural decoder numerically on the well-known two-dimensional toric code with phase-flip errors.

[Expression profiles and bioinformatic analysis of miRNA in human dental pulp cells during endothelial differentiation].

Science.gov (United States)

Gong, Qimei; Jiang, Hongwei; Wang, Jinming; Ling, Junqi

2014-05-01

To investigate the differential expression profile and bioinformatic analysis of microRNA (miRNA) in human dental pulp cells (DPC) during endothelial differentiation. DPC were cultured in endothelial induction medium (50 µg/L vascular endothelial growth factor, 10 µg/L basic fibroblast growth factor and 2% fetal calf serum) for 7 days. Meanwhile non-induced DPC were used as control.Quantitative real-time PCR (qRT-PCR) was applied to detect vascular endothelial marker genes [CD31, von Willebrand factor (vWF) and vascular endothelial-cadherin (VE-cadherin)] and in vitro tube formation on matrigel was used to analyze the angiogenic ability of differentiated cells. And then miRNA expression profiles of DPC were examined using miRNA microarray and then the differentially expressed miRNA were validated by qRT-PCR. Furthermore, bioinformatic analysis was employed to predict the target genes of miRNA and to analyze the possible biological functions and signaling pathways that were involved in DPC after induction. The relative mRNA level of CD31, vWF and VE-cadherin in the control group were (3.48 ± 0.22) ×10(-4), (3.13 ± 0.31) ×10(-4) and (39.60 ± 2.36) ×10(-4), and (19.57 ± 2.20) ×10(-4), (48.13 ± 0.54) ×10(-4) and (228.00 ± 8.89) ×10(-4) in the induced group. The expressions of CD31, vWF and VE-cadherin were increased significantly in endothelial induced DPC compared to the control group (P functions, such as the regulation of transcription, cell motion, blood vessel morphogenesis, angiogenesis and cytoskeletal protein, and signaling pathways including the mitogen-activated protein kinase (MAPK) and the Wnt signaling pathway. The differential miRNA expression identified in this study may be involved in governing DPC endothelial differentiation, thus contributing to the future research on regulatory mechanisms in dental pulp angiogenesis.

LDPC Decoding on GPU for Mobile Device

Directory of Open Access Journals (Sweden)

Yiqin Lu

2016-01-01

Full Text Available A flexible software LDPC decoder that exploits data parallelism for simultaneous multicode words decoding on the mobile device is proposed in this paper, supported by multithreading on OpenCL based graphics processing units. By dividing the check matrix into several parts to make full use of both the local memory and private memory on GPU and properly modify the code capacity each time, our implementation on a mobile phone shows throughputs above 100 Mbps and delay is less than 1.6 millisecond in decoding, which make high-speed communication like video calling possible. To realize efficient software LDPC decoding on the mobile device, the LDPC decoding feature on communication baseband chip should be replaced to save the cost and make it easier to upgrade decoder to be compatible with a variety of channel access schemes.

TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues.

Science.gov (United States)

Berillo, Olga; Régnier, Mireille; Ivashchenko, Anatoly

2014-01-01

microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents all received data in table formats that are easy to analyse further. The predicted data finds utility in molecular and evolutionary biology studies. They find use in studying miRNA binding sites in animals and plants. TmiRUSite and TmiROSite scripts are available for free from authors upon request and at https: //sites.google.com/site/malaheenee/downloads for download.

Evolutionary relationships between miRNA genes and their activity.

Science.gov (United States)

Zhu, Yan; Skogerbø, Geir; Ning, Qianqian; Wang, Zhen; Li, Biqing; Yang, Shuang; Sun, Hong; Li, Yixue

2012-12-22

The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained. In order to systematically understand the evolutionary relationship between miRNAs gene and their function, we classified human known miRNAs into eight groups based on their evolutionary ages estimated by maximum parsimony method. New miRNA genes with new functional sequences accumulated more dynamically in vertebrates than that observed in Drosophila. Different levels of evolutionary selection were observed over miRNA gene sequences with different time of origin. Most genic miRNAs differ from their host genes in time of origin, there is no particular relationship between the age of a miRNA and the age of its host genes, genic miRNAs are mostly younger than the corresponding host genes. MicroRNAs originated over different time-scales are often predicted/verified to target the same or overlapping sets of genes, opening the possibility of substantial functional redundancy among miRNAs of different ages. Higher degree of tissue specificity and lower expression level was found in young miRNAs. Our data showed that compared with protein coding genes, miRNA genes are more dynamic in terms of emergence and decay. Evolution patterns are quite different between miRNAs of different ages. MicroRNAs activity is under tight control with well-regulated expression increased and targeting decreased over time. Our work calls attention to the study of miRNA activity with a consideration of their origin time.

The serial message-passing schedule for LDPC decoding algorithms

Science.gov (United States)

Liu, Mingshan; Liu, Shanshan; Zhou, Yuan; Jiang, Xue

2015-12-01

The conventional message-passing schedule for LDPC decoding algorithms is the so-called flooding schedule. It has the disadvantage that the updated messages cannot be used until next iteration, thus reducing the convergence speed . In this case, the Layered Decoding algorithm (LBP) based on serial message-passing schedule is proposed. In this paper the decoding principle of LBP algorithm is briefly introduced, and then proposed its two improved algorithms, the grouped serial decoding algorithm (Grouped LBP) and the semi-serial decoding algorithm .They can improve LBP algorithm's decoding speed while maintaining a good decoding performance.

A defect in the CLIP1 gene (CLIP-170) can cause autosomal recessive intellectual disability

OpenAIRE

Larti, Farzaneh; Kahrizi, Kimia; Musante, Luciana; Hu, Hao; Papari, Elahe; Fattahi, Zohreh; Bazazzadegan, Niloofar; Liu, Zhe; Banan, Mehdi; Garshasbi, Masoud; Wienker, Thomas F; Hilger Ropers, H; Galjart, Niels; Najmabadi, Hossein

2015-01-01

In the context of a comprehensive research project, investigating novel autosomal recessive intellectual disability (ARID) genes, linkage analysis based on autozygosity mapping helped identify an intellectual disability locus on Chr.12q24, in an Iranian family (LOD score=3.7). Next-generation sequencing (NGS) following exon enrichment in this novel interval, detected a nonsense mutation (p.Q1010*) in the CLIP1 gene. CLIP1 encodes a member of microtubule (MT) plus-end tracking proteins, which ...

Improved Power Decoding of One-Point Hermitian Codes

DEFF Research Database (Denmark)

Puchinger, Sven; Bouw, Irene; Rosenkilde, Johan Sebastian Heesemann

2017-01-01

We propose a new partial decoding algorithm for one-point Hermitian codes that can decode up to the same number of errors as the Guruswami–Sudan decoder. Simulations suggest that it has a similar failure probability as the latter one. The algorithm is based on a recent generalization of the power...... decoding algorithm for Reed–Solomon codes and does not require an expensive root-finding step. In addition, it promises improvements for decoding interleaved Hermitian codes....

Decoding communities in networks.

Science.gov (United States)

Radicchi, Filippo

2018-02-01

According to a recent information-theoretical proposal, the problem of defining and identifying communities in networks can be interpreted as a classical communication task over a noisy channel: memberships of nodes are information bits erased by the channel, edges and nonedges in the network are parity bits introduced by the encoder but degraded through the channel, and a community identification algorithm is a decoder. The interpretation is perfectly equivalent to the one at the basis of well-known statistical inference algorithms for community detection. The only difference in the interpretation is that a noisy channel replaces a stochastic network model. However, the different perspective gives the opportunity to take advantage of the rich set of tools of coding theory to generate novel insights on the problem of community detection. In this paper, we illustrate two main applications of standard coding-theoretical methods to community detection. First, we leverage a state-of-the-art decoding technique to generate a family of quasioptimal community detection algorithms. Second and more important, we show that the Shannon's noisy-channel coding theorem can be invoked to establish a lower bound, here named as decodability bound, for the maximum amount of noise tolerable by an ideal decoder to achieve perfect detection of communities. When computed for well-established synthetic benchmarks, the decodability bound explains accurately the performance achieved by the best community detection algorithms existing on the market, telling us that only little room for their improvement is still potentially left.

Decoding communities in networks

Science.gov (United States)

Radicchi, Filippo

2018-02-01

According to a recent information-theoretical proposal, the problem of defining and identifying communities in networks can be interpreted as a classical communication task over a noisy channel: memberships of nodes are information bits erased by the channel, edges and nonedges in the network are parity bits introduced by the encoder but degraded through the channel, and a community identification algorithm is a decoder. The interpretation is perfectly equivalent to the one at the basis of well-known statistical inference algorithms for community detection. The only difference in the interpretation is that a noisy channel replaces a stochastic network model. However, the different perspective gives the opportunity to take advantage of the rich set of tools of coding theory to generate novel insights on the problem of community detection. In this paper, we illustrate two main applications of standard coding-theoretical methods to community detection. First, we leverage a state-of-the-art decoding technique to generate a family of quasioptimal community detection algorithms. Second and more important, we show that the Shannon's noisy-channel coding theorem can be invoked to establish a lower bound, here named as decodability bound, for the maximum amount of noise tolerable by an ideal decoder to achieve perfect detection of communities. When computed for well-established synthetic benchmarks, the decodability bound explains accurately the performance achieved by the best community detection algorithms existing on the market, telling us that only little room for their improvement is still potentially left.

Integrating CLIPS applications into heterogeneous distributed systems

Science.gov (United States)

Adler, Richard M.

1991-01-01

SOCIAL is an advanced, object-oriented development tool for integrating intelligent and conventional applications across heterogeneous hardware and software platforms. SOCIAL defines a family of 'wrapper' objects called agents, which incorporate predefined capabilities for distributed communication and control. Developers embed applications within agents and establish interactions between distributed agents via non-intrusive message-based interfaces. This paper describes a predefined SOCIAL agent that is specialized for integrating C Language Integrated Production System (CLIPS)-based applications. The agent's high-level Application Programming Interface supports bidirectional flow of data, knowledge, and commands to other agents, enabling CLIPS applications to initiate interactions autonomously, and respond to requests and results from heterogeneous remote systems. The design and operation of CLIPS agents are illustrated with two distributed applications that integrate CLIPS-based expert systems with other intelligent systems for isolating and mapping problems in the Space Shuttle Launch Processing System at the NASA Kennedy Space Center.

21 CFR 886.3100 - Ophthalmic tantalum clip.

Science.gov (United States)

2010-04-01

... blood vessels in the eye. (b) Classification. Class II (special controls). The device is exempt from the...) MEDICAL DEVICES OPHTHALMIC DEVICES Prosthetic Devices § 886.3100 Ophthalmic tantalum clip. (a) Identification. An ophthalmic tantalum clip is a malleable metallic device intended to be implanted permanently...

The effect of dys-1 mutation on miRNA expression profile in Caenorhabditis elegans during Shenzhou-8 mission

Science.gov (United States)

Xu, Dan; Sun, Yeqing; Gao, Ying; Xing, Yanfang

microRNAs (miRNAs) is reported to be sensitive to radiation exposure and altered gravity, involved in a variety of biological processes through negative regulation of gene expression. Dystrophin-like dys-1 gene is expressed and required in muscle tissue, which plays a vital role in mechanical transduction when gravity varies. In the present study, we investigated the effect of dys-1 mutation on miRNA expression profile in Caenorhabditis elegans (C. elegans) under space radiation associated with microgravity (R+M) and radiation alone (R) environment during Shenzhou-8 mission. We performed miRNA microarray analysis in dys-1 mutant and wide-type (WT) of dauer larvae and found that 27 miRNAs changed in abundance after spaceflight. Compared with WT, there was different miRNA expression pattern in different treatments in dys-1 mutant. Cel-miR-796 and miR-124 were reversely expressed under R+M and R environment in WT and dys-1 mutant, respectively, indicating they might be affected by microgravity. Mutation of dys-1 remarkably reduced the number of altered miRNAs under space environment, resulting in the decrease of genes in biological categories of “body morphogenesis”, “behavior”, “cell adhesion” and so on. Particularly, we found that those genes controlling regulation of locomotion in WT were lost in dys-1 mutant, while genes in positive regulation of developmental process only existed in dys-1 mutant. miR-796 was predicted to target genes ace-1 and dyc-1 that are functionally linked to dys-1. Integration analysis of miRNA and mRNA expression profile revealed that miR-56 and miR-124 were involved in behavior and locomotion by regulating different target genes under space environment, among which nep-11, deb-1, C07H4.1 and F11H8.2 might be associated with neuromuscular system. Our findings suggest that dys-1 could cause alteration of miRNAs and target genes, involved in regulating the response of C. elegans to space microgravity in neuromuscular system. This

miRNA Signatures of Insulin Resistance in Obesity.

Science.gov (United States)

Jones, Angela; Danielson, Kirsty M; Benton, Miles C; Ziegler, Olivia; Shah, Ravi; Stubbs, Richard S; Das, Saumya; Macartney-Coxson, Donia

2017-10-01

Extracellular microRNAs (miRNAs) represent functional biomarkers for obesity and related disorders; this study investigated plasma miRNAs in insulin resistance phenotypes in obesity. One hundred seventy-five miRNAs were analyzed in females with obesity (insulin sensitivity, n = 11; insulin resistance, n = 19; type 2 diabetes, n = 15) and without obesity (n = 12). Correlations between miRNA level and clinical parameters and levels of 15 miRNAs in a murine obesity model were investigated. One hundred six miRNAs were significantly (adjusted P ≤ 0.05) different between controls and at least one obesity phenotype, including miRNAs with the following attributes: previously reported roles in obesity and altered circulating levels (e.g., miR-122, miR-192); known roles in obesity but no reported changes in circulating levels (e.g., miR-378a); and no current reported role in, or association with, obesity (e.g., miR-28-5p, miR-374b, miR-32). The miRNAs in the latter group were found to be associated with extracellular vesicles. Forty-eight miRNAs showed significant correlations with clinical parameters; stepwise regression retained let-7b, miR-144-5p, miR-34a, and miR-532-5p in a model predictive of insulin resistance (R 2  = 0.57, P = 7.5 × 10 -8 ). Both miR-378a and miR-122 were perturbed in metabolically relevant tissues in a murine model of obesity. This study expands on the role of extracellular miRNAs in insulin-resistant phenotypes of obesity and identifies candidate miRNAs not previously associated with obesity. © 2017 The Obesity Society.

Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses.

Directory of Open Access Journals (Sweden)

Laura Ann Jacobs

Full Text Available Organisms are often exposed to environmental pressures that affect homeostasis, so it is important to understand the biological basis of stress-response. Various biological mechanisms have evolved to help cells cope with potentially cytotoxic changes in their environment. miRNAs are small non-coding RNAs which are able to regulate mRNA stability. It has been suggested that miRNAs may tip the balance between continued cytorepair and induction of apoptosis in response to stress. There is a wealth of data in the literature showing the effect of environmental stress on miRNAs, but it is scattered in a large number of disparate publications. Meta-analyses of this data would produce added insight into the molecular mechanisms of stress-response. To facilitate this we created and manually curated the miRStress database, which describes the changes in miRNA levels following an array of stress types in eukaryotic cells. Here we describe this database and validate the miRStress tool for analysing miRNAs that are regulated by stress. To validate the database we performed a cross-species analysis to identify miRNAs that respond to radiation. The analysis tool confirms miR-21 and miR-34a as frequently deregulated in response to radiation, but also identifies novel candidates as potentially important players in this stress response, including miR-15b, miR-19b, and miR-106a. Similarly, we used the miRStress tool to analyse hypoxia-responsive miRNAs. The most frequently deregulated miRNAs were miR-210 and miR-21, as expected. Several other miRNAs were also found to be associated with hypoxia, including miR-181b, miR-26a/b, miR-106a, miR-213 and miR-192. Therefore the miRStress tool has identified miRNAs with hitherto unknown or under-appreciated roles in the response to specific stress types. The miRStress tool, which can be used to uncover new insight into the biological roles of miRNAs, and also has the potential to unearth potential biomarkers for

A fast online hit verification method for the single ion hit system at GSI

International Nuclear Information System (INIS)

Du, G.; Fischer, B.; Barberet, P.; Heiss, M.

2006-01-01

For a single ion hit facility built to irradiate specific targets inside biological cells, it is necessary to prove that the ions hit the selected targets reliably because the ion hits usually cannot be seen. That ability is traditionally tested either indirectly by aiming at pre-etched tracks in a nuclear track detector or directly by making the ion tracks inside cells visible using a stain coupled to special proteins produced in response to ion hits. However, both methods are time consuming and hits can be verified only after the experiment. This means that targeting errors in the experiment cannot be corrected during the experiment. Therefore, we have developed a fast online hit verification method that measures the targeting accuracy electronically with a spatial resolution of ±1 μm before cell irradiation takes place. (authors)

On Lattice Sequential Decoding for The Unconstrained AWGN Channel

KAUST Repository

Abediseid, Walid

2012-10-01

In this paper, the performance limits and the computational complexity of the lattice sequential decoder are analyzed for the unconstrained additive white Gaussian noise channel. The performance analysis available in the literature for such a channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the lattice decoder. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement, and the search for low complexity receivers for the detection of lattice codes is considered a challenging problem. However, the low computational complexity advantage that sequential decoding promises, makes it an alternative solution to the lattice decoder. In this work, we characterize the performance and complexity tradeoff via the error exponent and the decoding complexity, respectively, of such a decoder as a function of the decoding parameter --- the bias term. For the above channel, we derive the cut-off volume-to-noise ratio that is required to achieve a good error performance with low decoding complexity.

On Lattice Sequential Decoding for The Unconstrained AWGN Channel

KAUST Repository

Abediseid, Walid

2013-04-04

In this paper, the performance limits and the computational complexity of the lattice sequential decoder are analyzed for the unconstrained additive white Gaussian noise channel. The performance analysis available in the literature for such a channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the \\\\textit{lattice decoder}. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement, and the search for low complexity receivers for the detection of lattice codes is considered a challenging problem. However, the low computational complexity advantage that sequential decoding promises, makes it an alternative solution to the lattice decoder. In this work, we characterize the performance and complexity tradeoff via the error exponent and the decoding complexity, respectively, of such a decoder as a function of the decoding parameter --- the bias term. For the above channel, we derive the cut-off volume-to-noise ratio that is required to achieve a good error performance with low decoding complexity.

On Lattice Sequential Decoding for The Unconstrained AWGN Channel

KAUST Repository

Abediseid, Walid; Alouini, Mohamed-Slim

2012-01-01

In this paper, the performance limits and the computational complexity of the lattice sequential decoder are analyzed for the unconstrained additive white Gaussian noise channel. The performance analysis available in the literature for such a channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the lattice decoder. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement, and the search for low complexity receivers for the detection of lattice codes is considered a challenging problem. However, the low computational complexity advantage that sequential decoding promises, makes it an alternative solution to the lattice decoder. In this work, we characterize the performance and complexity tradeoff via the error exponent and the decoding complexity, respectively, of such a decoder as a function of the decoding parameter --- the bias term. For the above channel, we derive the cut-off volume-to-noise ratio that is required to achieve a good error performance with low decoding complexity.

Interior point decoding for linear vector channels

International Nuclear Information System (INIS)

Wadayama, T

2008-01-01

In this paper, a novel decoding algorithm for low-density parity-check (LDPC) codes based on convex optimization is presented. The decoding algorithm, called interior point decoding, is designed for linear vector channels. The linear vector channels include many practically important channels such as inter-symbol interference channels and partial response channels. It is shown that the maximum likelihood decoding (MLD) rule for a linear vector channel can be relaxed to a convex optimization problem, which is called a relaxed MLD problem

Interior point decoding for linear vector channels

Energy Technology Data Exchange (ETDEWEB)

Wadayama, T [Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, Aichi, 466-8555 (Japan)], E-mail: wadayama@nitech.ac.jp

2008-01-15

In this paper, a novel decoding algorithm for low-density parity-check (LDPC) codes based on convex optimization is presented. The decoding algorithm, called interior point decoding, is designed for linear vector channels. The linear vector channels include many practically important channels such as inter-symbol interference channels and partial response channels. It is shown that the maximum likelihood decoding (MLD) rule for a linear vector channel can be relaxed to a convex optimization problem, which is called a relaxed MLD problem.

Symbol synchronization for the TDRSS decoder

Science.gov (United States)

Costello, D. J., Jr.

1983-01-01

Each 8 bits out of the Viterbi decoder correspond to one symbol of the R/S code. Synchronization must be maintained here so that each 8-bit symbol delivered to the R/S decoder corresponds to an 8-bit symbol from the R/S encoder. Lack of synchronization, would cause an error in almost every R/S symbol since even a - 1-bit sync slip shifts every bit in each 8-bit symbol by one position, therby confusing the mapping betweeen 8-bit sequences and symbols. The error correcting capability of the R/S code would be exceeded. Possible ways to correcting this condition include: (1) designing the R/S decoder to recognize the overload and shifting the output sequence of the inner decoder to establish a different sync state; (2) using the characteristics of the inner decoder to establish symbol synchronization for the outer code, with or without a deinterleaver and an interleaver; and (3) modifying the encoder to alternate periodically between two sets of generators.

A class of Sudan-decodable codes

DEFF Research Database (Denmark)

Nielsen, Rasmus Refslund

2000-01-01

In this article, Sudan's algorithm is modified into an efficient method to list-decode a class of codes which can be seen as a generalization of Reed-Solomon codes. The algorithm is specialized into a very efficient method for unique decoding. The code construction can be generalized based...... on algebraic-geometry codes and the decoding algorithms are generalized accordingly. Comparisons with Reed-Solomon and Hermitian codes are made....

Expression profiles of miRNA-122 and its target CAT1 in minipigs (Sus scrofa) fed a high-cholesterol diet

DEFF Research Database (Denmark)

Cirera Salicio, Susanna; Birck, Malene Muusfeldt; Busk, Peter Kamp

2010-01-01

The Göttingen minipig is an excellent model for studying effects of dietary high-fat intake on obesity. In this study, we analyzed the expression level of microRNA-122 (miRNA-122) and its target mRNA, CAT1, in intact young male minipigs fed either high-cholesterol or standard diet for 11 wk. Mi...... with a decrease in the expression of miRNA-122, confirming the implication of this microRNA in obesity. Gene expression levels of CAT1 did not differ between groups.......RNA-122 and CAT1 are known to be important regulators of lipid metabolism. The weight of the young minipigs was monitored once a week during the feeding period; measurements of total cholesterol, triglycerides, high-density lipoproteins, and low-density lipoproteins were recorded at 4 time points (8, 14...

New miRNA labeling method for bead-based quantification

Directory of Open Access Journals (Sweden)

Lanfranchi Gerolamo

2010-06-01

Full Text Available Abstract Background microRNAs (miRNAs are small single-stranded non-coding RNAs that act as crucial regulators of gene expression. Different methods have been developed for miRNA expression profiling in order to better understand gene regulation in normal and pathological conditions. miRNAs expression values obtained from large scale methodologies such as microarrays still need a validation step with alternative technologies. Results Here we have applied with an innovative approach, the Luminex® xMAP™ technology validate expression data of differentially expressed miRNAs obtained from high throughput arrays. We have developed a novel labeling system of small RNA molecules (below 200 nt, optimizing the sensitive cloning method for miRNAs, termed miRNA amplification profiling (mRAP. The Luminex expression patterns of three miRNAs (miR-23a, miR-27a and miR-199a in seven different cell lines have been validated by TaqMan miRNA assay. In all cases, bead-based meas were confirmed by the data obtained by TaqMan and microarray technologies. Conclusions We demonstrate that the measure of individual miRNA by the bead-based method is feasible, high speed, sensitive and low cost. The Luminex® xMAP™ technology also provides flexibility, since the central reaction can be scaled up with additional miRNA capturing beads, allowing validation of many differentially expressed miRNAs obtained from microarrays in a single experiment. We propose this technology as an alternative method to qRT-PCR for validating miRNAs expression data obtained with high-throughput technologies.

Multi-stage decoding for multi-level block modulation codes

Science.gov (United States)

Lin, Shu

1991-01-01

In this paper, we investigate various types of multi-stage decoding for multi-level block modulation codes, in which the decoding of a component code at each stage can be either soft-decision or hard-decision, maximum likelihood or bounded-distance. Error performance of codes is analyzed for a memoryless additive channel based on various types of multi-stage decoding, and upper bounds on the probability of an incorrect decoding are derived. Based on our study and computation results, we find that, if component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. In particular, we find that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum decoding of the overall code is very small: only a fraction of dB loss in SNR at the probability of an incorrect decoding for a block of 10(exp -6). Multi-stage decoding of multi-level modulation codes really offers a way to achieve the best of three worlds, bandwidth efficiency, coding gain, and decoding complexity.

Percutaneous interventional mitral regurgitation treatment using the Mitra-Clip system

DEFF Research Database (Denmark)

Boekstegers, P; Hausleiter, J; Baldus, S

2014-01-01

The interventional treatment of mitral valve regurgitation by the MitraClip procedure has grown rapidly in Germany and Europe during the past years. The MitraClip procedure has the potential to treat high-risk patients with secondary mitral valve regurgitation and poor left ventricular function....... Furthermore, patients with primary mitral valve regurgitation may be treated successfully by the MitraClip procedure in case of high surgical risk or in very old patients. At the same time it has been emphasised that the MitraClip interventional treatment is still at an early stage of clinical development....... The largest clinical experience with the MitraClip procedure so far is probably present in some German cardiovascular centers, which here summarise their recommendations on the current indications and procedural steps of the MitraClip treatment. These recommendations of the AGIK and ALKK may present a basis...

Clip reconstruction of a large right MCA bifurcation aneurysm. Case report

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Giovani A.

2014-06-01

Full Text Available We report a case of complex large middle cerebral artery (MCA bifurcation aneurysm that ruptured during dissection from the very adherent MCA branches but was successfully clipped and the MCA bifurcation reconstructed using 4 Yasargill clips. Through a right pterional craniotomy the sylvian fissure was largely opened as to allow enough workspace for clipping the aneurysm and placing a temporary clip on M1. The pacient recovered very well after surgery and was discharged after 1 week with no neurological deficit. Complex MCA bifurcation aneurysms can be safely reconstructed using regular clips, without the need of using fenestrated clips or complex by-pass procedures.

On Rational Interpolation-Based List-Decoding and List-Decoding Binary Goppa Codes

DEFF Research Database (Denmark)

Beelen, Peter; Høholdt, Tom; Nielsen, Johan Sebastian Rosenkilde

2013-01-01

We derive the Wu list-decoding algorithm for generalized Reed–Solomon (GRS) codes by using Gröbner bases over modules and the Euclidean algorithm as the initial algorithm instead of the Berlekamp–Massey algorithm. We present a novel method for constructing the interpolation polynomial fast. We gi...... and a duality in the choice of parameters needed for decoding, both in the case of GRS codes and in the case of Goppa codes....

MTUS1 tumor suppressor and its miRNA regulators in fibroadenoma and breast cancer.

Science.gov (United States)

Kara, Murat; Kaplan, Mehmet; Bozgeyik, Ibrahim; Ozcan, Onder; Celik, Ozgur Ilhan; Bozgeyik, Esra; Yumrutas, Onder

2016-08-10

Breast cancer is major public health problem predominantly effects female population. Current therapeutic approaches to deal with breast cancer are still lack of effectiveness. Thus, identifying/developing novel strategies to fight against breast cancer is very important. The frequent deletions at 8p21.3-22 chromosomal location nearby D8S254 marker enabled the discovery of a novel tumor suppressor gene, MTUS1. Subsequently, MTUS1 was demonstrated to be less expressed in a variety cancer types including breast cancer. Also, it is obvious that gene expression is widely regulated by miRNAs. Here, we aimed to report differential expression of MTUS1 and its regulatory miRNAs in breast cancer and fibroadenoma tissues. Dynamic analysis of MTUS1 expression levels and its miRNAs regulators were attained by Fluidigm 96×96 Dynamic Array Expression chips and reactions were performed in Fluidigm BioMark™ HD System qPCR. Consequently, MTUS1 mRNA levels were significantly diminished in breast cancer tissues and elevated in fibroadenoma tissues. Also, among MTUS1 targeting miRNAs, miR-183-5p was identified to be overexpressed in breast cancer and down-regulated in fibroadenoma tissues. Also, expression levels of MTUS1 and miR-183-5p were well correlated with clinical parameters. In particular, MTUS1 expression was found to be diminished and miR-183-5p expression was elevated with the advancing stage. In conclusion, as a potential therapeutic target, miR-183-5p can be a chief regulator of MTUS1 and MTUS1-miR-183-5p axis may have significant influence in the pathology of breast cancer. Copyright © 2016 Elsevier B.V. All rights reserved.

A Systematic Analysis on mRNA and MicroRNA Expression in Runting and Stunting Chickens

Science.gov (United States)

Xu, Haiping; Xu, Zhenqiang; Ma, Jinge; Li, Bixiao; Lin, Shudai; Nie, Qinghua; Luo, Qingbin; Zhang, Xiquan

2015-01-01

Runting and stunting syndrome (RSS), which is characterized by lower body weight, widely occurs in broilers. Some RSS chickens simply exhibit slow growth without pathological changes. An increasing number of studies indicate that broiler strains differ in susceptibility to infectious diseases, most likely due to their genetic differences. The objective of this study was to detect the differentially expressed miRNAs and mRNAs in RSS and normal chickens. By integrating miRNA with mRNA expression profiling, potential molecular mechanisms involved in RSS could be further explored. Twenty-two known miRNAs and 1,159 genes were differentially expressed in RSS chickens compared with normal chickens (P chicken liver albeit with reduced abundance. Dual-luciferase reporter assay indicated that gga-miR-30b/c directly target CARS through binding to its 3′UTR. The miR-30b/c: CARS regulation mainly occurred in liver. In thigh muscle and the hypothalamus, miR-30b/c are expressed at higher levels in RSS chickens compared with normal chickens from 2 to 6 w of age, and notably significant differences are observed at 4 w of age. PMID:26010155

Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis

Directory of Open Access Journals (Sweden)

Barker Jeffery L

2009-08-01

Full Text Available Abstract Background Cortical development is a complex process that includes sequential generation of neuronal progenitors, which proliferate and migrate to form the stratified layers of the developing cortex. To identify the individual microRNAs (miRNAs and mRNAs that may regulate the genetic network guiding the earliest phase of cortical development, the expression profiles of rat neuronal progenitors obtained at embryonic day 11 (E11, E12 and E13 were analyzed. Results Neuronal progenitors were purified from telencephalic dissociates by a positive-selection strategy featuring surface labeling with tetanus-toxin and cholera-toxin followed by fluorescence-activated cell sorting. Microarray analyses revealed the fractions of miRNAs and mRNAs that were up-regulated or down-regulated in these neuronal progenitors at the beginning of cortical development. Nearly half of the dynamically expressed miRNAs were negatively correlated with the expression of their predicted target mRNAs. Conclusion These data support a regulatory role for miRNAs during the transition from neuronal progenitors into the earliest differentiating cortical neurons. In addition, by supplying a robust data set in which miRNA and mRNA profiles originate from the same purified cell type, this empirical study may facilitate the development of new algorithms to integrate various "-omics" data sets.

Encoder-decoder optimization for brain-computer interfaces.

Science.gov (United States)

Merel, Josh; Pianto, Donald M; Cunningham, John P; Paninski, Liam

2015-06-01

Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors, such as a cursor on a computer screen. It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector. Co-adaptation is the process whereby a user learns to control the system in conjunction with the decoder adapting to learn the user's neural patterns. We provide a mathematical framework for co-adaptation and relate co-adaptation to the joint optimization of the user's control scheme ("encoding model") and the decoding algorithm's parameters. When the assumptions of that framework are respected, co-adaptation cannot yield better performance than that obtainable by an optimal initial choice of fixed decoder, coupled with optimal user learning. For a specific case, we provide numerical methods to obtain such an optimized decoder. We demonstrate our approach in a model brain-computer interface system using an online prosthesis simulator, a simple human-in-the-loop pyschophysics setup which provides a non-invasive simulation of the BCI setting. These experiments support two claims: that users can learn encoders matched to fixed, optimal decoders and that, once learned, our approach yields expected performance advantages.

Encoder-decoder optimization for brain-computer interfaces.

Directory of Open Access Journals (Sweden)

Josh Merel

2015-06-01

Full Text Available Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors, such as a cursor on a computer screen. It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector. Co-adaptation is the process whereby a user learns to control the system in conjunction with the decoder adapting to learn the user's neural patterns. We provide a mathematical framework for co-adaptation and relate co-adaptation to the joint optimization of the user's control scheme ("encoding model" and the decoding algorithm's parameters. When the assumptions of that framework are respected, co-adaptation cannot yield better performance than that obtainable by an optimal initial choice of fixed decoder, coupled with optimal user learning. For a specific case, we provide numerical methods to obtain such an optimized decoder. We demonstrate our approach in a model brain-computer interface system using an online prosthesis simulator, a simple human-in-the-loop pyschophysics setup which provides a non-invasive simulation of the BCI setting. These experiments support two claims: that users can learn encoders matched to fixed, optimal decoders and that, once learned, our approach yields expected performance advantages.

Iterative Decoding of Concatenated Codes: A Tutorial

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Phillip A. Regalia

2005-05-01

Full Text Available The turbo decoding algorithm of a decade ago constituted a milestone in error-correction coding for digital communications, and has inspired extensions to generalized receiver topologies, including turbo equalization, turbo synchronization, and turbo CDMA, among others. Despite an accrued understanding of iterative decoding over the years, the “turbo principle” remains elusive to master analytically, thereby inciting interest from researchers outside the communications domain. In this spirit, we develop a tutorial presentation of iterative decoding for parallel and serial concatenated codes, in terms hopefully accessible to a broader audience. We motivate iterative decoding as a computationally tractable attempt to approach maximum-likelihood decoding, and characterize fixed points in terms of a “consensus” property between constituent decoders. We review how the decoding algorithm for both parallel and serial concatenated codes coincides with an alternating projection algorithm, which allows one to identify conditions under which the algorithm indeed converges to a maximum-likelihood solution, in terms of particular likelihood functions factoring into the product of their marginals. The presentation emphasizes a common framework applicable to both parallel and serial concatenated codes.

Joint Decoding of Concatenated VLEC and STTC System

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Chen Huijun

2008-01-01

Full Text Available Abstract We consider the decoding of wireless communication systems with both source coding in the application layer and channel coding in the physical layer for high-performance transmission over fading channels. Variable length error correcting codes (VLECs and space time trellis codes (STTCs are used to provide bandwidth efficient data compression as well as coding and diversity gains. At the receiver, an iterative joint source and space time decoding scheme are developed to utilize redundancy in both STTC and VLEC to improve overall decoding performance. Issues such as the inseparable systematic information in the symbol level, the asymmetric trellis structure of VLEC, and information exchange between bit and symbol domains have been considered in the maximum a posteriori probability (MAP decoding algorithm. Simulation results indicate that the developed joint decoding scheme achieves a significant decoding gain over the separate decoding in fading channels, whether or not the channel information is perfectly known at the receiver. Furthermore, how rate allocation between STTC and VLEC affects the performance of the joint source and space-time decoder is investigated. Different systems with a fixed overall information rate are studied. It is shown that for a system with more redundancy dedicated to the source code and a higher order modulation of STTC, the joint decoding yields better performance, though with increased complexity.

Joint Decoding of Concatenated VLEC and STTC System

Directory of Open Access Journals (Sweden)

Huijun Chen

2008-07-01

Full Text Available We consider the decoding of wireless communication systems with both source coding in the application layer and channel coding in the physical layer for high-performance transmission over fading channels. Variable length error correcting codes (VLECs and space time trellis codes (STTCs are used to provide bandwidth efficient data compression as well as coding and diversity gains. At the receiver, an iterative joint source and space time decoding scheme are developed to utilize redundancy in both STTC and VLEC to improve overall decoding performance. Issues such as the inseparable systematic information in the symbol level, the asymmetric trellis structure of VLEC, and information exchange between bit and symbol domains have been considered in the maximum a posteriori probability (MAP decoding algorithm. Simulation results indicate that the developed joint decoding scheme achieves a significant decoding gain over the separate decoding in fading channels, whether or not the channel information is perfectly known at the receiver. Furthermore, how rate allocation between STTC and VLEC affects the performance of the joint source and space-time decoder is investigated. Different systems with a fixed overall information rate are studied. It is shown that for a system with more redundancy dedicated to the source code and a higher order modulation of STTC, the joint decoding yields better performance, though with increased complexity.

FPGA Realization of Memory 10 Viterbi Decoder

DEFF Research Database (Denmark)

Paaske, Erik; Bach, Thomas Bo; Andersen, Jakob Dahl

1997-01-01

sequence mode when feedback from the Reed-Solomon decoder is available. The Viterbi decoder is realized using two Altera FLEX 10K50 FPGA's. The overall operating speed is 30 kbit/s, and since up to three iterations are performed for each frame and only one decoder is used, the operating speed...

Hardware Implementation Of Line Clipping A lgorithm By Using FPGA

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Amar Dawod

2013-04-01

Full Text Available The computer graphics system performance is increasing faster than any other computing application. Algorithms for line clipping against convex polygons and lines have been studied for a long time and many research papers have been published so far. In spite of the latest graphical hardware development and significant increase of performance the clipping is still a bottleneck of any graphical system. So its implementation in hardware is essential for real time applications. In this paper clipping operation is discussed and a hardware implementation of the line clipping algorithm is presented and finally formulated and tested using Field Programmable Gate Arrays (FPGA. The designed hardware unit consists of two parts : the first is positional code generator unit and the second is the clipping unit. Finally it is worth mentioning that the  designed unit is capable of clipping (232524 line segments per second.       

Speed Biases With Real-Life Video Clips

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Federica Rossi

2018-03-01

Full Text Available We live almost literally immersed in an artificial visual world, especially motion pictures. In this exploratory study, we asked whether the best speed for reproducing a video is its original, shooting speed. By using adjustment and double staircase methods, we examined speed biases in viewing real-life video clips in three experiments, and assessed their robustness by manipulating visual and auditory factors. With the tested stimuli (short clips of human motion, mixed human-physical motion, physical motion and ego-motion, speed underestimation was the rule rather than the exception, although it depended largely on clip content, ranging on average from 2% (ego-motion to 32% (physical motion. Manipulating display size or adding arbitrary soundtracks did not modify these speed biases. Estimated speed was not correlated with estimated duration of these same video clips. These results indicate that the sense of speed for real-life video clips can be systematically biased, independently of the impression of elapsed time. Measuring subjective visual tempo may integrate traditional methods that assess time perception: speed biases may be exploited to develop a simple, objective test of reality flow, to be used for example in clinical and developmental contexts. From the perspective of video media, measuring speed biases may help to optimize video reproduction speed and validate “natural” video compression techniques based on sub-threshold temporal squeezing.

High Speed Frame Synchronization and Viterbi Decoding

DEFF Research Database (Denmark)

Paaske, Erik; Justesen, Jørn; Larsen, Knud J.

1996-01-01

The purpose of Phase 1 of the study is to describe the system structure and algorithms in sufficient detail to allow drawing the high level architecture of units containing frame synchronization and Viterbi decoding. The systems we consider are high data rate space communication systems. Also...... components. Node synchronization performed within a Viterbi decoder is discussed, and algorithms for frame synchronization are described and analyzed. We present a list of system configurations that we find potentially useful. Further, the high level architecture of units that contain frame synchronization...... and various other functions needed in a complete system is presented. Two such units are described, one for placement before the Viterbi decoder and another for placement after the decoder. The high level architectures of three possible implementations of Viterbi decoders are described: The first...

High Speed Frame Synchronization and Viterbi Decoding

DEFF Research Database (Denmark)

Paaske, Erik; Justesen, Jørn; Larsen, Knud J.

1998-01-01

The study has been divided into two phases. The purpose of Phase 1 of the study was to describe the system structure and algorithms in sufficient detail to allow drawing the high level architecture of units containing frame synchronization and Viterbi decoding. After selection of which specific...... potentially useful.Algorithms for frame synchronization are described and analyzed. Further, the high level architecture of units that contain frame synchronization and various other functions needed in a complete system is presented. Two such units are described, one for placement before the Viterbi decoder...... towards a realization in an FPGA.Node synchronization performed within a Viterbi decoder is discussed, and the high level architectures of three possible implementations of Viterbi decoders are described: The first implementation uses a number of commercially available decoders while the the two others...

Health Information Technology (HIT) Adaptation: Refocusing on the Journey to Successful HIT Implementation.

Science.gov (United States)

Yen, Po-Yin; McAlearney, Ann Scheck; Sieck, Cynthia J; Hefner, Jennifer L; Huerta, Timothy R

2017-09-07

In past years, policies and regulations required hospitals to implement advanced capabilities of certified electronic health records (EHRs) in order to receive financial incentives. This has led to accelerated implementation of health information technologies (HIT) in health care settings. However, measures commonly used to evaluate the success of HIT implementation, such as HIT adoption, technology acceptance, and clinical quality, fail to account for complex sociotechnical variability across contexts and the different trajectories within organizations because of different implementation plans and timelines. We propose a new focus, HIT adaptation, to illuminate factors that facilitate or hinder the connection between use of the EHR and improved quality of care as well as to explore the trajectory of changes in the HIT implementation journey as it is impacted by frequent system upgrades and optimizations. Future research should develop instruments to evaluate the progress of HIT adaptation in both its longitudinal design and its focus on adaptation progress rather than on one cross-sectional outcome, allowing for more generalizability and knowledge transfer. ©Po-Yin Yen, Ann Scheck McAlearney, Cynthia J Sieck, Jennifer L Hefner, Timothy R Huerta. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 07.09.2017.

A Scalable Architecture of a Structured LDPC Decoder

Science.gov (United States)

Lee, Jason Kwok-San; Lee, Benjamin; Thorpe, Jeremy; Andrews, Kenneth; Dolinar, Sam; Hamkins, Jon

2004-01-01

We present a scalable decoding architecture for a certain class of structured LDPC codes. The codes are designed using a small (n,r) protograph that is replicated Z times to produce a decoding graph for a (Z x n, Z x r) code. Using this architecture, we have implemented a decoder for a (4096,2048) LDPC code on a Xilinx Virtex-II 2000 FPGA, and achieved decoding speeds of 31 Mbps with 10 fixed iterations. The implemented message-passing algorithm uses an optimized 3-bit non-uniform quantizer that operates with 0.2dB implementation loss relative to a floating point decoder.

A method of handing down surgical clipping technique for cerebral aneurysm

International Nuclear Information System (INIS)

Idei, Masaru; Yamane, Kanji; Okita, Shinji; Kumano, Kiyoshi; Nakae, Ryuta

2009-01-01

Meticulous clipping techniques are essential to obtain good results. Recently, the introduction of intravascular surgery for cerebral aneurysms has decreased the number of the direct clipping surgeries. And the increasing number of the lawsuits against doctors further discourages young surgeons from attempting clipping. As a result, young neurosurgeons, have less experience performing clipping. Therefore, we must learn clipping techniques from expert neurosurgeons under the limitation of having fewer opportunities to perform clipping surgery. In this paper, I present my experiences and discuss ways to obtain techniques for clipping surgery. I performed surgical clipping in 19 cases, 12 unruptured and 7 ruptured aneurysms, 7 males and 12 females aged from 36 to 79 years old (mean 61.9 years). Postoperatively, there were no symptomatic complications, but there were 2 asymptomatic infarctions that were revealed on CT scan. Intraoperative premature rupture occurred in 1 patient with a ruptured aneurysm. Techniques of manipulation with micro-forceps, suction and spatula are required for successful clipping. Off-the-job training of dissecting chicken wing arteries and rat abdominal aortas and vena cavas is useful. Moreover, actual experiences of surgical operations are essential. Surgical experiences raise the motivation of young neurosurgeons and encourage them to train more. We believe that this benign cycle contributes to meticulous surgical skills. (author)

Semantic Labeling of Nonspeech Audio Clips

Directory of Open Access Journals (Sweden)

Xiaojuan Ma

2010-01-01

Full Text Available Human communication about entities and events is primarily linguistic in nature. While visual representations of information are shown to be highly effective as well, relatively little is known about the communicative power of auditory nonlinguistic representations. We created a collection of short nonlinguistic auditory clips encoding familiar human activities, objects, animals, natural phenomena, machinery, and social scenes. We presented these sounds to a broad spectrum of anonymous human workers using Amazon Mechanical Turk and collected verbal sound labels. We analyzed the human labels in terms of their lexical and semantic properties to ascertain that the audio clips do evoke the information suggested by their pre-defined captions. We then measured the agreement with the semantically compatible labels for each sound clip. Finally, we examined which kinds of entities and events, when captured by nonlinguistic acoustic clips, appear to be well-suited to elicit information for communication, and which ones are less discriminable. Our work is set against the broader goal of creating resources that facilitate communication for people with some types of language loss. Furthermore, our data should prove useful for future research in machine analysis/synthesis of audio, such as computational auditory scene analysis, and annotating/querying large collections of sound effects.

Clip, connect, clone

DEFF Research Database (Denmark)

Fujima, Jun; Lunzer, Aran; Hornbæk, Kasper

2010-01-01

using three mechanisms: clipping of input and result elements from existing applications to form cells on a spreadsheet; connecting these cells using formulas, thus enabling result transfer between applications; and cloning cells so that multiple requests can be handled side by side. We demonstrate...

Evaluation framework for K-best sphere decoders

KAUST Repository

Shen, Chungan

2010-08-01

While Maximum-Likelihood (ML) is the optimum decoding scheme for most communication scenarios, practical implementation difficulties limit its use, especially for Multiple Input Multiple Output (MIMO) systems with a large number of transmit or receive antennas. Tree-searching type decoder structures such as Sphere decoder and K-best decoder present an interesting trade-off between complexity and performance. Many algorithmic developments and VLSI implementations have been reported in literature with widely varying performance to area and power metrics. In this semi-tutorial paper we present a holistic view of different Sphere decoding techniques and K-best decoding techniques, identifying the key algorithmic and implementation trade-offs. We establish a consistent benchmark framework to investigate and compare the delay cost, power cost, and power-delay-product cost incurred by each method. Finally, using the framework, we propose and analyze a novel architecture and compare that to other published approaches. Our goal is to explicitly elucidate the overall advantages and disadvantages of each proposed algorithms in one coherent framework. © 2010 World Scientific Publishing Company.

Heterogeneity of miRNA expression in localized prostate cancer with clinicopathological correlations

DEFF Research Database (Denmark)

Zedan, Ahmed Hussein; Blavnsfeldt, Søren Garm; Hansen, Torben Frøstrup

2017-01-01

).RESULTS: Four miRNAs (miRNA-21, miRNA-34a, miRNA-125, and miRNA-126) were significantly upregulated in PCa compared to benign prostatic hyperplasia (BPH), and except for miRNA-21 these miRNAs documented a positive correlation between the expression level in PCa cores and their matched BPH cores, (r > 0......-free survival (p = 0.016).CONCLUSION: The present study documents significant upregulation of the expression of miRNA-21, miRNA-34a, miRNA-125, and miRNA-126 in PCa compared to BPH and suggests a possible prognostic value associated with the expression of miRNA-143. The results, however, document intra...

Heterogeneity of miRNA expression in localized prostate cancer with clinicopathological correlations

DEFF Research Database (Denmark)

Zedan, Ahmed Hussein; Blavnsfeldt, Søren Garm; Hansen, Torben Frøstrup

2017-01-01

). RESULTS: Four miRNAs (miRNA-21, miRNA-34a, miRNA-125, and miRNA-126) were significantly upregulated in PCa compared to benign prostatic hyperplasia (BPH), and except for miRNA-21 these miRNAs documented a positive correlation between the expression level in PCa cores and their matched BPH cores, (r > 0......-free survival (p = 0.016). CONCLUSION: The present study documents significant upregulation of the expression of miRNA-21, miRNA-34a, miRNA-125, and miRNA-126 in PCa compared to BPH and suggests a possible prognostic value associated with the expression of miRNA-143. The results, however, document intra...

Exosomes as miRNA Carriers: Formation–Function–Future

Science.gov (United States)

Yu, Xiaojie; Odenthal, Margarete; Fries, Jochen W. U.

2016-01-01

Exosomes, which are one of the smallest extracellular vesicles released from cells, have been shown to carry different nucleic acids, including microRNAs (miRNAs). miRNAs significantly regulate cell growth and metabolism by posttranscriptional inhibition of gene expression. The rapidly changing understanding of exosomes’ formation and function in delivering miRNAs from cell to cell has prompted us to review current knowledge in exosomal miRNA secretion mechanisms as well as possible therapeutic applications for personalized medicine. PMID:27918449

Exosomes as miRNA Carriers: Formation–Function–Future

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Xiaojie Yu

2016-12-01

Full Text Available Exosomes, which are one of the smallest extracellular vesicles released from cells, have been shown to carry different nucleic acids, including microRNAs (miRNAs. miRNAs significantly regulate cell growth and metabolism by posttranscriptional inhibition of gene expression. The rapidly changing understanding of exosomes’ formation and function in delivering miRNAs from cell to cell has prompted us to review current knowledge in exosomal miRNA secretion mechanisms as well as possible therapeutic applications for personalized medicine.

Orientation decoding: Sense in spirals?

Science.gov (United States)

Clifford, Colin W G; Mannion, Damien J

2015-04-15

The orientation of a visual stimulus can be successfully decoded from the multivariate pattern of fMRI activity in human visual cortex. Whether this capacity requires coarse-scale orientation biases is controversial. We and others have advocated the use of spiral stimuli to eliminate a potential coarse-scale bias-the radial bias toward local orientations that are collinear with the centre of gaze-and hence narrow down the potential coarse-scale biases that could contribute to orientation decoding. The usefulness of this strategy is challenged by the computational simulations of Carlson (2014), who reported the ability to successfully decode spirals of opposite sense (opening clockwise or counter-clockwise) from the pooled output of purportedly unbiased orientation filters. Here, we elaborate the mathematical relationship between spirals of opposite sense to confirm that they cannot be discriminated on the basis of the pooled output of unbiased or radially biased orientation filters. We then demonstrate that Carlson's (2014) reported decoding ability is consistent with the presence of inadvertent biases in the set of orientation filters; biases introduced by their digital implementation and unrelated to the brain's processing of orientation. These analyses demonstrate that spirals must be processed with an orientation bias other than the radial bias for successful decoding of spiral sense. Copyright © 2014 Elsevier Inc. All rights reserved.

Grasp movement decoding from premotor and parietal cortex.

Science.gov (United States)

Townsend, Benjamin R; Subasi, Erk; Scherberger, Hansjörg

2011-10-05

Despite recent advances in harnessing cortical motor-related activity to control computer cursors and robotic devices, the ability to decode and execute different grasping patterns remains a major obstacle. Here we demonstrate a simple Bayesian decoder for real-time classification of grip type and wrist orientation in macaque monkeys that uses higher-order planning signals from anterior intraparietal cortex (AIP) and ventral premotor cortex (area F5). Real-time decoding was based on multiunit signals, which had similar tuning properties to cells in previous single-unit recording studies. Maximum decoding accuracy for two grasp types (power and precision grip) and five wrist orientations was 63% (chance level, 10%). Analysis of decoder performance showed that grip type decoding was highly accurate (90.6%), with most errors occurring during orientation classification. In a subsequent off-line analysis, we found small but significant performance improvements (mean, 6.25 percentage points) when using an optimized spike-sorting method (superparamagnetic clustering). Furthermore, we observed significant differences in the contributions of F5 and AIP for grasp decoding, with F5 being better suited for classification of the grip type and AIP contributing more toward decoding of object orientation. However, optimum decoding performance was maximal when using neural activity simultaneously from both areas. Overall, these results highlight quantitative differences in the functional representation of grasp movements in AIP and F5 and represent a first step toward using these signals for developing functional neural interfaces for hand grasping.

O2-GIDNC: Beyond instantly decodable network coding

KAUST Repository

Aboutorab, Neda

2013-06-01

In this paper, we are concerned with extending the graph representation of generalized instantly decodable network coding (GIDNC) to a more general opportunistic network coding (ONC) scenario, referred to as order-2 GIDNC (O2-GIDNC). In the O2-GIDNC scheme, receivers can store non-instantly decodable packets (NIDPs) comprising two of their missing packets, and use them in a systematic way for later decodings. Once this graph representation is found, it can be used to extend the GIDNC graph-based analyses to the proposed O2-GIDNC scheme with a limited increase in complexity. In the proposed O2-GIDNC scheme, the information of the stored NIDPs at the receivers and the decoding opportunities they create can be exploited to improve the broadcast completion time and decoding delay compared to traditional GIDNC scheme. The completion time and decoding delay minimizing algorithms that can operate on the new O2-GIDNC graph are further described. The simulation results show that our proposed O2-GIDNC improves the completion time and decoding delay performance of the traditional GIDNC. © 2013 IEEE.

On decoding of multi-level MPSK modulation codes

Science.gov (United States)

Lin, Shu; Gupta, Alok Kumar

1990-01-01

The decoding problem of multi-level block modulation codes is investigated. The hardware design of soft-decision Viterbi decoder for some short length 8-PSK block modulation codes is presented. An effective way to reduce the hardware complexity of the decoder by reducing the branch metric and path metric, using a non-uniform floating-point to integer mapping scheme, is proposed and discussed. The simulation results of the design are presented. The multi-stage decoding (MSD) of multi-level modulation codes is also investigated. The cases of soft-decision and hard-decision MSD are considered and their performance are evaluated for several codes of different lengths and different minimum squared Euclidean distances. It is shown that the soft-decision MSD reduces the decoding complexity drastically and it is suboptimum. The hard-decision MSD further simplifies the decoding while still maintaining a reasonable coding gain over the uncoded system, if the component codes are chosen properly. Finally, some basic 3-level 8-PSK modulation codes using BCH codes as component codes are constructed and their coding gains are found for hard decision multistage decoding.

Current MitraClip experience, safety and feasibility in the Netherlands

NARCIS (Netherlands)

Rahhab, Z.; Kortlandt, F. A.; Velu, J. F.; Schurer, R. A. J.; Delgado, V.; Tonino, P.; Boven, A. J.; van den Branden, B. J. L.; Kraaijeveld, A. O.; Voskuil, M.; Hoorntje, J.; van Wely, M. [=Marleen; van Houwelingen, K.; Bleeker, G. B.; Rensing, B.; Kardys, I.; Baan, J.; van der Heyden, J. A. S.; van Mieghem, N. M.

2017-01-01

Purpose Data on MitraClip procedural safety and efficacy in the Netherlands are scarce. We aim to provide an overview of the Dutch MitraClip experience. Methods We pooled anonymised demographic and procedural data of 1151 consecutive MitraClip patients, from 13 Dutch hospitals. Data was collected by

Multi-stage decoding of multi-level modulation codes

Science.gov (United States)

Lin, Shu; Kasami, Tadao; Costello, Daniel J., Jr.

1991-01-01

Various types of multi-stage decoding for multi-level modulation codes are investigated. It is shown that if the component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. Particularly, it is shown that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum soft-decision decoding of the code is very small, only a fraction of dB loss in signal to noise ratio at a bit error rate (BER) of 10(exp -6).

Heterogeneity of miRNA expression in localized prostate cancer with clinicopathological correlations.

Directory of Open Access Journals (Sweden)

Ahmed Hussein Zedan

Full Text Available In the last decade microRNAs (miRNAs have been widely investigated in prostate cancer (PCa and have shown to be promising biomarkers in diagnostic, prognostic and predictive settings. However, tumor heterogeneity may influence miRNA expression. The aims of this study were to assess the impact of tumor heterogeneity, as demonstrated by a panel of selected miRNAs in PCa, and to correlate miRNA expression with risk profile and patient outcome.Prostatectomy specimens and matched, preoperative needle biopsies from a retrospective cohort of 49 patients, who underwent curatively intended surgery for localized PCa, were investigated with a panel of 6 miRNAs (miRNA-21, miRNA-34a, miRNA-125b, miRNA-126, miRNA-143, and miRNA-145 using tissue micro-array (TMA and in situ hybridization (ISH. Inter- and intra-patient variation was assessed using intra-class correlation (ICC.Four miRNAs (miRNA-21, miRNA-34a, miRNA-125, and miRNA-126 were significantly upregulated in PCa compared to benign prostatic hyperplasia (BPH, and except for miRNA-21 these miRNAs documented a positive correlation between the expression level in PCa cores and their matched BPH cores, (r > 0.72. The ICC varied from 0.451 to 0.764, with miRNA-34a showing an intra-tumoral heterogeneity accounting for less than 50% of the total variation. Regarding clinicopathological outcomes, only miRNA-143 showed potential as a prognostic marker with a higher expression correlating with longer relapse-free survival (p = 0.016.The present study documents significant upregulation of the expression of miRNA-21, miRNA-34a, miRNA-125, and miRNA-126 in PCa compared to BPH and suggests a possible prognostic value associated with the expression of miRNA-143. The results, however, document intra-tumoral heterogeneity in the expression of various miRNAs calling for caution when using these tumor tissue biomarkers in prognostic and predictive settings.

Diagnostic applications of nail clippings.

Science.gov (United States)

Stephen, Sasha; Tosti, Antonella; Rubin, Adam I

2015-04-01

"Nail clipping is a simple technique for diagnosis of several nail unit dermatoses. This article summarizes the practical approach, utility, and histologic findings of a nail clipping in evaluation of onychomycosis, nail unit psoriasis, onychomatricoma, subungual hematoma, melanonychia, and nail cosmetics, and the forensic applications of this easily obtained specimen. It reviews important considerations in optimizing specimen collection, processing methods, and efficacy of special stains in several clinical contexts. Readers will develop a greater understanding and ease of application of this indispensable procedure in assessing nail unit dermatoses." Copyright © 2015 Elsevier Inc. All rights reserved.

Binary Systematic Network Coding for Progressive Packet Decoding

OpenAIRE

Jones, Andrew L.; Chatzigeorgiou, Ioannis; Tassi, Andrea

2015-01-01

We consider binary systematic network codes and investigate their capability of decoding a source message either in full or in part. We carry out a probability analysis, derive closed-form expressions for the decoding probability and show that systematic network coding outperforms conventional net- work coding. We also develop an algorithm based on Gaussian elimination that allows progressive decoding of source packets. Simulation results show that the proposed decoding algorithm can achieve ...

Power decoding Reed-Solomon codes up to the Johnson radius

DEFF Research Database (Denmark)

Rosenkilde, Johan Sebastian Heesemann

2018-01-01

Power decoding, or "decoding using virtual interleaving" is a technique for decoding Reed-Solomon codes up to the Sudan radius. Since the method's inception, it has been an open question if it is possible to use this approach to decode up to the Johnson radius - the decoding radius of the Guruswami...

Application of Beyond Bound Decoding for High Speed Optical Communications

DEFF Research Database (Denmark)

Li, Bomin; Larsen, Knud J.; Vegas Olmos, Juan José

2013-01-01

This paper studies the application of beyond bound decoding method for high speed optical communications. This hard-decision decoding method outperforms traditional minimum distance decoding method, with a total net coding gain of 10.36 dB.......This paper studies the application of beyond bound decoding method for high speed optical communications. This hard-decision decoding method outperforms traditional minimum distance decoding method, with a total net coding gain of 10.36 dB....

Dirty Hits

OpenAIRE

Clarke, Louise

2010-01-01

Issue 9 of the Saatchi Gallery Magazine: Art&Music is dedicated to Sex. The article Dirty Hits invited a cross-section of contemporary artists and musicians to answer: What makes a dirty hit? As one of the artists invited, I wrote an autobiographical piece to reveal how these fumbling, feral sexual experiences of my childhood landscape, along with irrational superstition and folk law inform my life and underpin my work. The article also included an artwork: Louise Clarke, Sip (2009)

Polar Coding with CRC-Aided List Decoding

Science.gov (United States)

2015-08-01

TECHNICAL REPORT 2087 August 2015 Polar Coding with CRC-Aided List Decoding David Wasserman Approved...list decoding . RESULTS Our simulation results show that polar coding can produce results very similar to the FEC used in the Digital Video...standard. RECOMMENDATIONS In any application for which the DVB-S2 FEC is considered, polar coding with CRC-aided list decod - ing with N = 65536

Quantum walks with infinite hitting times

International Nuclear Information System (INIS)

Krovi, Hari; Brun, Todd A.

2006-01-01

Hitting times are the average time it takes a walk to reach a given final vertex from a given starting vertex. The hitting time for a classical random walk on a connected graph will always be finite. We show that, by contrast, quantum walks can have infinite hitting times for some initial states. We seek criteria to determine if a given walk on a graph will have infinite hitting times, and find a sufficient condition, which for discrete time quantum walks is that the degeneracy of the evolution operator be greater than the degree of the graph. The set of initial states which give an infinite hitting time form a subspace. The phenomenon of infinite hitting times is in general a consequence of the symmetry of the graph and its automorphism group. Using the irreducible representations of the automorphism group, we derive conditions such that quantum walks defined on this graph must have infinite hitting times for some initial states. In the case of the discrete walk, if this condition is satisfied the walk will have infinite hitting times for any choice of a coin operator, and we give a class of graphs with infinite hitting times for any choice of coin. Hitting times are not very well defined for continuous time quantum walks, but we show that the idea of infinite hitting-time walks naturally extends to the continuous time case as well

miRNA genes of an invasive vector mosquito, Aedes albopictus.

Directory of Open Access Journals (Sweden)

Jinbao Gu

Full Text Available Aedes albopictus, a vector of Dengue and Chikungunya viruses, is a robust invasive species in both tropical and temperate environments. MicroRNAs (miRNAs regulate gene expression and biological processes including embryonic development, innate immunity and infection. While a number of miRNAs have been discovered in some mosquitoes, no comprehensive effort has been made to characterize them from different developmental stages from a single species. Systematic analysis of miRNAs in Ae. albopictus will improve our understanding of its basic biology and inform novel strategies to prevent virus transmission. Between 10-14 million Illumina sequencing reads per sample were obtained from embryos, larvae, pupae, adult males, sugar-fed and blood-fed adult females. A total of 119 miRNA genes represented by 215 miRNA or miRNA star (miRNA* sequences were identified, 15 of which are novel. Eleven, two, and two of the newly-discovered miRNA genes appear specific to Aedes, Culicinae, and Culicidae, respectively. A number of miRNAs accumulate predominantly in one or two developmental stages and the large number that showed differences in abundance following a blood meal likely are important in blood-induced mosquito biology. Gene Ontology (GO analysis of the targets of all Ae. albopictus miRNAs provides a useful starting point for the study of their functions in mosquitoes. This study is the first systematic analysis of miRNAs based on deep-sequencing of small RNA samples of all developmental stages of a mosquito species. A number of miRNAs are related to specific physiological states, most notably, pre- and post-blood feeding. The distribution of lineage-specific miRNAs is consistent with mosquito phylogeny and the presence of a number of Aedes-specific miRNAs likely reflects the divergence between the Aedes and Culex genera.

77 FR 23250 - HIT Standards Committee; Schedule for the Assessment of HIT Policy Committee Recommendations

Science.gov (United States)

2012-04-18

... DEPARTMENT OF HEALTH AND HUMAN SERVICES HIT Standards Committee; Schedule for the Assessment of HIT Policy Committee Recommendations AGENCY: Office of the National Coordinator for Health Information... 2009 mandates that the HIT Standards Committee develop a schedule for the assessment of policy...

76 FR 25355 - HIT Standards Committee; Schedule for the Assessment of HIT Policy Committee Recommendations

Science.gov (United States)

2011-05-04

... DEPARTMENT OF HEALTH AND HUMAN SERVICES HIT Standards Committee; Schedule for the Assessment of HIT Policy Committee Recommendations AGENCY: Office of the National Coordinator for Health Information... 2009 mandates that the HIT Standards Committee develop a schedule for the assessment of policy...

78 FR 29134 - HIT Standards Committee; Schedule for the Assessment of HIT Policy Committee Recommendations

Science.gov (United States)

2013-05-17

... DEPARTMENT OF HEALTH AND HUMAN SERVICES HIT Standards Committee; Schedule for the Assessment of HIT Policy Committee Recommendations AGENCY: Office of the National Coordinator for Health Information... 2009 mandates that the HIT Standards Committee develop a schedule for the assessment of policy...

Statistical properties and pre-hit dynamics of price limit hits in the Chinese stock markets.

Science.gov (United States)

Wan, Yu-Lei; Xie, Wen-Jie; Gu, Gao-Feng; Jiang, Zhi-Qiang; Chen, Wei; Xiong, Xiong; Zhang, Wei; Zhou, Wei-Xing

2015-01-01

Price limit trading rules are adopted in some stock markets (especially emerging markets) trying to cool off traders' short-term trading mania on individual stocks and increase market efficiency. Under such a microstructure, stocks may hit their up-limits and down-limits from time to time. However, the behaviors of price limit hits are not well studied partially due to the fact that main stock markets such as the US markets and most European markets do not set price limits. Here, we perform detailed analyses of the high-frequency data of all A-share common stocks traded on the Shanghai Stock Exchange and the Shenzhen Stock Exchange from 2000 to 2011 to investigate the statistical properties of price limit hits and the dynamical evolution of several important financial variables before stock price hits its limits. We compare the properties of up-limit hits and down-limit hits. We also divide the whole period into three bullish periods and three bearish periods to unveil possible differences during bullish and bearish market states. To uncover the impacts of stock capitalization on price limit hits, we partition all stocks into six portfolios according to their capitalizations on different trading days. We find that the price limit trading rule has a cooling-off effect (object to the magnet effect), indicating that the rule takes effect in the Chinese stock markets. We find that price continuation is much more likely to occur than price reversal on the next trading day after a limit-hitting day, especially for down-limit hits, which has potential practical values for market practitioners.

CLIPS - C LANGUAGE INTEGRATED PRODUCTION SYSTEM (IBM PC VERSION WITH CLIPSITS)

Science.gov (United States)

Riley, , .

1994-01-01

The C Language Integrated Production System, CLIPS, is a shell for developing expert systems. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. The primary design goals for CLIPS are portability, efficiency, and functionality. For these reasons, the program is written in C. CLIPS meets or outperforms most micro- and minicomputer based artificial intelligence tools. CLIPS is a forward chaining rule-based language. The program contains an inference engine and a language syntax that provide a framework for the construction of an expert system. It also includes tools for debugging an application. CLIPS is based on the Rete algorithm, which enables very efficient pattern matching. The collection of conditions and actions to be taken if the conditions are met is constructed into a rule network. As facts are asserted either prior to or during a session, CLIPS pattern-matches the number of fields. Wildcards and variables are supported for both single and multiple fields. CLIPS syntax allows the inclusion of externally defined functions (outside functions which are written in a language other than CLIPS). CLIPS itself can be embedded in a program such that the expert system is available as a simple subroutine call. Advanced features found in CLIPS version 4.3 include an integrated microEMACS editor, the ability to generate C source code from a CLIPS rule base to produce a dedicated executable, binary load and save capabilities for CLIPS rule bases, and the utility program CRSV (Cross-Reference, Style, and Verification) designed to facilitate the development and maintenance of large rule bases. Five machine versions are available. Each machine version includes the source and the executable for that machine. The UNIX version includes the source and binaries for IBM RS/6000, Sun3 series, and Sun4 series computers. The UNIX, DEC VAX, and DEC RISC Workstation versions are line oriented. The PC version and the Macintosh

Decoding of concatenated codes with interleaved outer codes

DEFF Research Database (Denmark)

Justesen, Jørn; Høholdt, Tom; Thommesen, Christian

2004-01-01

Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved (N, K) Reed-Solomon codes, which allows close to N-K errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes.......Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved (N, K) Reed-Solomon codes, which allows close to N-K errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes....

miRNA and Degradome Sequencing Reveal miRNA and Their Target Genes That May Mediate Shoot Growth in Spur Type Mutant “Yanfu 6”

Science.gov (United States)

Song, Chunhui; Zhang, Dong; Zheng, Liwei; Zhang, Jie; Zhang, Baojuan; Luo, Wenwen; Li, Youmei; Li, Guangfang; Ma, Juanjuan; Han, Mingyu

2017-01-01

The spur-type growth habit in apple trees is characterized by short internodes, increased number of fruiting spurs, and compact growth that promotes flowering and facilitates management practices, such as pruning. The molecular mechanisms responsible for regulating spur-type growth have not been elucidated. In the present study, miRNAs and the expression of their potential target genes were evaluated in shoot tips of “Nagafu 2” (CF) and spur-type bud mutation “Yanfu 6” (YF). A total of 700 mature miRNAs were identified, including 202 known apple miRNAs and 498 potential novel miRNA candidates. A comparison of miRNA expression in CF and YF revealed 135 differentially expressed genes, most of which were downregulated in YF. YF also had lower levels of GA, ZR, IAA, and ABA hormones, relative to CF. Exogenous applications of GA promoted YF shoot growth. Based on the obtained results, a regulatory network involving plant hormones, miRNA, and their potential target genes is proposed for the molecular mechanism regulating the growth of YF. miRNA164, miRNA166, miRNA171, and their potential targets, and associated plant hormones, appear to regulate shoot apical meristem (SAM) growth. miRNA159, miRNA167, miRNA396, and their potential targets, and associated plant hormones appear to regulate cell division and internode length. This study provides a foundation for further studies designed to elucidate the mechanism underlying spur-type apple architecture. PMID:28424721

Image transmission system using adaptive joint source and channel decoding

Science.gov (United States)

Liu, Weiliang; Daut, David G.

2005-03-01

In this paper, an adaptive joint source and channel decoding method is designed to accelerate the convergence of the iterative log-dimain sum-product decoding procedure of LDPC codes as well as to improve the reconstructed image quality. Error resilience modes are used in the JPEG2000 source codec, which makes it possible to provide useful source decoded information to the channel decoder. After each iteration, a tentative decoding is made and the channel decoded bits are then sent to the JPEG2000 decoder. Due to the error resilience modes, some bits are known to be either correct or in error. The positions of these bits are then fed back to the channel decoder. The log-likelihood ratios (LLR) of these bits are then modified by a weighting factor for the next iteration. By observing the statistics of the decoding procedure, the weighting factor is designed as a function of the channel condition. That is, for lower channel SNR, a larger factor is assigned, and vice versa. Results show that the proposed joint decoding methods can greatly reduce the number of iterations, and thereby reduce the decoding delay considerably. At the same time, this method always outperforms the non-source controlled decoding method up to 5dB in terms of PSNR for various reconstructed images.

Entropy-based model for miRNA isoform analysis.

Directory of Open Access Journals (Sweden)

Shengqin Wang

Full Text Available MiRNAs have been widely studied due to their important post-transcriptional regulatory roles in gene expression. Many reports have demonstrated the evidence of miRNA isoform products (isomiRs in high-throughput small RNA sequencing data. However, the biological function involved in these molecules is still not well investigated. Here, we developed a Shannon entropy-based model to estimate isomiR expression profiles of high-throughput small RNA sequencing data extracted from miRBase webserver. By using the Kolmogorov-Smirnov statistical test (KS test, we demonstrated that the 5p and 3p miRNAs present more variants than the single arm miRNAs. We also found that the isomiR variant, except the 3' isomiR variant, is strongly correlated with Minimum Free Energy (MFE of pre-miRNA, suggesting the intrinsic feature of pre-miRNA should be one of the important factors for the miRNA regulation. The functional enrichment analysis showed that the miRNAs with high variation, particularly the 5' end variation, are enriched in a set of critical functions, supporting these molecules should not be randomly produced. Our results provide a probabilistic framework for miRNA isoforms analysis, and give functional insights into pre-miRNA processing.

Iterative channel decoding of FEC-based multiple-description codes.

Science.gov (United States)

Chang, Seok-Ho; Cosman, Pamela C; Milstein, Laurence B

2012-03-01

Multiple description coding has been receiving attention as a robust transmission framework for multimedia services. This paper studies the iterative decoding of FEC-based multiple description codes. The proposed decoding algorithms take advantage of the error detection capability of Reed-Solomon (RS) erasure codes. The information of correctly decoded RS codewords is exploited to enhance the error correction capability of the Viterbi algorithm at the next iteration of decoding. In the proposed algorithm, an intradescription interleaver is synergistically combined with the iterative decoder. The interleaver does not affect the performance of noniterative decoding but greatly enhances the performance when the system is iteratively decoded. We also address the optimal allocation of RS parity symbols for unequal error protection. For the optimal allocation in iterative decoding, we derive mathematical equations from which the probability distributions of description erasures can be generated in a simple way. The performance of the algorithm is evaluated over an orthogonal frequency-division multiplexing system. The results show that the performance of the multiple description codes is significantly enhanced.

Modified Decoding Algorithm of LLR-SPA

Directory of Open Access Journals (Sweden)

Zhongxun Wang

2014-09-01

Full Text Available In wireless sensor networks, the energy consumption is mainly occurred in the stage of information transmission. The Low Density Parity Check code can make full use of the channel information to save energy. Because of the widely used decoding algorithm of the Low Density Parity Check code, this paper proposes a new decoding algorithm which is based on the LLR-SPA (Sum-Product Algorithm in Log-Likelihood-domain to improve the accuracy of the decoding algorithm. In the modified algorithm, a piecewise linear function is used to approximate the complicated Jacobi correction term in LLR-SPA decoding algorithm. Construct the tangent by the tangency point to the function of Jacobi correction term, which is based on the first order Taylor Series. In this way, the proposed piecewise linear approximation offers almost a perfect match to the function of Jacobi correction term. Meanwhile, the proposed piecewise linear approximation could avoid the operation of logarithmic which is more suitable for practical application. The simulation results show that the proposed algorithm could improve the decoding accuracy greatly without noticeable variation of the computational complexity.

Assay reproducibility in clinical studies of plasma miRNA.

Directory of Open Access Journals (Sweden)

Jonathan Rice

Full Text Available There are increasing reports of plasma miRNAs as biomarkers of human disease but few standards in methodologic reporting, leading to inconsistent data. We systematically reviewed plasma miRNA studies published between July 2013-June 2014 to assess methodology. Six parameters were investigated: time to plasma extraction, methods of RNA extraction, type of miRNA, quantification, cycle threshold (Ct setting, and methods of statistical analysis. We compared these data with a proposed standard methodologic technique. Beginning with initial screening for 380 miRNAs using microfluidic array technology and validation in an additional cohort of patients, we compared 11 miRNAs that exhibited differential expression between 16 patients with benign colorectal neoplasms (advanced adenomas and 16 patients without any neoplasm (controls. Plasma was isolated immediately, 12, 24, 48, or 72 h following phlebotomy. miRNA was extracted using two different techniques (Trizol LS with pre-amplification or modified miRNeasy. We performed Taqman-based RT-PCR assays for the 11 miRNAs with subsequent analyses using a variable Ct setting or a fixed Ct set at 0.01, 0.03, 0.05, or 0.5. Assays were performed in duplicate by two different operators. RNU6 was the internal reference. Systematic review yielded 74 manuscripts meeting inclusion criteria. One manuscript (1.4% documented all 6 methodological parameters, while < 5% of studies listed Ct setting. In our proposed standard technique, plasma extraction ≤12 h provided consistent ΔCt. miRNeasy extraction yielded higher miRNA concentrations and fewer non-expressed miRNAs compared to Trizol LS (1/704 miRNAs [0.14%] vs 109/704 miRNAs [15%], not expressed, respectively. A fixed Ct bar setting of 0.03 yielded the most reproducible data, provided that <10% miRNA were non-expressed. There was no significant intra-operator variability. There was significant inter-operator variation using Trizol LS extraction, while this was

Real-time minimal-bit-error probability decoding of convolutional codes

Science.gov (United States)

Lee, L.-N.

1974-01-01

A recursive procedure is derived for decoding of rate R = 1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit, subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e., fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications, such as in the inner coding system for concatenated coding.

Real-time minimal bit error probability decoding of convolutional codes

Science.gov (United States)

Lee, L. N.

1973-01-01

A recursive procedure is derived for decoding of rate R=1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e. fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications such as in the inner coding system for concatenated coding.

N6-adenosine methylation in MiRNAs.

Directory of Open Access Journals (Sweden)

Tea Berulava

Full Text Available Methylation of N6-adenosine (m6A has been observed in many different classes of RNA, but its prevalence in microRNAs (miRNAs has not yet been studied. Here we show that a knockdown of the m6A demethylase FTO affects the steady-state levels of several miRNAs. Moreover, RNA immunoprecipitation with an anti-m6A-antibody followed by RNA-seq revealed that a significant fraction of miRNAs contains m6A. By motif searches we have discovered consensus sequences discriminating between methylated and unmethylated miRNAs. The epigenetic modification of an epigenetic modifier as described here adds a new layer to the complexity of the posttranscriptional regulation of gene expression.

Receiver-based recovery of clipped ofdm signals for papr reduction: A bayesian approach

KAUST Repository

Ali, Anum

2014-01-01

Clipping is one of the simplest peak-to-average power ratio reduction schemes for orthogonal frequency division multiplexing (OFDM). Deliberately clipping the transmission signal degrades system performance, and clipping mitigation is required at the receiver for information restoration. In this paper, we acknowledge the sparse nature of the clipping signal and propose a low-complexity Bayesian clipping estimation scheme. The proposed scheme utilizes a priori information about the sparsity rate and noise variance for enhanced recovery. At the same time, the proposed scheme is robust against inaccurate estimates of the clipping signal statistics. The undistorted phase property of the clipped signal, as well as the clipping likelihood, is utilized for enhanced reconstruction. Furthermore, motivated by the nature of modern OFDM-based communication systems, we extend our clipping reconstruction approach to multiple antenna receivers and multi-user OFDM.We also address the problem of channel estimation from pilots contaminated by the clipping distortion. Numerical findings are presented that depict favorable results for the proposed scheme compared to the established sparse reconstruction schemes.

MiRNA expression patterns predict survival in glioblastoma

International Nuclear Information System (INIS)

Niyazi, Maximilian; Belka, Claus; Zehentmayr, Franz; Niemöller, Olivier M; Eigenbrod, Sabina; Kretzschmar, Hans; Osthoff, Klaus-Schulze; Tonn, Jörg-Christian; Atkinson, Mike; Mörtl, Simone

2011-01-01

In order to define new prognostic subgroups in patients with glioblastoma a miRNA screen (> 1000 miRNAs) from paraffin tissues followed by a bio-mathematical analysis was performed. 35 glioblastoma patients treated between 7/2005 - 8/2008 at a single institution with surgery and postoperative radio(chemo)therapy were included in this retrospective analysis. For microarray analysis the febit biochip 'Geniom ® Biochip MPEA homo-sapiens' was used. Total RNA was isolated from FFPE tissue sections and 1100 different miRNAs were analyzed. It was possible to define a distinct miRNA expression pattern allowing for a separation of distinct prognostic subgroups. The defined miRNA pattern was significantly associated with early death versus long-term survival (split at 450 days) (p = 0.01). The pattern and the prognostic power were both independent of the MGMT status. At present, this is the first dataset defining a prognostic role of miRNA expression patterns in patients with glioblastoma. Having defined such a pattern, a prospective validation of this observation is required

Statistical Properties and Pre-Hit Dynamics of Price Limit Hits in the Chinese Stock Markets

Science.gov (United States)

Wan, Yu-Lei; Xie, Wen-Jie; Gu, Gao-Feng; Jiang, Zhi-Qiang; Chen, Wei; Xiong, Xiong; Zhang, Wei; Zhou, Wei-Xing

2015-01-01

Price limit trading rules are adopted in some stock markets (especially emerging markets) trying to cool off traders’ short-term trading mania on individual stocks and increase market efficiency. Under such a microstructure, stocks may hit their up-limits and down-limits from time to time. However, the behaviors of price limit hits are not well studied partially due to the fact that main stock markets such as the US markets and most European markets do not set price limits. Here, we perform detailed analyses of the high-frequency data of all A-share common stocks traded on the Shanghai Stock Exchange and the Shenzhen Stock Exchange from 2000 to 2011 to investigate the statistical properties of price limit hits and the dynamical evolution of several important financial variables before stock price hits its limits. We compare the properties of up-limit hits and down-limit hits. We also divide the whole period into three bullish periods and three bearish periods to unveil possible differences during bullish and bearish market states. To uncover the impacts of stock capitalization on price limit hits, we partition all stocks into six portfolios according to their capitalizations on different trading days. We find that the price limit trading rule has a cooling-off effect (object to the magnet effect), indicating that the rule takes effect in the Chinese stock markets. We find that price continuation is much more likely to occur than price reversal on the next trading day after a limit-hitting day, especially for down-limit hits, which has potential practical values for market practitioners. PMID:25874716

Direct migration motion estimation and mode decision to decoder for a low-complexity decoder Wyner-Ziv video coding

Science.gov (United States)

Lei, Ted Chih-Wei; Tseng, Fan-Shuo

2017-07-01

This paper addresses the problem of high-computational complexity decoding in traditional Wyner-Ziv video coding (WZVC). The key focus is the migration of two traditionally high-computationally complex encoder algorithms, namely motion estimation and mode decision. In order to reduce the computational burden in this process, the proposed architecture adopts the partial boundary matching algorithm and four flexible types of block mode decision at the decoder. This approach does away with the need for motion estimation and mode decision at the encoder. The experimental results show that the proposed padding block-based WZVC not only decreases decoder complexity to approximately one hundredth that of the state-of-the-art DISCOVER decoding but also outperforms DISCOVER codec by up to 3 to 4 dB.

Novel Insights into miRNA in Lung and Heart Inflammatory Diseases

Directory of Open Access Journals (Sweden)

Amit Kishore

2014-01-01

Full Text Available MicroRNAs (miRNAs are noncoding regulatory sequences that govern posttranscriptional inhibition of genes through binding mainly at regulatory regions. The regulatory mechanism of miRNAs are influenced by complex crosstalk among single nucleotide polymorphisms (SNPs within miRNA seed region and epigenetic modifications. Circulating miRNAs exhibit potential characteristics as stable biomarker. Functionally, miRNAs are involved in basic regulatory mechanisms of cells including inflammation. Thus, miRNA dysregulation, resulting in aberrant expression of a gene, is suggested to play an important role in disease susceptibility. This review focuses on the role of miRNA as diagnostic marker in pathogenesis of lung inflammatory diseases and in cardiac remodelling events during inflammation. From recent reports, In this context, the information about the models in which miRNAs expression were investigated including types of biological samples, as well as on the methods for miRNA validation and prediction/definition of their gene targets are emphasized in the review. Besides disease pathogenesis, promising role of miRNAs in early disease diagnosis and prognostication is also discussed. However, some miRNAs are also indicated with protective role. Thus, identifications and usage of such potential miRNAs as well as disruption of disease susceptible miRNAs using antagonists, antagomirs, are imperative and may provide a novel therapeutic approach towards combating the disease progression.

CLIPS/Ada: An Ada-based tool for building expert systems

Science.gov (United States)

White, W. A.

1990-01-01

Clips/Ada is a production system language and a development environment. It is functionally equivalent to the CLIPS tool. CLIPS/Ada was developed in order to provide a means of incorporating expert system technology into projects where the use of the Ada language had been mandated. A secondary purpose was to glean information about the Ada language and its compilers. Specifically, whether or not the language and compilers were mature enough to support AI applications. The CLIPS/Ada tool is coded entirely in Ada and is designed to be used by Ada systems that require expert reasoning.

MiR-27a suppresses triglyceride accumulation and affects gene mRNA expression associated with fat metabolism in dairy goat mammary gland epithelial cells.

Science.gov (United States)

Lin, Xian-Zi; Luo, Jun; Zhang, Li-Ping; Wang, Wei; Shi, Heng-Bo; Zhu, Jiang-Jiang

2013-05-25

MicroRNAs (miRNAs), a well-defined group of small RNAs containing about 22 nucleotides, participate in various biological metabolic processes. miR-27a is a miRNA that is known to regulate fat synthesis and differentiation in preadipocyte cells. However, little is known regarding the role that miR-27a plays in regulating goat milk fat synthesis. In this study, we determined the miR-27a expression profile in goat mammary gland and found that miR-27a expression was correlated with the lactation cycle. Additionally, prolactin promoted miR-27a expression in goat mammary gland epithelial cells. Further functional analysis showed that over-expression of miR-27a down-regulated triglyceride accumulation and decreased the ratio of unsaturated/saturated fatty acid in mammary gland epithelial cells. miR-27a also significantly affected mRNA expression related to milk fat metabolism. Specifically, over-expression of miR-27a reduced gene mRNA expression associated with triglyceride synthesis by suppressing PPARγ protein levels. This study provides the first experimental evidence that miR-27a regulates triglyceride synthesis in goat mammary gland epithelial cells and improves our understanding about the importance of miRNAs in milk fat synthesis. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

Study of bifurcation behavior of two-dimensional turbo product code decoders

International Nuclear Information System (INIS)

He Yejun; Lau, Francis C.M.; Tse, Chi K.

2008-01-01

Turbo codes, low-density parity-check (LDPC) codes and turbo product codes (TPCs) are high performance error-correction codes which employ iterative algorithms for decoding. Under different conditions, the behaviors of the decoders are different. While the nonlinear dynamical behaviors of turbo code decoders and LDPC decoders have been reported in the literature, the dynamical behavior of TPC decoders is relatively unexplored. In this paper, we investigate the behavior of the iterative algorithm of a two-dimensional TPC decoder when the input signal-to-noise ratio (SNR) varies. The quantity to be measured is the mean square value of the posterior probabilities of the information bits. Unlike turbo decoders or LDPC decoders, TPC decoders do not produce a clear 'waterfall region'. This is mainly because the TPC decoding algorithm does not converge to 'indecisive' fixed points even at very low SNR values

Architecture for time or transform domain decoding of reed-solomon codes

Science.gov (United States)

Shao, Howard M. (Inventor); Truong, Trieu-Kie (Inventor); Hsu, In-Shek (Inventor); Deutsch, Leslie J. (Inventor)

1989-01-01

Two pipeline (255,233) RS decoders, one a time domain decoder and the other a transform domain decoder, use the same first part to develop an errata locator polynomial .tau.(x), and an errata evaluator polynominal A(x). Both the time domain decoder and transform domain decoder have a modified GCD that uses an input multiplexer and an output demultiplexer to reduce the number of GCD cells required. The time domain decoder uses a Chien search and polynomial evaluator on the GCD outputs .tau.(x) and A(x), for the final decoding steps, while the transform domain decoder uses a transform error pattern algorithm operating on .tau.(x) and the initial syndrome computation S(x), followed by an inverse transform algorithm in sequence for the final decoding steps prior to adding the received RS coded message to produce a decoded output message.

tRNA's wobble decoding of the genome: 40 years of modification.

Science.gov (United States)

Agris, Paul F; Vendeix, Franck A P; Graham, William D

2007-02-09

The genetic code is degenerate, in that 20 amino acids are encoded by 61 triplet codes. In 1966, Francis Crick hypothesized that the cell's limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis. Post-transcriptional modifications at tRNA's wobble position 34, especially modifications of uridine 34, enable wobble to occur. The Modified Wobble Hypothesis proposed in 1991 that specific modifications of a tRNA wobble nucleoside shape the anticodon architecture in such a manner that interactions were restricted to the complementary base plus a single wobble pairing for amino acids with twofold degenerate codons. However, chemically different modifications at position 34 would expand the ability of a tRNA to read three or even four of the fourfold degenerate codons. One foundation of Crick's Wobble Hypothesis was that a near-constant geometry of canonical base-pairing be maintained in forming all three base-pairs between the tRNA anticodon and mRNA codon on the ribosome. In accepting an aminoacyl-tRNA, the ribosome requires maintenance of a specific geometry for the anticodon-codon base-pairing. However, it is the post-transcriptional modifications at tRNA wobble position 34 and purine 37, 3'-adjacent to the anticodon, that pre-structure the anticodon domain to ensure the correct codon binding. The modifications create both the architecture and the stability needed for decoding through restraints on anticodon stereochemistry and conformational space, and through selective hydrogen bonding. A physicochemical understanding of modified nucleoside contributions to the tRNA anticodon domain architecture and its decoding of the genome has advanced RNA world evolutionary theory, the principles of RNA chemistry, and the application of this knowledge to the introduction of new amino acids to proteins.

Developing Health Information Technology (HIT) Programs and HIT Curriculum: The Southern Polytechnic State University Experience

Science.gov (United States)

Zhang, Chi; Reichgelt, Han; Rutherfoord, Rebecca H.; Wang, Andy Ju An

2014-01-01

Health Information Technology (HIT) professionals are in increasing demand as healthcare providers need help in the adoption and meaningful use of Electronic Health Record (EHR) systems while the HIT industry needs workforce skilled in HIT and EHR development. To respond to this increasing demand, the School of Computing and Software Engineering…

Decoding subjective mental states from fMRI activity patterns

International Nuclear Information System (INIS)

Tamaki, Masako; Kamitani, Yukiyasu

2011-01-01

In recent years, functional magnetic resonance imaging (fMRI) decoding has emerged as a powerful tool to read out detailed stimulus features from multi-voxel brain activity patterns. Moreover, the method has been extended to perform a primitive form of 'mind-reading,' by applying a decoder 'objectively' trained using stimulus features to more 'subjective' conditions. In this paper, we first introduce basic procedures for fMRI decoding based on machine learning techniques. Second, we discuss the source of information used for decoding, in particular, the possibility of extracting information from subvoxel neural structures. We next introduce two experimental designs for decoding subjective mental states: the 'objective-to-subjective design' and the 'subjective-to-subjective design.' Then, we illustrate recent studies on the decoding of a variety of mental states, such as, attention, awareness, decision making, memory, and mental imagery. Finally, we discuss the challenges and new directions of fMRI decoding. (author)

Reference miRNAs for miRNAome analysis of urothelial carcinomas.

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Nadine Ratert

Full Text Available BACKGROUND/OBJECTIVE: Reverse transcription quantitative real-time PCR (RT-qPCR is widely used in microRNA (miRNA expression studies on cancer. To compensate for the analytical variability produced by the multiple steps of the method, relative quantification of the measured miRNAs is required, which is based on normalization to endogenous reference genes. No study has been performed so far on reference miRNAs for normalization of miRNA expression in urothelial carcinoma. The aim of this study was to identify suitable reference miRNAs for miRNA expression studies by RT-qPCR in urothelial carcinoma. METHODS: Candidate reference miRNAs were selected from 24 urothelial carcinoma and normal bladder tissue samples by miRNA microarrays. The usefulness of these candidate reference miRNAs together with the commonly for normalization purposes used small nuclear RNAs RNU6B, RNU48, and Z30 were thereafter validated by RT-qPCR in 58 tissue samples and analyzed by the algorithms geNorm, NormFinder, and BestKeeper. PRINCIPAL FINDINGS: Based on the miRNA microarray data, a total of 16 miRNAs were identified as putative reference genes. After validation by RT-qPCR, miR-101, miR-125a-5p, miR-148b, miR-151-5p, miR-181a, miR-181b, miR-29c, miR-324-3p, miR-424, miR-874, RNU6B, RNU48, and Z30 were used for geNorm, NormFinder, and BestKeeper analyses that gave different combinations of recommended reference genes for normalization. CONCLUSIONS: The present study provided the first systematic analysis for identifying suitable reference miRNAs for miRNA expression studies of urothelial carcinoma by RT-qPCR. Different combinations of reference genes resulted in reliable expression data for both strongly and less strongly altered miRNAs. Notably, RNU6B, which is the most frequently used reference gene for miRNA studies, gave inaccurate normalization. The combination of four (miR-101, miR-125a-5p, miR-148b, and miR-151-5p or three (miR-148b, miR-181b, and miR-874

21 CFR 882.4190 - Clip forming/cutting instrument.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Clip forming/cutting instrument. 882.4190 Section 882.4190 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES.../cutting instrument. (a) Identification. A clip forming/cutting instrument is a device used by the...

Study of bifurcation behavior of two-dimensional turbo product code decoders

Energy Technology Data Exchange (ETDEWEB)

He Yejun [Department of Electronic and Information Engineering, Hong Kong Polytechnic University, Hunghom, Hong Kong (China); Lau, Francis C.M. [Department of Electronic and Information Engineering, Hong Kong Polytechnic University, Hunghom, Hong Kong (China)], E-mail: encmlau@polyu.edu.hk; Tse, Chi K. [Department of Electronic and Information Engineering, Hong Kong Polytechnic University, Hunghom, Hong Kong (China)

2008-04-15

Turbo codes, low-density parity-check (LDPC) codes and turbo product codes (TPCs) are high performance error-correction codes which employ iterative algorithms for decoding. Under different conditions, the behaviors of the decoders are different. While the nonlinear dynamical behaviors of turbo code decoders and LDPC decoders have been reported in the literature, the dynamical behavior of TPC decoders is relatively unexplored. In this paper, we investigate the behavior of the iterative algorithm of a two-dimensional TPC decoder when the input signal-to-noise ratio (SNR) varies. The quantity to be measured is the mean square value of the posterior probabilities of the information bits. Unlike turbo decoders or LDPC decoders, TPC decoders do not produce a clear 'waterfall region'. This is mainly because the TPC decoding algorithm does not converge to 'indecisive' fixed points even at very low SNR values.

Interpolation decoding method with variable parameters for fractal image compression

International Nuclear Information System (INIS)

He Chuanjiang; Li Gaoping; Shen Xiaona

2007-01-01

The interpolation fractal decoding method, which is introduced by [He C, Yang SX, Huang X. Progressive decoding method for fractal image compression. IEE Proc Vis Image Signal Process 2004;3:207-13], involves generating progressively the decoded image by means of an interpolation iterative procedure with a constant parameter. It is well-known that the majority of image details are added at the first steps of iterations in the conventional fractal decoding; hence the constant parameter for the interpolation decoding method must be set as a smaller value in order to achieve a better progressive decoding. However, it needs to take an extremely large number of iterations to converge. It is thus reasonable for some applications to slow down the iterative process at the first stages of decoding and then to accelerate it afterwards (e.g., at some iteration as we need). To achieve the goal, this paper proposed an interpolation decoding scheme with variable (iteration-dependent) parameters and proved the convergence of the decoding process mathematically. Experimental results demonstrate that the proposed scheme has really achieved the above-mentioned goal

Sub-quadratic decoding of one-point hermitian codes

DEFF Research Database (Denmark)

Nielsen, Johan Sebastian Rosenkilde; Beelen, Peter

2015-01-01

We present the first two sub-quadratic complexity decoding algorithms for one-point Hermitian codes. The first is based on a fast realization of the Guruswami-Sudan algorithm using state-of-the-art algorithms from computer algebra for polynomial-ring matrix minimization. The second is a power...... decoding algorithm: an extension of classical key equation decoding which gives a probabilistic decoding algorithm up to the Sudan radius. We show how the resulting key equations can be solved by the matrix minimization algorithms from computer algebra, yielding similar asymptotic complexities....

Decoding resistant hypertension signalling pathways.

Science.gov (United States)

Parreira, Ricardo Cambraia; Lacerda, Leandro Heleno Guimarães; Vasconcellos, Rebecca; Lima, Swiany Silveira; Santos, Anderson Kenedy; Fontana, Vanessa; Sandrim, Valéria Cristina; Resende, Rodrigo Ribeiro

2017-12-01

Resistant hypertension (RH) is a clinical condition in which the hypertensive patient has become resistant to drug therapy and is often associated with increased cardiovascular morbidity and mortality. Several signalling pathways have been studied and related to the development and progression of RH: modulation of sympathetic activity by leptin and aldosterone, primary aldosteronism, arterial stiffness, endothelial dysfunction and variations in the renin-angiotensin-aldosterone system (RAAS). miRNAs comprise a family of small non-coding RNAs that participate in the regulation of gene expression at post-transcriptional level. miRNAs are involved in the development of both cardiovascular damage and hypertension. Little is known of the molecular mechanisms that lead to development and progression of this condition. This review aims to cover the potential roles of miRNAs in the mechanisms associated with the development and consequences of RH, and explore the current state of the art of diagnostic and therapeutic tools based on miRNA approaches. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Dramatic changes in 67 miRNAs during initiation of first wave of spermatogenesis in Mus musculus testis: global regulatory insights generated by miRNA-mRNA network analysis.

Science.gov (United States)

Sree, Sreesha; Radhakrishnan, Karthika; Indu, Sivankutty; Kumar, Pradeep G

2014-09-01

We mapped global changes in miRNA and mRNA profiles spanning the first wave of spermatogenesis using prepubertal (Postnatal Day 8 [P8]), pubertal (P16), and adolescent (P24) Mus musculus testes and identified the differential expression of 67 miRNAs and 8226 mRNAs. These two data sets were integrated into miRNA-dependent regulatory networks based on miRWalk predictions. In a network representing the P8 to P16 transition, downregulation of four miRNAs and upregulation of 19 miRNAs were linked with 81 upregulated target mRNAs and 228 downregulated target mRNAs, respectively. Furthermore, during the P16 to P24 transition, two miRNAs were downregulated, and eight miRNAs were upregulated, which linked with 64 upregulated mRNAs and 389 downregulated mRNAs, respectively. Only three of the miRNAs present in the network (miR-34b-5p, miR-34c, and miR-449a) showed a progressive increase from P8 through P16 to P24, while the remaining miRNAs in the network showed statistically significant changes in their levels either during the P8 to P16 transition or during the P16 to P24 transition. Analysis of the chromosomal location of these differentially expressed miRNAs showed that 14 out of 25 miRNAs upregulated from P8 to P16, and 18 out of 40 miRNAs upregulated from P8 to P24 were X-linked. This is suggestive of their escape from meiotic sex chromosome inactivation and postmeiotic sex chromatin. This integrated network of miRNA-level and mRNA-level changes in mouse testis during the first wave of spermatogenesis is expected to build a base for evaluating the role of miRNA-mediated gene expression regulation in maturing mammalian testis. © 2014 by the Society for the Study of Reproduction, Inc.

Dynamics of intracellular information decoding.

Science.gov (United States)

Kobayashi, Tetsuya J; Kamimura, Atsushi

2011-10-01

A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity.

Decoding intention at sensorimotor timescales.

Directory of Open Access Journals (Sweden)

Mathew Salvaris

Full Text Available The ability to decode an individual's intentions in real time has long been a 'holy grail' of research on human volition. For example, a reliable method could be used to improve scientific study of voluntary action by allowing external probe stimuli to be delivered at different moments during development of intention and action. Several Brain Computer Interface applications have used motor imagery of repetitive actions to achieve this goal. These systems are relatively successful, but only if the intention is sustained over a period of several seconds; much longer than the timescales identified in psychophysiological studies for normal preparation for voluntary action. We have used a combination of sensorimotor rhythms and motor imagery training to decode intentions in a single-trial cued-response paradigm similar to those used in human and non-human primate motor control research. Decoding accuracy of over 0.83 was achieved with twelve participants. With this approach, we could decode intentions to move the left or right hand at sub-second timescales, both for instructed choices instructed by an external stimulus and for free choices generated intentionally by the participant. The implications for volition are considered.

Dynamics of intracellular information decoding

International Nuclear Information System (INIS)

Kobayashi, Tetsuya J; Kamimura, Atsushi

2011-01-01

A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export.

Science.gov (United States)

Müller-McNicoll, Michaela; Botti, Valentina; de Jesus Domingues, Antonio M; Brandl, Holger; Schwich, Oliver D; Steiner, Michaela C; Curk, Tomaz; Poser, Ina; Zarnack, Kathi; Neugebauer, Karla M

2016-03-01

Nuclear export factor 1 (NXF1) exports mRNA to the cytoplasm after recruitment to mRNA by specific adaptor proteins. How and why cells use numerous different export adaptors is poorly understood. Here we critically evaluate members of the SR protein family (SRSF1-7) for their potential to act as NXF1 adaptors that couple pre-mRNA processing to mRNA export. Consistent with this proposal, >1000 endogenous mRNAs required individual SR proteins for nuclear export in vivo. To address the mechanism, transcriptome-wide RNA-binding profiles of NXF1 and SRSF1-7 were determined in parallel by individual-nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP). Quantitative comparisons of RNA-binding sites showed that NXF1 and SR proteins bind mRNA targets at adjacent sites, indicative of cobinding. SRSF3 emerged as the most potent NXF1 adaptor, conferring sequence specificity to RNA binding by NXF1 in last exons. Interestingly, SRSF3 and SRSF7 were shown to bind different sites in last exons and regulate 3' untranslated region length in an opposing manner. Both SRSF3 and SRSF7 promoted NXF1 recruitment to mRNA. Thus, SRSF3 and SRSF7 couple alternative splicing and polyadenylation to NXF1-mediated mRNA export, thereby controlling the cytoplasmic abundance of transcripts with alternative 3' ends. © 2016 Müller-McNicoll et al.; Published by Cold Spring Harbor Laboratory Press.

Performance breakdown in optimal stimulus decoding.

Science.gov (United States)

Lubomir Kostal; Lansky, Petr; Pilarski, Stevan

2015-06-01

One of the primary goals of neuroscience is to understand how neurons encode and process information about their environment. The problem is often approached indirectly by examining the degree to which the neuronal response reflects the stimulus feature of interest. In this context, the methods of signal estimation and detection theory provide the theoretical limits on the decoding accuracy with which the stimulus can be identified. The Cramér-Rao lower bound on the decoding precision is widely used, since it can be evaluated easily once the mathematical model of the stimulus-response relationship is determined. However, little is known about the behavior of different decoding schemes with respect to the bound if the neuronal population size is limited. We show that under broad conditions the optimal decoding displays a threshold-like shift in performance in dependence on the population size. The onset of the threshold determines a critical range where a small increment in size, signal-to-noise ratio or observation time yields a dramatic gain in the decoding precision. We demonstrate the existence of such threshold regions in early auditory and olfactory information coding. We discuss the origin of the threshold effect and its impact on the design of effective coding approaches in terms of relevant population size.

miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

KAUST Repository

Liew, Yi Jin

2016-02-12

MicroRNAs (miRNAs) are small regulatory RNAs that are involved in many biological process in eukaryotes. They play a crucial role in modulating genetic expression of their targets, which makes them integral components of transcriptional regulatory networks. As sponges (phylum Porifera) are commonly considered the most basal metazoan, the in-depth capture of miRNAs from these organisms provides additional clues to the evolution of miRNA families in metazoans. Here, we identified the core proteins involved in the biogenesis of miRNAs, and obtained evidence for bona fide miRNA sequences for two marine sponges Stylissa carteri and Xestospongia testudinaria (11 and 19 respectively). Our analysis identified several miRNAs that are conserved amongst demosponges, and revealed that all of the novel miRNAs identified in these two species are specific to the class Demospongiae.

miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

KAUST Repository

Liew, Yi Jin; Ryu, Tae Woo; Aranda, Manuel; Ravasi, Timothy

2016-01-01

MicroRNAs (miRNAs) are small regulatory RNAs that are involved in many biological process in eukaryotes. They play a crucial role in modulating genetic expression of their targets, which makes them integral components of transcriptional regulatory networks. As sponges (phylum Porifera) are commonly considered the most basal metazoan, the in-depth capture of miRNAs from these organisms provides additional clues to the evolution of miRNA families in metazoans. Here, we identified the core proteins involved in the biogenesis of miRNAs, and obtained evidence for bona fide miRNA sequences for two marine sponges Stylissa carteri and Xestospongia testudinaria (11 and 19 respectively). Our analysis identified several miRNAs that are conserved amongst demosponges, and revealed that all of the novel miRNAs identified in these two species are specific to the class Demospongiae.

High-throughput miRNA profiling of human melanoma blood samples

Directory of Open Access Journals (Sweden)

Rass Knuth

2010-06-01

Full Text Available Abstract Background MicroRNA (miRNA signatures are not only found in cancer tissue but also in blood of cancer patients. Specifically, miRNA detection in blood offers the prospect of a non-invasive analysis tool. Methods Using a microarray based approach we screened almost 900 human miRNAs to detect miRNAs that are deregulated in their expression in blood cells of melanoma patients. We analyzed 55 blood samples, including 20 samples of healthy individuals, 24 samples of melanoma patients as test set, and 11 samples of melanoma patients as independent validation set. Results A hypothesis test based approch detected 51 differentially regulated miRNAs, including 21 miRNAs that were downregulated in blood cells of melanoma patients and 30 miRNAs that were upregulated in blood cells of melanoma patients as compared to blood cells of healthy controls. The tets set and the independent validation set of the melanoma samples showed a high correlation of fold changes (0.81. Applying hierarchical clustering and principal component analysis we found that blood samples of melanoma patients and healthy individuals can be well differentiated from each other based on miRNA expression analysis. Using a subset of 16 significant deregulated miRNAs, we were able to reach a classification accuracy of 97.4%, a specificity of 95% and a sensitivity of 98.9% by supervised analysis. MiRNA microarray data were validated by qRT-PCR. Conclusions Our study provides strong evidence for miRNA expression signatures of blood cells as useful biomarkers for melanoma.

Combinatorial Control of mRNA Fates by RNA-Binding Proteins and Non-Coding RNAs

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Valentina Iadevaia

2015-09-01

Full Text Available Post-transcriptional control of gene expression is mediated by RNA-binding proteins (RBPs and small non-coding RNAs (e.g., microRNAs that bind to distinct elements in their mRNA targets. Here, we review recent examples describing the synergistic and/or antagonistic effects mediated by RBPs and miRNAs to determine the localisation, stability and translation of mRNAs in mammalian cells. From these studies, it is becoming increasingly apparent that dynamic rearrangements of RNA-protein complexes could have profound implications in human cancer, in synaptic plasticity, and in cellular differentiation.

Clinical experience of titanium cerebral aneurysm clips. Evaluation of artifact of CT and MRI

International Nuclear Information System (INIS)

Ninomiya, Takashi; Kato, Yoko; Sano, Hirotoshi

1996-01-01

The titanium aneurysm clips manufactured by AESCULAP Company are expected to be useful, not only for clinical applications, but also for reducing artifacts in post-operative CT and MRI. We carried out an investigation of the behavior of the new Yasargil titanium clips in a 1.5T MR imager. The new titanium clips showed considerably smaller clip-induced MR and CT artifacts than phynox and elgiloy clips. No movement of the titanium clips was seen by introducing them to the MR imager. Subsequent to these experimental studies, we applied titanium clips to 25 cerebral aneurysms. Post-operative CT, especially helical scanning CT and MR showed minimal artifacts, leading to the conclusion that the titanium clips are better than the other types of clips for the evaluation of post-operative neuroradiological images. (author)

Real-time SHVC software decoding with multi-threaded parallel processing

Science.gov (United States)

Gudumasu, Srinivas; He, Yuwen; Ye, Yan; He, Yong; Ryu, Eun-Seok; Dong, Jie; Xiu, Xiaoyu

2014-09-01

This paper proposes a parallel decoding framework for scalable HEVC (SHVC). Various optimization technologies are implemented on the basis of SHVC reference software SHM-2.0 to achieve real-time decoding speed for the two layer spatial scalability configuration. SHVC decoder complexity is analyzed with profiling information. The decoding process at each layer and the up-sampling process are designed in parallel and scheduled by a high level application task manager. Within each layer, multi-threaded decoding is applied to accelerate the layer decoding speed. Entropy decoding, reconstruction, and in-loop processing are pipeline designed with multiple threads based on groups of coding tree units (CTU). A group of CTUs is treated as a processing unit in each pipeline stage to achieve a better trade-off between parallelism and synchronization. Motion compensation, inverse quantization, and inverse transform modules are further optimized with SSE4 SIMD instructions. Simulations on a desktop with an Intel i7 processor 2600 running at 3.4 GHz show that the parallel SHVC software decoder is able to decode 1080p spatial 2x at up to 60 fps (frames per second) and 1080p spatial 1.5x at up to 50 fps for those bitstreams generated with SHVC common test conditions in the JCT-VC standardization group. The decoding performance at various bitrates with different optimization technologies and different numbers of threads are compared in terms of decoding speed and resource usage, including processor and memory.

High-throughput GPU-based LDPC decoding

Science.gov (United States)

Chang, Yang-Lang; Chang, Cheng-Chun; Huang, Min-Yu; Huang, Bormin

2010-08-01

Low-density parity-check (LDPC) code is a linear block code known to approach the Shannon limit via the iterative sum-product algorithm. LDPC codes have been adopted in most current communication systems such as DVB-S2, WiMAX, WI-FI and 10GBASE-T. LDPC for the needs of reliable and flexible communication links for a wide variety of communication standards and configurations have inspired the demand for high-performance and flexibility computing. Accordingly, finding a fast and reconfigurable developing platform for designing the high-throughput LDPC decoder has become important especially for rapidly changing communication standards and configurations. In this paper, a new graphic-processing-unit (GPU) LDPC decoding platform with the asynchronous data transfer is proposed to realize this practical implementation. Experimental results showed that the proposed GPU-based decoder achieved 271x speedup compared to its CPU-based counterpart. It can serve as a high-throughput LDPC decoder.

Current perspectives in microRNAs (miRNA)

CERN Document Server

Ying, Shao-Yao

2008-01-01

In this book, many new perspectives of the miRNA research are reviewed and discussed. These new findings provide significant insight into the various mechanisms of miRNAs and offer a great opportunity in developing new therapeutic interventions.

The miRNA biogenesis in marine bivalves

Directory of Open Access Journals (Sweden)

Umberto Rosani

2016-03-01

Full Text Available Small non-coding RNAs include powerful regulators of gene expression, transposon mobility and virus activity. Among the various categories, mature microRNAs (miRNAs guide the translational repression and decay of several targeted mRNAs. The biogenesis of miRNAs depends on few gene products, essentially conserved from basal to higher metazoans, whose protein domains allow specific interactions with dsRNA. Here, we report the identification of key genes responsible of the miRNA biogenesis in 32 bivalves, with particular attention to the aquaculture species Mytilus galloprovincialis and Crassostrea gigas. In detail, we have identified and phylogenetically compared eight evolutionary conserved proteins: DROSHA, DGCR8, EXP5, RAN, DICER TARBP2, AGO and PIWI. In mussels, we recognized several other proteins participating in the miRNA biogenesis or in the subsequent RNA silencing. According to digital expression analysis, these genes display low and not inducible expression levels in adult mussels and oysters whereas they are considerably expressed during development. As miRNAs play an important role also in the antiviral responses, knowledge on their production and regulative effects can shed light on essential molecular processes and provide new hints for disease prevention in bivalves.

miRNA delivery for skin wound healing.

Science.gov (United States)

Meng, Zhao; Zhou, Dezhong; Gao, Yongsheng; Zeng, Ming; Wang, Wenxin

2017-12-19

The wound healing has remained a worldwide challenge as one of significant public health problems. Pathological scars and chronic wounds caused by injury, aging or diabetes lead to impaired tissue repair and regeneration. Due to the unique biological wound environment, the wound healing is a highly complicated process, efficient and targeted treatments are still lacking. Hence, research-driven to discover more efficient therapeutics is a highly urgent demand. Recently, the research results have revealed that microRNA (miRNA) is a promising tool in therapeutic and diagnostic fields because miRNA is an essential regulator in cellular physiology and pathology. Therefore, new technologies for wound healing based on miRNA have been developed and miRNA delivery has become a significant research topic in the field of gene delivery. Copyright © 2017. Published by Elsevier B.V.

Identification of microRNAs controlling hepatic mRNA levels for metabolic genes during the metabolic transition from embryonic to posthatch development in the chicken.

Science.gov (United States)

Hicks, Julie A; Porter, Tom E; Liu, Hsiao-Ching

2017-09-05

The transition from embryonic to posthatch development in the chicken represents a massive metabolic switch from primarily lipolytic to primarily lipogenic metabolism. This metabolic switch is essential for the chick to successfully transition from the metabolism of stored egg yolk to the utilization of carbohydrate-based feed. However, regulation of this metabolic switch is not well understood. We hypothesized that microRNAs (miRNAs) play an important role in the metabolic switch that is essential to efficient growth of chickens. We used high-throughput RNA sequencing to characterize expression profiles of mRNA and miRNA in liver during late embryonic and early posthatch development of the chicken. This extensive data set was used to define the contributions of microRNAs to the metabolic switch during development that is critical to growth and nutrient utilization in chickens. We found that expression of over 800 mRNAs and 30 miRNAs was altered in the embryonic liver between embryonic day 18 and posthatch day 3, and many of these differentially expressed mRNAs and miRNAs are associated with metabolic processes. We confirmed the regulation of some of these mRNAs by miRNAs expressed in a reciprocal pattern using luciferase reporter assays. Finally, through the use of yeast one-hybrid screens, we identified several proteins that likely regulate expression of one of these important miRNAs. Integration of the upstream regulatory mechanisms governing miRNA expression along with monitoring the downstream effects of this expression will ultimately allow for the construction of complete miRNA regulatory networks associated with the hepatic metabolic switch in chickens. Our findings support a key role for miRNAs in controlling the metabolic switch that occurs between embryonic and posthatch development in the chicken.

An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells

Directory of Open Access Journals (Sweden)

Nam Seungyoon

2012-12-01

Full Text Available Abstract Background A major goal of the field of systems biology is to translate genome-wide profiling data (e.g., mRNAs, miRNAs into interpretable functional networks. However, employing a systems biology approach to better understand the complexities underlying drug resistance phenotypes in cancer continues to represent a significant challenge to the field. Previously, we derived two drug-resistant breast cancer sublines (tamoxifen- and fulvestrant-resistant cell lines from the MCF7 breast cancer cell line and performed genome-wide mRNA and microRNA profiling to identify differential molecular pathways underlying acquired resistance to these important antiestrogens. In the current study, to further define molecular characteristics of acquired antiestrogen resistance we constructed an “integrative network”. We combined joint miRNA-mRNA expression profiles, cancer contexts, miRNA-target mRNA relationships, and miRNA upstream regulators. In particular, to reduce the probability of false positive connections in the network, experimentally validated, rather than prediction-oriented, databases were utilized to obtain connectivity. Also, to improve biological interpretation, cancer contexts were incorporated into the network connectivity. Results Based on the integrative network, we extracted “substructures” (network clusters representing the drug resistant states (tamoxifen- or fulvestrant-resistance cells compared to drug sensitive state (parental MCF7 cells. We identified un-described network clusters that contribute to antiestrogen resistance consisting of miR-146a, -27a, -145, -21, -155, -15a, -125b, and let-7s, in addition to the previously described miR-221/222. Conclusions By integrating miRNA-related network, gene/miRNA expression and text-mining, the current study provides a computational-based systems biology approach for further investigating the molecular mechanism underlying antiestrogen resistance in breast cancer cells. In

Tissue-dependent paired expression of miRNAs

OpenAIRE

Ro, Seungil; Park, Chanjae; Young, David; Sanders, Kenton M.; Yan, Wei

2007-01-01

It is believed that depending on the thermodynamic stability of the 5′-strand and the 3′-strand in the stem-loop structure of a precursor microRNA (pre-miRNA), cells preferentially select the less stable one (called the miRNA or guide strand) and destroy the other one (called the miRNA* or passenger strand). However, our expression profiling analyses revealed that both strands could be co-accumulated as miRNA pairs in some tissues while being subjected to strand selection in other tissues. Ou...

Remission of migraine after clipping of saccular intracranial aneurysms

DEFF Research Database (Denmark)

Lebedeva, E R; Busygina, A V; Kolotvinov, V S

2015-01-01

interview. The remission rates of migraine and tension-type headache (TTH) in these patients were compared to 92 patients from a headache center. Diagnoses were made according to the ICHD-2. RESULTS: During 1 year preceding rupture 51 patients with SIA had migraine. During the year after clipping......BACKGROUND: Unruptured saccular intracranial aneurysm (SIA) is associated with an increased prevalence of migraine, but it is unclear whether this is altered by clipping of the aneurysm. The aim of our study was to determine whether remission rate of migraine and other recurrent headaches...... was greater in patients with SIA after clipping than in controls. METHODS: We prospectively studied 87 SIA patients with migraine or other recurrent headaches. They were interviewed about headaches in the preceding year before and 1 year after clipping using a validated semi-structured neurologist conducted...

Film clips and narrative text as subjective emotion elicitation techniques.

Science.gov (United States)

Zupan, Barbra; Babbage, Duncan R

2017-01-01

Film clips and narrative text are useful techniques in eliciting emotion in a laboratory setting but have not been examined side-by-side using the same methodology. This study examined the self-identification of emotions elicited by film clip and narrative text stimuli to confirm that selected stimuli appropriately target the intended emotions. Seventy participants viewed 30 film clips, and 40 additional participants read 30 narrative texts. Participants identified the emotion experienced (happy, sad, angry, fearful, neutral-six stimuli each). Eighty-five percent of participants self-identified the target emotion for at least two stimuli for all emotion categories of film clips, except angry (only one) and for all categories of narrative text, except fearful (only one). The most effective angry text was correctly identified 74% of the time. Film clips were more effective in eliciting all target emotions in participants for eliciting the correct emotion (angry), intensity rating (happy, sad), or both (fearful).

Neuroprosthetic Decoder Training as Imitation Learning.

Science.gov (United States)

Merel, Josh; Carlson, David; Paninski, Liam; Cunningham, John P

2016-05-01

Neuroprosthetic brain-computer interfaces function via an algorithm which decodes neural activity of the user into movements of an end effector, such as a cursor or robotic arm. In practice, the decoder is often learned by updating its parameters while the user performs a task. When the user's intention is not directly observable, recent methods have demonstrated value in training the decoder against a surrogate for the user's intended movement. Here we show that training a decoder in this way is a novel variant of an imitation learning problem, where an oracle or expert is employed for supervised training in lieu of direct observations, which are not available. Specifically, we describe how a generic imitation learning meta-algorithm, dataset aggregation (DAgger), can be adapted to train a generic brain-computer interface. By deriving existing learning algorithms for brain-computer interfaces in this framework, we provide a novel analysis of regret (an important metric of learning efficacy) for brain-computer interfaces. This analysis allows us to characterize the space of algorithmic variants and bounds on their regret rates. Existing approaches for decoder learning have been performed in the cursor control setting, but the available design principles for these decoders are such that it has been impossible to scale them to naturalistic settings. Leveraging our findings, we then offer an algorithm that combines imitation learning with optimal control, which should allow for training of arbitrary effectors for which optimal control can generate goal-oriented control. We demonstrate this novel and general BCI algorithm with simulated neuroprosthetic control of a 26 degree-of-freedom model of an arm, a sophisticated and realistic end effector.

Neuroprosthetic Decoder Training as Imitation Learning.

Directory of Open Access Journals (Sweden)

Josh Merel

2016-05-01

Full Text Available Neuroprosthetic brain-computer interfaces function via an algorithm which decodes neural activity of the user into movements of an end effector, such as a cursor or robotic arm. In practice, the decoder is often learned by updating its parameters while the user performs a task. When the user's intention is not directly observable, recent methods have demonstrated value in training the decoder against a surrogate for the user's intended movement. Here we show that training a decoder in this way is a novel variant of an imitation learning problem, where an oracle or expert is employed for supervised training in lieu of direct observations, which are not available. Specifically, we describe how a generic imitation learning meta-algorithm, dataset aggregation (DAgger, can be adapted to train a generic brain-computer interface. By deriving existing learning algorithms for brain-computer interfaces in this framework, we provide a novel analysis of regret (an important metric of learning efficacy for brain-computer interfaces. This analysis allows us to characterize the space of algorithmic variants and bounds on their regret rates. Existing approaches for decoder learning have been performed in the cursor control setting, but the available design principles for these decoders are such that it has been impossible to scale them to naturalistic settings. Leveraging our findings, we then offer an algorithm that combines imitation learning with optimal control, which should allow for training of arbitrary effectors for which optimal control can generate goal-oriented control. We demonstrate this novel and general BCI algorithm with simulated neuroprosthetic control of a 26 degree-of-freedom model of an arm, a sophisticated and realistic end effector.

Current MitraClip experience, safety and feasibility in the Netherlands

OpenAIRE

Rahhab, Z.; Kortlandt, F.A.; Velu, J.F.; Schurer, R.A.J.; Delgado, V.; Tonino, P.; Boven, A.J. van; Branden, B.J.L. Van den; Kraaijeveld, A.O.; Voskuil, M.; Hoorntje, J.; Wely, M.H. van; Houwelingen, K. van; Bleeker, G.B.; Rensing, B.

2017-01-01

PURPOSE: Data on MitraClip procedural safety and efficacy in the Netherlands are scarce. We aim to provide an overview of the Dutch MitraClip experience. METHODS: We pooled anonymised demographic and procedural data of 1151 consecutive MitraClip patients, from 13 Dutch hospitals. Data was collected by product specialists in collaboration with local operators. Effect on mitral regurgitation was intra-procedurally assessed by transoesophageal echocardiography. Technical success and device succe...

Iterative List Decoding of Concatenated Source-Channel Codes

Directory of Open Access Journals (Sweden)

Hedayat Ahmadreza

2005-01-01

Full Text Available Whenever variable-length entropy codes are used in the presence of a noisy channel, any channel errors will propagate and cause significant harm. Despite using channel codes, some residual errors always remain, whose effect will get magnified by error propagation. Mitigating this undesirable effect is of great practical interest. One approach is to use the residual redundancy of variable length codes for joint source-channel decoding. In this paper, we improve the performance of residual redundancy source-channel decoding via an iterative list decoder made possible by a nonbinary outer CRC code. We show that the list decoding of VLC's is beneficial for entropy codes that contain redundancy. Such codes are used in state-of-the-art video coders, for example. The proposed list decoder improves the overall performance significantly in AWGN and fully interleaved Rayleigh fading channels.

miRNAs in Human Subcutaneous Adipose Tissue

DEFF Research Database (Denmark)

Kristensen, Malene M.; Davidsen, Peter K.; Vigelso, Andreas

2017-01-01

Objective Obesity is central in the development of insulin resistance. However, the underlying mechanisms still need elucidation. Dysregulated microRNAs (miRNAs; post-transcriptional regulators) in adipose tissue may present an important link. Methods The miRNA expression in subcutaneous adipose ...

On Lattice Sequential Decoding for The Unconstrained AWGN Channel

KAUST Repository

Abediseid, Walid; Alouini, Mohamed-Slim

2013-01-01

channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the \\textit{lattice decoder}. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement

Performance-complexity tradeoff in sequential decoding for the unconstrained AWGN channel

KAUST Repository

Abediseid, Walid

2013-06-01

In this paper, the performance limits and the computational complexity of the lattice sequential decoder are analyzed for the unconstrained additive white Gaussian noise channel. The performance analysis available in the literature for such a channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the lattice decoder. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement, and the search for low complexity receivers for the detection of lattice codes is considered a challenging problem. However, the low computational complexity advantage that sequential decoding promises, makes it an alternative solution to the lattice decoder. In this work, we characterize the performance and complexity tradeoff via the error exponent and the decoding complexity, respectively, of such a decoder as a function of the decoding parameter - the bias term. For the above channel, we derive the cut-off volume-to-noise ratio that is required to achieve a good error performance with low decoding complexity. © 2013 IEEE.

The role of miRNAs in endometrial cancer.

Science.gov (United States)

Vasilatou, Diamantina; Sioulas, Vasileios D; Pappa, Vasiliki; Papageorgiou, Sotirios G; Vlahos, Nikolaos F

2015-01-01

miRNAs are small noncoding RNAs that regulate gene expression at the post-transcriptional level. Since their discovery, miRNAs have been associated with every cell function including malignant transformation and metastasis. Endometrial cancer is the most common gynecologic malignancy. However, improvement should be made in interobserver agreement on histological typing and individualized therapeutic approaches. This article summarizes the role of miRNAs in endometrial cancer pathogenesis and treatment.

Multiple-hit parameter estimation in monolithic detectors.

Science.gov (United States)

Hunter, William C J; Barrett, Harrison H; Lewellen, Tom K; Miyaoka, Robert S

2013-02-01

We examine a maximum-a-posteriori method for estimating the primary interaction position of gamma rays with multiple interaction sites (hits) in a monolithic detector. In assessing the performance of a multiple-hit estimator over that of a conventional one-hit estimator, we consider a few different detector and readout configurations of a 50-mm-wide square cerium-doped lutetium oxyorthosilicate block. For this study, we use simulated data from SCOUT, a Monte-Carlo tool for photon tracking and modeling scintillation- camera output. With this tool, we determine estimate bias and variance for a multiple-hit estimator and compare these with similar metrics for a one-hit maximum-likelihood estimator, which assumes full energy deposition in one hit. We also examine the effect of event filtering on these metrics; for this purpose, we use a likelihood threshold to reject signals that are not likely to have been produced under the assumed likelihood model. Depending on detector design, we observe a 1%-12% improvement of intrinsic resolution for a 1-or-2-hit estimator as compared with a 1-hit estimator. We also observe improved differentiation of photopeak events using a 1-or-2-hit estimator as compared with the 1-hit estimator; more than 6% of photopeak events that were rejected by likelihood filtering for the 1-hit estimator were accurately identified as photopeak events and positioned without loss of resolution by a 1-or-2-hit estimator; for PET, this equates to at least a 12% improvement in coincidence-detection efficiency with likelihood filtering applied.

Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes

Science.gov (United States)

Lin, Shu

1998-01-01

A code trellis is a graphical representation of a code, block or convolutional, in which every path represents a codeword (or a code sequence for a convolutional code). This representation makes it possible to implement Maximum Likelihood Decoding (MLD) of a code with reduced decoding complexity. The most well known trellis-based MLD algorithm is the Viterbi algorithm. The trellis representation was first introduced and used for convolutional codes [23]. This representation, together with the Viterbi decoding algorithm, has resulted in a wide range of applications of convolutional codes for error control in digital communications over the last two decades. There are two major reasons for this inactive period of research in this area. First, most coding theorists at that time believed that block codes did not have simple trellis structure like convolutional codes and maximum likelihood decoding of linear block codes using the Viterbi algorithm was practically impossible, except for very short block codes. Second, since almost all of the linear block codes are constructed algebraically or based on finite geometries, it was the belief of many coding theorists that algebraic decoding was the only way to decode these codes. These two reasons seriously hindered the development of efficient soft-decision decoding methods for linear block codes and their applications to error control in digital communications. This led to a general belief that block codes are inferior to convolutional codes and hence, that they were not useful. Chapter 2 gives a brief review of linear block codes. The goal is to provide the essential background material for the development of trellis structure and trellis-based decoding algorithms for linear block codes in the later chapters. Chapters 3 through 6 present the fundamental concepts, finite-state machine model, state space formulation, basic structural properties, state labeling, construction procedures, complexity, minimality, and

Singer product apertures—A coded aperture system with a fast decoding algorithm

International Nuclear Information System (INIS)

Byard, Kevin; Shutler, Paul M.E.

2017-01-01

A new type of coded aperture configuration that enables fast decoding of the coded aperture shadowgram data is presented. Based on the products of incidence vectors generated from the Singer difference sets, we call these Singer product apertures. For a range of aperture dimensions, we compare experimentally the performance of three decoding methods: standard decoding, induction decoding and direct vector decoding. In all cases the induction and direct vector methods are several orders of magnitude faster than the standard method, with direct vector decoding being significantly faster than induction decoding. For apertures of the same dimensions the increase in speed offered by direct vector decoding over induction decoding is better for lower throughput apertures.

Singer product apertures—A coded aperture system with a fast decoding algorithm

Energy Technology Data Exchange (ETDEWEB)

Byard, Kevin, E-mail: kevin.byard@aut.ac.nz [School of Economics, Faculty of Business, Economics and Law, Auckland University of Technology, Auckland 1142 (New Zealand); Shutler, Paul M.E. [National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616 (Singapore)

2017-06-01

A new type of coded aperture configuration that enables fast decoding of the coded aperture shadowgram data is presented. Based on the products of incidence vectors generated from the Singer difference sets, we call these Singer product apertures. For a range of aperture dimensions, we compare experimentally the performance of three decoding methods: standard decoding, induction decoding and direct vector decoding. In all cases the induction and direct vector methods are several orders of magnitude faster than the standard method, with direct vector decoding being significantly faster than induction decoding. For apertures of the same dimensions the increase in speed offered by direct vector decoding over induction decoding is better for lower throughput apertures.

Comparison of Sonography versus Digital Breast Tomosynthesis to Locate Intramammary Marker Clips.

Science.gov (United States)

Schulz-Wendtland, R; Dankerl, P; Dilbat, G; Bani, M; Fasching, P A; Heusinger, K; Lux, M P; Loehberg, C R; Jud, S M; Rauh, C; Bayer, C M; Beckmann, M W; Wachter, D L; Uder, M; Meier-Meitinger, M; Brehm, B

2015-01-01

Introduction: This study aimed to compare the accuracy of sonography versus digital breast tomosynthesis to locate intramammary marker clips placed under ultrasound guidance. Patients and Methods: Fifty patients with suspicion of breast cancer (lesion diameter less than 2 cm [cT1]) had ultrasound-guided core needle biopsy with placement of a marker clip in the center of the tumor. Intramammary marker clips were subsequently located with both sonography and digital breast tomosynthesis. Results: Sonography detected no dislocation of intrammammary marker clips in 42 of 50 patients (84 %); dislocation was reported in 8 patients (16 %) with a maximum dislocation of 7 mm along the x-, y- or z-axis. Digital breast tomosynthesis showed accurate placement without dislocation of the intramammary marker clip in 48 patients (96 %); 2 patients (4 %) had a maximum clip dislocation of 3 mm along the x-, y- or z-axis (p tomosynthesis could improve the accuracy when locating intramammary marker clips compared to sonography and could, in future, be used to complement or even completely replace sonography.

Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment

International Nuclear Information System (INIS)

Stankevicius, Vaidotas; Vasauskas, Gintautas; Bulotiene, Danute; Butkyte, Stase; Jarmalaite, Sonata; Rotomskis, Ricardas; Suziedelis, Kestutis

2016-01-01

The extracellular matrix (ECM), one of the key components of tumor microenvironment, has a tremendous impact on cancer development and highly influences tumor cell features. ECM affects vital cellular functions such as cell differentiation, migration, survival and proliferation. Gene and protein expression levels are regulated in cell-ECM interaction dependent manner as well. The rate of unsuccessful clinical trials, based on cell culture research models lacking the ECM microenvironment, indicates the need for alternative models and determines the shift to three-dimensional (3D) laminin rich ECM models, better simulating tissue organization. Recognized advantages of 3D models suggest the development of new anticancer treatment strategies. This is among the most promising directions of 3D cell cultures application. However, detailed analysis at the molecular level of 2D/3D cell cultures and tumors in vivo is still needed to elucidate cellular pathways most promising for the development of targeted therapies. In order to elucidate which biological pathways are altered during microenvironmental shift we have analyzed whole genome mRNA and miRNA expression differences in LLC1 cells cultured in 2D or 3D culture conditions. In our study we used DNA microarrays for whole genome analysis of mRNA and miRNA expression differences in LLC1 cells cultivated in 2D or 3D culture conditions. Next, we indicated the most common enriched functional categories using KEGG pathway enrichment analysis. Finally, we validated the microarray data by quantitative PCR in LLC1 cells cultured under 2D or 3D conditions or LLC1 tumors implanted in experimental animals. Microarray gene expression analysis revealed that 1884 genes and 77 miRNAs were significantly altered in LLC1 cells after 48 h cell growth under 2D and ECM based 3D cell growth conditions. Pathway enrichment results indicated metabolic pathway, MAP kinase, cell adhesion and immune response as the most significantly altered

Fast decoding algorithms for coded aperture systems

International Nuclear Information System (INIS)

Byard, Kevin

2014-01-01

Fast decoding algorithms are described for a number of established coded aperture systems. The fast decoding algorithms for all these systems offer significant reductions in the number of calculations required when reconstructing images formed by a coded aperture system and hence require less computation time to produce the images. The algorithms may therefore be of use in applications that require fast image reconstruction, such as near real-time nuclear medicine and location of hazardous radioactive spillage. Experimental tests confirm the efficacy of the fast decoding techniques

Evaluation of circulating miRNAs during late pregnancy in the mare.

Directory of Open Access Journals (Sweden)

Shavahn C Loux

Full Text Available MicroRNAs (miRNAs are small, non-coding RNAs which are produced throughout the body. Individual tissues tend to have a specific expression profile and excrete many of these miRNAs into circulation. These circulating miRNAs may be diagnostically valuable biomarkers for assessing the presence of disease while minimizing invasive testing. In women, numerous circulating miRNAs have been identified which change significantly during pregnancy-related complications (e.g. chorioamnionitis, eclampsia, recurrent pregnancy loss; however, no prior work has been done in this area in the horse. To identify pregnancy-specific miRNAs, we collected serial whole blood samples in pregnant mares at 8, 9, 10 m of gestation and post-partum, as well as from non-pregnant (diestrous mares. In total, we evaluated a panel of 178 miRNAs using qPCR, eventually identifying five miRNAs of interest. One miRNA (miR-374b was differentially regulated through late gestation and four miRNAs (miR-454, miR-133b, miR-486-5p and miR-204b were differentially regulated between the pregnant and non-pregnant samples. We were able to identify putative targets for the differentially regulated miRNAs using two separate target prediction programs, miRDB and Ingenuity Pathway Analysis. The targets for the miRNAs differentially regulated during pregnancy were predicted to be involved in signaling pathways such as the STAT3 pathway and PI3/AKT signaling pathway, as well as more endocrine-based pathways, including the GnRH, prolactin and insulin signaling pathways. In summary, this study provides novel information about the changes occurring in circulating miRNAs during normal pregnancy, as well as attempting to predict the biological effects induced by these miRNAs.

Adding run history to CLIPS

Science.gov (United States)

Tuttle, Sharon M.; Eick, Christoph F.

1991-01-01

To debug a C Language Integrated Production System (CLIPS) program, certain 'historical' information about a run is needed. It would be convenient for system builders to have the capability to request such information. We will discuss how historical Rete networks can be used for answering questions that help a system builder detect the cause of an error in a CLIPS program. Moreover, the cost of maintaining a historical Rete network is compared with that for a classical Rete network. We will demonstrate that the cost for assertions is only slightly higher for a historical Rete network. The cost for handling retraction could be significantly higher; however, we will show that by using special data structures that rely on hashing, it is also possible to implement retractions efficiently.

LDPC-based iterative joint source-channel decoding for JPEG2000.

Science.gov (United States)

Pu, Lingling; Wu, Zhenyu; Bilgin, Ali; Marcellin, Michael W; Vasic, Bane

2007-02-01

A framework is proposed for iterative joint source-channel decoding of JPEG2000 codestreams. At the encoder, JPEG2000 is used to perform source coding with certain error-resilience (ER) modes, and LDPC codes are used to perform channel coding. During decoding, the source decoder uses the ER modes to identify corrupt sections of the codestream and provides this information to the channel decoder. Decoding is carried out jointly in an iterative fashion. Experimental results indicate that the proposed method requires fewer iterations and improves overall system performance.

Deep Learning Methods for Improved Decoding of Linear Codes

Science.gov (United States)

Nachmani, Eliya; Marciano, Elad; Lugosch, Loren; Gross, Warren J.; Burshtein, David; Be'ery, Yair

2018-02-01

The problem of low complexity, close to optimal, channel decoding of linear codes with short to moderate block length is considered. It is shown that deep learning methods can be used to improve a standard belief propagation decoder, despite the large example space. Similar improvements are obtained for the min-sum algorithm. It is also shown that tying the parameters of the decoders across iterations, so as to form a recurrent neural network architecture, can be implemented with comparable results. The advantage is that significantly less parameters are required. We also introduce a recurrent neural decoder architecture based on the method of successive relaxation. Improvements over standard belief propagation are also observed on sparser Tanner graph representations of the codes. Furthermore, we demonstrate that the neural belief propagation decoder can be used to improve the performance, or alternatively reduce the computational complexity, of a close to optimal decoder of short BCH codes.

miRNA profiling of naive, effector and memory CD8 T cells.

Directory of Open Access Journals (Sweden)

Haoquan Wu

Full Text Available microRNAs have recently emerged as master regulators of gene expression during development and cell differentiation. Although profound changes in gene expression also occur during antigen-induced T cell differentiation, the role of miRNAs in the process is not known. We compared the miRNA expression profiles between antigen-specific naïve, effector and memory CD8+ T cells using 3 different methods--small RNA cloning, miRNA microarray analysis and real-time PCR. Although many miRNAs were expressed in all the T cell subsets, the frequency of 7 miRNAs (miR-16, miR-21, miR-142-3p, miR-142-5p, miR-150, miR-15b and let-7f alone accounted for approximately 60% of all miRNAs, and their expression was several fold higher than the other expressed miRNAs. Global downregulation of miRNAs (including 6/7 dominantly expressed miRNAs was observed in effector T cells compared to naïve cells and the miRNA expression levels tended to come back up in memory T cells. However, a few miRNAs, notably miR-21 were higher in effector and memory T cells compared to naïve T cells. These results suggest that concomitant with profound changes in gene expression, miRNA profile also changes dynamically during T cell differentiation. Sequence analysis of the cloned mature miRNAs revealed an extensive degree of end polymorphism. While 3'end polymorphisms dominated, heterogeneity at both ends, resembling drosha/dicer processing shift was also seen in miR-142, suggesting a possible novel mechanism to generate new miRNA and/or to diversify miRNA target selection. Overall, our results suggest that dynamic changes in the expression of miRNAs may be important for the regulation of gene expression during antigen-induced T cell differentiation. Our study also suggests possible novel mechanisms for miRNA biogenesis and function.

Bayesian population decoding of spiking neurons.

Science.gov (United States)

Gerwinn, Sebastian; Macke, Jakob; Bethge, Matthias

2009-01-01

The timing of action potentials in spiking neurons depends on the temporal dynamics of their inputs and contains information about temporal fluctuations in the stimulus. Leaky integrate-and-fire neurons constitute a popular class of encoding models, in which spike times depend directly on the temporal structure of the inputs. However, optimal decoding rules for these models have only been studied explicitly in the noiseless case. Here, we study decoding rules for probabilistic inference of a continuous stimulus from the spike times of a population of leaky integrate-and-fire neurons with threshold noise. We derive three algorithms for approximating the posterior distribution over stimuli as a function of the observed spike trains. In addition to a reconstruction of the stimulus we thus obtain an estimate of the uncertainty as well. Furthermore, we derive a 'spike-by-spike' online decoding scheme that recursively updates the posterior with the arrival of each new spike. We use these decoding rules to reconstruct time-varying stimuli represented by a Gaussian process from spike trains of single neurons as well as neural populations.

Bayesian population decoding of spiking neurons

Directory of Open Access Journals (Sweden)

Sebastian Gerwinn

2009-10-01

Full Text Available The timing of action potentials in spiking neurons depends on the temporal dynamics of their inputs and contains information about temporal fluctuations in the stimulus. Leaky integrate-and-fire neurons constitute a popular class of encoding models, in which spike times depend directly on the temporal structure of the inputs. However, optimal decoding rules for these models have only been studied explicitly in the noiseless case. Here, we study decoding rules for probabilistic inference of a continuous stimulus from the spike times of a population of leaky integrate-and-fire neurons with threshold noise. We derive three algorithms for approximating the posterior distribution over stimuli as a function of the observed spike trains. In addition to a reconstruction of the stimulus we thus obtain an estimate of the uncertainty as well. Furthermore, we derive a `spike-by-spike' online decoding scheme that recursively updates the posterior with the arrival of each new spike. We use these decoding rules to reconstruct time-varying stimuli represented by a Gaussian process from spike trains of single neurons as well as neural populations.

A CLIPS expert system for clinical flow cytometry data analysis

Science.gov (United States)

Salzman, G. C.; Duque, R. E.; Braylan, R. C.; Stewart, C. C.

1990-01-01

An expert system is being developed using CLIPS to assist clinicians in the analysis of multivariate flow cytometry data from cancer patients. Cluster analysis is used to find subpopulations representing various cell types in multiple datasets each consisting of four to five measurements on each of 5000 cells. CLIPS facts are derived from results of the clustering. CLIPS rules are based on the expertise of Drs. Stewart, Duque, and Braylan. The rules incorporate certainty factors based on case histories.

Extravasal occlusion of large vessels with titanic clips: efficiency, indications, and contraindications.

Science.gov (United States)

Vasilenko, Yu V; Kim, A I; Kotov, S A

2002-11-01

The mechanism of extravasal occlusion of blood vessels with titanic clips "Atrauclip" and "Ligaclip extra" was studied in order to reveal indications and contraindications to their use. Occlusion with the clips of both types was ineffective in vessels with a diameter of >7.0 mm. Arteritis or the presence of an intravascular occlusion facility in the vessel were also the contraindications for clip occlusion. In overcases the procedure of occlusion with titanic clips was efficient and atraumatic.

Three phase full wave dc motor decoder

Science.gov (United States)

Studer, P. A. (Inventor)

1977-01-01

A three phase decoder for dc motors is disclosed which employs an extremely simple six transistor circuit to derive six properly phased output signals for fullwave operation of dc motors. Six decoding transistors are coupled at their base-emitter junctions across a resistor network arranged in a delta configuration. Each point of the delta configuration is coupled to one of three position sensors which sense the rotational position of the motor. A second embodiment of the invention is disclosed in which photo-optical isolators are used in place of the decoding transistors.

Evaluation of a new high-dimensional miRNA profiling platform

Directory of Open Access Journals (Sweden)

Lamblin Anne-Francoise

2009-08-01

Full Text Available Abstract Background MicroRNAs (miRNAs are a class of approximately 22 nucleotide long, widely expressed RNA molecules that play important regulatory roles in eukaryotes. To investigate miRNA function, it is essential that methods to quantify their expression levels be available. Methods We evaluated a new miRNA profiling platform that utilizes Illumina's existing robust DASL chemistry as the basis for the assay. Using total RNA from five colon cancer patients and four cell lines, we evaluated the reproducibility of miRNA expression levels across replicates and with varying amounts of input RNA. The beta test version was comprised of 735 miRNA targets of Illumina's miRNA profiling application. Results Reproducibility between sample replicates within a plate was good (Spearman's correlation 0.91 to 0.98 as was the plate-to-plate reproducibility replicates run on different days (Spearman's correlation 0.84 to 0.98. To determine whether quality data could be obtained from a broad range of input RNA, data obtained from amounts ranging from 25 ng to 800 ng were compared to those obtained at 200 ng. No effect across the range of RNA input was observed. Conclusion These results indicate that very small amounts of starting material are sufficient to allow sensitive miRNA profiling using the Illumina miRNA high-dimensional platform. Nonlinear biases were observed between replicates, indicating the need for abundance-dependent normalization. Overall, the performance characteristics of the Illumina miRNA profiling system were excellent.

Decoding and Encoding Facial Expressions in Preschool-Age Children.

Science.gov (United States)

Zuckerman, Miron; Przewuzman, Sylvia J.

1979-01-01

Preschool-age children drew, decoded, and encoded facial expressions depicting five different emotions. Accuracy of drawing, decoding and encoding each of the five emotions was consistent across the three tasks; decoding ability was correlated with drawing ability among female subjects, but neither of these abilities was correlated with encoding…

Belief propagation decoding of quantum channels by passing quantum messages

International Nuclear Information System (INIS)

Renes, Joseph M

2017-01-01

The belief propagation (BP) algorithm is a powerful tool in a wide range of disciplines from statistical physics to machine learning to computational biology, and is ubiquitous in decoding classical error-correcting codes. The algorithm works by passing messages between nodes of the factor graph associated with the code and enables efficient decoding of the channel, in some cases even up to the Shannon capacity. Here we construct the first BP algorithm which passes quantum messages on the factor graph and is capable of decoding the classical–quantum channel with pure state outputs. This gives explicit decoding circuits whose number of gates is quadratic in the code length. We also show that this decoder can be modified to work with polar codes for the pure state channel and as part of a decoder for transmitting quantum information over the amplitude damping channel. These represent the first explicit capacity-achieving decoders for non-Pauli channels. (fast track communication)

Belief propagation decoding of quantum channels by passing quantum messages

Science.gov (United States)

Renes, Joseph M.

2017-07-01

The belief propagation (BP) algorithm is a powerful tool in a wide range of disciplines from statistical physics to machine learning to computational biology, and is ubiquitous in decoding classical error-correcting codes. The algorithm works by passing messages between nodes of the factor graph associated with the code and enables efficient decoding of the channel, in some cases even up to the Shannon capacity. Here we construct the first BP algorithm which passes quantum messages on the factor graph and is capable of decoding the classical-quantum channel with pure state outputs. This gives explicit decoding circuits whose number of gates is quadratic in the code length. We also show that this decoder can be modified to work with polar codes for the pure state channel and as part of a decoder for transmitting quantum information over the amplitude damping channel. These represent the first explicit capacity-achieving decoders for non-Pauli channels.

Molecular clips based on propanediurea : synthesis and physical properties

NARCIS (Netherlands)

Jansen, Robertus Johannes

2002-01-01

This thesis describes the synthesis and physical properties of a series of molecular clips derived from the concave molecule propanediurea. These molecular clips are cavity-containing receptors that can bind a variety of aromatic guests. This binding is a result of hydrogen bonding and pi-pi

Bayesian Recovery of Clipped OFDM Signals: A Receiver-based Approach

KAUST Repository

Al-Rabah, Abdullatif R.

2013-05-01

Recently, orthogonal frequency-division multiplexing (OFDM) has been adopted for high-speed wireless communications due to its robustness against multipath fading. However, one of the main fundamental drawbacks of OFDM systems is the high peak-to-average-power ratio (PAPR). Several techniques have been proposed for PAPR reduction. Most of these techniques require transmitter-based (pre-compensated) processing. On the other hand, receiver-based alternatives would save the power and reduce the transmitter complexity. By keeping this in mind, a possible approach is to limit the amplitude of the OFDM signal to a predetermined threshold and equivalently a sparse clipping signal is added. Then, estimating this clipping signal at the receiver to recover the original signal. In this work, we propose a Bayesian receiver-based low-complexity clipping signal recovery method for PAPR reduction. The method is able to i) effectively reduce the PAPR via simple clipping scheme at the transmitter side, ii) use Bayesian recovery algorithm to reconstruct the clipping signal at the receiver side by measuring part of subcarriers, iii) perform well in the absence of statistical information about the signal (e.g. clipping level) and the noise (e.g. noise variance), and at the same time iv is energy efficient due to its low complexity. Specifically, the proposed recovery technique is implemented in data-aided based. The data-aided method collects clipping information by measuring reliable 
data subcarriers, thus makes full use of spectrum for data transmission without the need for tone reservation. The study is extended further to discuss how to improve the recovery of the clipping signal utilizing some features of practical OFDM systems i.e., the oversampling and the presence of multiple receivers. Simulation results demonstrate the superiority of the proposed technique over other recovery algorithms. The overall objective is to show that the receiver-based Bayesian technique is highly

Wig1 prevents cellular senescence by regulating p21 mRNA decay through control of RISC recruitment.

Science.gov (United States)

Kim, Bong Cho; Lee, Hyung Chul; Lee, Je-Jung; Choi, Chang-Min; Kim, Dong-Kwan; Lee, Jae Cheol; Ko, Young-Gyu; Lee, Jae-Seon

2012-11-14

Premature senescence, a key strategy used to suppress carcinogenesis, can be driven by p53/p21 proteins in response to various stresses. Here, we demonstrate that Wig1 plays a critical role in this process through regulation of p21 mRNA stability. Wig1 controls the association of Argonaute2 (Ago2), a central component of the RNA-induced silencing complex (RISC), with target p21 mRNA via binding of the stem-loop structure near the microRNA (miRNA) target site. Depletion of Wig1 prohibited miRNA-mediated p21 mRNA decay and resulted in premature senescence. Wig1 plays an essential role in cell proliferation, as demonstrated in tumour xenografts in mice, and Wig1 and p21 mRNA levels are inversely correlated in human normal and cancer tissues. Together, our data indicate a novel role of Wig1 in RISC target accessibility, which is a key step in RNA-mediated gene silencing. In addition, these findings indicate that fine-tuning of p21 levels by Wig1 is essential for the prevention of cellular senescence.

Understanding and Applying Psychology through Use of News Clippings.

Science.gov (United States)

Rider, Elizabeth A.

1992-01-01

Discusses a student project for psychology courses in which students collect newspaper clippings that illustrate psychological concepts. Explains that the students record the source and write a brief description of the clipping, explaining how it relates to a psychological concept or theory. Includes results of student evaluations of the…

The SVT Hit Buffer

International Nuclear Information System (INIS)

Belforte, S.; Dell'Orso, M.; Donati, S.

1996-01-01

The Hit Buffer is part of the Silicon Vertex Tracker, a trigger processor dedicated to the reconstruction of particle trajectories in the Silicon Vertex Detector and the Central Tracking Chamber of the Collider Detector at Fermilab. The Hit Buffer is a high speed data-traffic node, where thousands of words are received in arbitrary order and simultaneously organized in an internal structured data base, to be later promptly retrieved and delivered in response to specific requests. The Hit Buffer is capable of processing data at a rate of 25 MHz, thanks to the use of special fast devices like Cache-Tag RAMs and high performance Erasable Programmable Logic Devices from the XILINX XC7300 family

Sympathetic block by metal clips may be a reversible operation

DEFF Research Database (Denmark)

Thomsen, Lars L; Mikkelsen, Rasmus T; Derejko, Miroslawa

2014-01-01

, but the question of reversibility remains controversial. Two recent experimental studies found severe histological signs of nerve damage 4-6 weeks after clip removal, but they only used conventional histopathological staining methods. METHODS: Thoracoscopic clipping of the sympathetic trunk was performed in adult...... the sympathetic chain vary tremendously. Most surgeons transect or resect the sympathetic chain, but application of a metal clip that blocks transmission of nerve impulses in the sympathetic chain is used increasingly worldwide. This approach offers potential reversibility if patients regret surgery...... suggests in theory that application of metal clips to the sympathetic chain is a reversible procedure if only the observation period is prolonged. Further studies with longer periods between application and removal as well as investigations of nerve conduction should be encouraged, because we do not know...

Heparin-independent, PF4-dependent binding of HIT antibodies to platelets: implications for HIT pathogenesis.

Science.gov (United States)

Padmanabhan, Anand; Jones, Curtis G; Bougie, Daniel W; Curtis, Brian R; McFarland, Janice G; Wang, Demin; Aster, Richard H

2015-01-01

Antibodies specific for platelet factor 4 (PF4)/heparin complexes are the hallmark of heparin-induced thrombocytopenia and thrombosis (HIT), but many antibody-positive patients have normal platelet counts. The basis for this is not fully understood, but it is believed that antibodies testing positive in the serotonin release assay (SRA) are the most likely to cause disease. We addressed this issue by characterizing PF4-dependent binding of HIT antibodies to intact platelets and found that most antibodies testing positive in the SRA, but none of those testing negative, bind to and activate platelets when PF4 is present without any requirement for heparin (P HIT antibodies recognize PF4 in a complex with heparin, only a subset of these antibodies recognize more subtle epitopes induced in PF4 when it binds to CS, the major platelet glycosaminoglycan. Antibodies having this property could explain "delayed HIT" seen in some individuals after discontinuation of heparin and the high risk for thrombosis that persists for weeks in patients recovered from HIT. © 2015 by The American Society of Hematology.

Identification and target prediction of miRNAs specifically expressed in rat neural tissue

Directory of Open Access Journals (Sweden)

Tu Kang

2009-05-01

Full Text Available Abstract Background MicroRNAs (miRNAs are a large group of RNAs that play important roles in regulating gene expression and protein translation. Several studies have indicated that some miRNAs are specifically expressed in human, mouse and zebrafish tissues. For example, miR-1 and miR-133 are specifically expressed in muscles. Tissue-specific miRNAs may have particular functions. Although previous studies have reported the presence of human, mouse and zebrafish tissue-specific miRNAs, there have been no detailed reports of rat tissue-specific miRNAs. In this study, Home-made rat miRNA microarrays which established in our previous study were used to investigate rat neural tissue-specific miRNAs, and mapped their target genes in rat tissues. This study will provide information for the functional analysis of these miRNAs. Results In order to obtain as complete a picture of specific miRNA expression in rat neural tissues as possible, customized miRNA microarrays with 152 selected miRNAs from miRBase were used to detect miRNA expression in 14 rat tissues. After a general clustering analysis, 14 rat tissues could be clearly classified into neural and non-neural tissues based on the obtained expression profiles with p values Conclusion Our work provides a global view of rat neural tissue-specific miRNA profiles and a target map of miRNAs, which is expected to contribute to future investigations of miRNA regulatory mechanisms in neural systems.

Deciphering the role of a miRNA in rice domestication

Directory of Open Access Journals (Sweden)

Swetha Chenna

2017-10-01

Full Text Available MicroRNAs (miRNAs are a class of 21 nt non-coding small RNAs (sRNAs produced from endogenously expressed MIR genes. miRNAs are mostly involved in development and disease resistance. We are interested in identifying key miRNAs that are differentially expressed among wild and cultivated rice species. Analysis of sRNA datasets from two wild species (O. nivara and O. rufipogon and one cultivated species of rice (O. sativa var. indica Pusa Basmati-1, revealed a surprisingly higher abundance of small RNAs originating from Chromosome 2 in wild rice species. This locus codes for a novel 22 nt miRNA. This novel miRNA was found to be highly abundant in flag leaf of wild species, a tissue that usually provides 70% of energy required for grain filling. This miRNA targets a group of proteins (Os03g0273200, Os01g0827300, Os01g0850700, Os11g0708100 and Os01g0842500 which are involved in secondary metabolite production, although a functional significance of this interaction has not been understood. The expression of these targets also differs across the species. Typical of 22 nt miRNAs, the identified miRNA also triggers a secondary cascade silencing by producing small interfering RNAs (siRNAs from target mRNAs in O. nivara. These secondary siRNAs are observed only among wild rice species but not in cultivated rice. Currently we are using a range of genetic, biochemical and molecular techniques to understand role of this novel miRNA in domestication of rice.

Differential expression of miRNAs and their relation to active tuberculosis.

Science.gov (United States)

Xu, Zhihong; Zhou, Aiping; Ni, Jinjing; Zhang, Qiufen; Wang, Ying; Lu, Jie; Wu, Wenjuan; Karakousis, Petros C; Lu, Shuihua; Yao, Yufeng

2015-07-01

The aim of this work was to screen miRNA signatures dysregulated in tuberculosis to improve our understanding of the biological role of miRNAs involved in the disease. Datasets deposited in publically available databases from microarray studies on infectious diseases and malignancies were retrieved, screened, and subjected to further analysis. Effect sizes were combined using the inverse-variance model and between-study heterogeneity was evaluated by the random effects model. 35 miRNAs were differentially expressed (12 up-regulated, 23 down-regulated; p tuberculosis and other infectious diseases. 15 miRNAs were found to be significantly differentially regulated (7 up-regulated, 8 down-regulated; p tuberculosis and malignancies. Most of the miRNA signatures identified in this study were found to be involved in immune responses and metabolism. Expression of these miRNA signatures in serum samples from TB subjects (n = 11) as well as healthy controls (n = 10) was examined by TaqMan miRNA array. Taken together, the results revealed differential expression of miRNAs in TB, but available datasets are limited and these miRNA signatures should be validated in future studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

The influence of clipping frequency on reserve carbohydrates and ...

African Journals Online (AJOL)

Increasing the frequency of clipping over a 12 week period resulted in decreasing root and stubble weight at the end of the 12 week period. During the regrowth period, following the clipping treatment, the aerial dry matter production was found to increase with the more lenient treatments. Keywords: weights|dry ...

Exploration of miRNA families for hypotheses generation.

KAUST Repository

Kamanu, T.K.; Radovanovic, Aleksandar; Archer, John A.C.; Bajic, Vladimir B.

2013-01-01

species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.

Decoding Algorithms for Random Linear Network Codes

DEFF Research Database (Denmark)

Heide, Janus; Pedersen, Morten Videbæk; Fitzek, Frank

2011-01-01

We consider the problem of efficient decoding of a random linear code over a finite field. In particular we are interested in the case where the code is random, relatively sparse, and use the binary finite field as an example. The goal is to decode the data using fewer operations to potentially...... achieve a high coding throughput, and reduce energy consumption.We use an on-the-fly version of the Gauss-Jordan algorithm as a baseline, and provide several simple improvements to reduce the number of operations needed to perform decoding. Our tests show that the improvements can reduce the number...

Suture retraction technique to prevent parent vessel obstruction following aneurysm tandem clipping.

Science.gov (United States)

Rayan, Tarek; Amin-Hanjani, Sepideh

2015-08-01

With large or giant aneurysms, the use of multiple tandem clips can be essential for complete obliteration of the aneurysm. One potential disadvantage, however, is the considerable cumulative weight of these clips, which may lead to kinking of the underlying parent vessels and obstruction of flow. The authors describe a simple technique to address this problem, guided by intraoperative blood flow measurements, in a patient with a ruptured near-giant 2.2 × 1.7-cm middle cerebral artery bifurcation aneurysm that was treated with the tandem clipping technique. A total of 11 clips were applied in a vertical stacked fashion. The cumulative weight of the clips caused kinking of the temporal M2 branch of the bifurcation with reduction of flow. A 4-0 Nurolon suture tie was applied to the hub of one of the clips and was tethered to the dura of the sphenoid ridge by a small mini-clip and reinforced by application of tissue sealant. The patient underwent intraoperative indocyanine green videoangiography as well as catheter angiography, which demonstrated complete aneurysmal obliteration and preservation of vessel branches. Postoperative angiography confirmed patency of the bifurcation vessels with mild vasospasm. The patient had a full recovery with no postoperative complications and was neurologically intact at her 6-month follow-up. The suture retraction technique allows a simple solution to parent vessel obstruction following aneurysm tandem clipping, in conjunction with the essential guidance provided by intraoperative flow measurements.

Simultaneous inhibition of multiple oncogenic miRNAs by a multi-potent microRNA sponge.

Science.gov (United States)

Jung, Jaeyun; Yeom, Chanjoo; Choi, Yeon-Sook; Kim, Sinae; Lee, EunJi; Park, Min Ji; Kang, Sang Wook; Kim, Sung Bae; Chang, Suhwan

2015-08-21

The roles of oncogenic miRNAs are widely recognized in many cancers. Inhibition of single miRNA using antagomiR can efficiently knock-down a specific miRNA. However, the effect is transient and often results in subtle phenotype, as there are other miRNAs contribute to tumorigenesis. Here we report a multi-potent miRNA sponge inhibiting multiple miRNAs simultaneously. As a model system, we targeted miR-21, miR-155 and miR-221/222, known as oncogenic miRNAs in multiple tumors including breast and pancreatic cancers. To achieve efficient knockdown, we generated perfect and bulged-matched miRNA binding sites (MBS) and introduced multiple copies of MBS, ranging from one to five, in the multi-potent miRNA sponge. Luciferase reporter assay showed the multi-potent miRNA sponge efficiently inhibited 4 miRNAs in breast and pancreatic cancer cells. Furthermore, a stable and inducible version of the multi-potent miRNA sponge cell line showed the miRNA sponge efficiently reduces the level of 4 target miRNAs and increase target protein level of these oncogenic miRNAs. Finally, we showed the miRNA sponge sensitize cells to cancer drug and attenuate cell migratory activity. Altogether, our study demonstrates the multi-potent miRNA sponge is a useful tool to examine the functional impact of simultaneous inhibition of multiple miRNAs and proposes a therapeutic potential.

A systematic review of discomfort due to toe or ear clipping in laboratory rodents

Science.gov (United States)

Geessink, Florentine J.; Brouwer, Michelle A. E.; Tillema, Alice; Ritskes-Hoitinga, Merel

2017-01-01

Toe clipping and ear clipping (also ear notching or ear punching) are frequently used methods for individual identification of laboratory rodents. These procedures potentially cause severe discomfort, which can reduce animal welfare and distort experimental results. However, no systematic summary of the evidence on this topic currently exists. We conducted a systematic review of the evidence for discomfort due to toe or ear clipping in rodents. The review methodology was pre-specified in a registered review protocol. The population, intervention, control, outcome (PICO) question was: In rodents, what is the effect of toe clipping or ear clipping, compared with no clipping or sham clipping, on welfare-related outcomes? Through a systematic search in PubMed, Embase, Web of Science and grey literature, we identified seven studies on the effect of ear clipping on animal welfare, and five such studies on toe clipping. Studies were included in the review if they contained original data from an in vivo experiment in rodents, assessing the effect of toe clipping or ear clipping on a welfare-related outcome. Case studies and studies applying unsuitable co-interventions were excluded. Study quality was appraised using an extended version of SYstematic Review Centre for Laboratory animal Experimentation (SYRCLE)’s risk of bias tool for animal studies. Study characteristics and outcome measures were highly heterogeneous, and there was an unclear or high risk of bias in all studies. We therefore present a narrative synthesis of the evidence identified. None of the studies reported a sample size calculation. Out of over 60 different outcomes, we found evidence of discomfort due to ear clipping in the form of increased respiratory volume, vocalization and blood pressure. For toe clipping, increased vocalization and decreased motor activity in pups were found, as well as long-term effects in the form of reduced grip strength and swimming ability in adults. In conclusion, there

Diet and lifestyle factors associated with miRNA expression in colorectal tissue

Directory of Open Access Journals (Sweden)

Slattery ML

2016-12-01

Full Text Available Martha L Slattery,1 Jennifer S Herrick,1 Lila E Mullany,1 John R Stevens,2 Roger K Wolff1 1Department of Internal Medicine, The University of Utah, Salt Lake City, 2Department of Mathematics and Statistics, Utah State University, Logan, UT, USA Abstract: MicroRNAs (miRNAs are small non-protein-coding RNA molecules that regulate gene expression. Diet and lifestyle factors have been hypothesized to be involved in the regulation of miRNA expression. In this study it was hypothesized that diet and lifestyle factors are associated with miRNA expression. Data from 1,447 cases of colorectal cancer to evaluate 34 diet and lifestyle variables using miRNA expression in normal colorectal mucosa as well as for differential expression between paired carcinoma and normal tissue were used. miRNA data were obtained using an Agilent platform. Multiple comparisons were adjusted for using the false discovery rate q-value. There were 250 miRNAs differentially expressed between carcinoma and normal colonic tissue by level of carbohydrate intake and 198 miRNAs differentially expressed by the level of sucrose intake. Of these miRNAs, 166 miRNAs were differentially expressed for both carbohydrate intake and sucrose intake. Ninety-nine miRNAs were differentially expressed by the level of whole grain intake in normal colonic mucosa. Level of oxidative balance score was associated with 137 differentially expressed miRNAs between carcinoma and paired normal rectal mucosa. Additionally, 135 miRNAs were differentially expressed in colon tissue based on recent NSAID use. Other dietary factors, body mass index, waist and hip circumference, and long-term physical activity levels did not alter miRNA expression after adjustment for multiple comparisons. These results suggest that diet and lifestyle factors regulate miRNA level. They provide additional support for the influence of carbohydrate, sucrose, whole grains, NSAIDs, and oxidative balance score on colorectal cancer risk

Peak reduction and clipping mitigation in OFDM by augmented compressive sensing

KAUST Repository

Al-Safadi, Ebrahim B.

2012-07-01

This work establishes the design, analysis, and fine-tuning of a peak-to-average-power-ratio (PAPR) reducing system, based on compressed sensing (CS) at the receiver of a peak-reducing sparse clipper applied to an orthogonal frequency-division multiplexing (OFDM) signal at the transmitter. By exploiting the sparsity of clipping events in the time domain relative to a predefined clipping threshold, the method depends on partially observing the frequency content of the clipping distortion over reserved tones to estimate the remaining distortion. The approach has the advantage of eliminating the computational complexity at the transmitter and reducing the overall complexity of the system compared to previous methods which incorporate pilots to cancel nonlinear distortion. Data-based augmented CS methods are also proposed that draw upon available phase and support information from data tones for enhanced estimation and cancelation of clipping noise. This enables signal recovery under more severe clipping scenarios and hence lower PAPR can be achieved compared to conventional CS techniques. © 2012 IEEE.

Peak reduction and clipping mitigation in OFDM by augmented compressive sensing

KAUST Repository

Al-Safadi, Ebrahim B.; Al-Naffouri, Tareq Y.

2012-01-01

This work establishes the design, analysis, and fine-tuning of a peak-to-average-power-ratio (PAPR) reducing system, based on compressed sensing (CS) at the receiver of a peak-reducing sparse clipper applied to an orthogonal frequency-division multiplexing (OFDM) signal at the transmitter. By exploiting the sparsity of clipping events in the time domain relative to a predefined clipping threshold, the method depends on partially observing the frequency content of the clipping distortion over reserved tones to estimate the remaining distortion. The approach has the advantage of eliminating the computational complexity at the transmitter and reducing the overall complexity of the system compared to previous methods which incorporate pilots to cancel nonlinear distortion. Data-based augmented CS methods are also proposed that draw upon available phase and support information from data tones for enhanced estimation and cancelation of clipping noise. This enables signal recovery under more severe clipping scenarios and hence lower PAPR can be achieved compared to conventional CS techniques. © 2012 IEEE.

Exploring miRNA based approaches in cancer diagnostics and therapeutics.

Science.gov (United States)

Mishra, Shivangi; Yadav, Tanuja; Rani, Vibha

2016-02-01

MicroRNAs (miRNAs), a highly conserved class of tissue specific, small non-protein coding RNAs maintain cell homeostasis by negative gene regulation. Proper controlling of miRNA expression is required for a balanced physiological environment, as these small molecules influence almost every genetic pathway from cell cycle checkpoint, cell proliferation to apoptosis, with a wide range of target genes. Deregulation in miRNAs expression correlates with various cancers by acting as tumor suppressors and oncogenes. Although promising therapies exist to control tumor development and progression, there is a lack of efficient diagnostic and therapeutic approaches for delineating various types of cancer. The molecularly different tumors can be differentiated by specific miRNA profiling as their phenotypic signatures, which can hence be exploited to surmount the diagnostic and therapeutic challenges. Present review discusses the involvement of miRNAs in oncogenesis with the analysis of patented research available on miRNAs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Catheter Entrapment During Posterior Mitral Leaflet Pushing Maneuver for MitraClip Implantation.

Science.gov (United States)

Castrodeza, Javier; Amat-Santos, Ignacio J; Tobar, Javier; Varela-Falcón, Luis H

2016-06-01

MitraClip (Abbott Vascular) therapy has been reported to be an effective procedure for mitral regurgitation, especially in high-risk patients. Recently, the novel pushing maneuver technique has been described for approaching restricted and short posterior leaflets with a pigtail catheter in order to facilitate grasping of the clip. However, complications or unexpected situations may occur. We report the case of an 84-year-old patient who underwent MitraClip implantation wherein the pushing maneuver was complicated by the clip accidentally gripping the pigtail catheter along with the two leaflets.

Preoperative simulation for the planning of microsurgical clipping of intracranial aneurysms.

Science.gov (United States)

Marinho, Paulo; Vermandel, Maximilien; Bourgeois, Philippe; Lejeune, Jean-Paul; Mordon, Serge; Thines, Laurent

2014-12-01

The safety and success of intracranial aneurysm (IA) surgery could be improved through the dedicated application of simulation covering the procedure from the 3-dimensional (3D) description of the surgical scene to the visual representation of the clip application. We aimed in this study to validate the technical feasibility and clinical relevance of such a protocol. All patients preoperatively underwent 3D magnetic resonance imaging and 3D computed tomography angiography to build 3D reconstructions of the brain, cerebral arteries, and surrounding cranial bone. These 3D models were segmented and merged using Osirix, a DICOM image processing application. This provided the surgical scene that was subsequently imported into Blender, a modeling platform for 3D animation. Digitized clips and appliers could then be manipulated in the virtual operative environment, allowing the visual simulation of clipping. This simulation protocol was assessed in a series of 10 IAs by 2 neurosurgeons. The protocol was feasible in all patients. The visual similarity between the surgical scene and the operative view was excellent in 100% of the cases, and the identification of the vascular structures was accurate in 90% of the cases. The neurosurgeons found the simulation helpful for planning the surgical approach (ie, the bone flap, cisternal opening, and arterial tree exposure) in 100% of the cases. The correct number of final clip(s) needed was predicted from the simulation in 90% of the cases. The preoperatively expected characteristics of the optimal clip(s) (ie, their number, shape, size, and orientation) were validated during surgery in 80% of the cases. This study confirmed that visual simulation of IA clipping based on the processing of high-resolution 3D imaging can be effective. This is a new and important step toward the development of a more sophisticated integrated simulation platform dedicated to cerebrovascular surgery.

Oppositional Decoding as an Act of Resistance.

Science.gov (United States)

Steiner, Linda

1988-01-01

Argues that contributors to the "No Comment" feature of "Ms." magazine are engaging in oppositional decoding and speculates on why this is a satisfying group process. Also notes such decoding presents another challenge to the idea that mass media has the same effect on all audiences. (SD)

miRNA regulation of LDL-cholesterol metabolism.

Science.gov (United States)

Goedeke, Leigh; Wagschal, Alexandre; Fernández-Hernando, Carlos; Näär, Anders M

2016-12-01

In the past decade, microRNAs (miRNAs) have emerged as key regulators of circulating levels of lipoproteins. Specifically, recent work has uncovered the role of miRNAs in controlling the levels of atherogenic low-density lipoprotein LDL (LDL)-cholesterol by post-transcriptionally regulating genes involved in very low-density lipoprotein (VLDL) secretion, cholesterol biosynthesis, and hepatic LDL receptor (LDLR) expression. Interestingly, several of these miRNAs are located in genomic loci associated with abnormal levels of circulating lipids in humans. These findings reinforce the interest of targeting this subset of non-coding RNAs as potential therapeutic avenues for regulating plasma cholesterol and triglyceride (TAG) levels. In this review, we will discuss how these new miRNAs represent potential pre-disposition factors for cardiovascular disease (CVD), and putative therapeutic targets in patients with cardiometabolic disorders. This article is part of a Special Issue entitled: MicroRNAs and lipid/energy metabolism and related diseases edited by Carlos Fernández-Hernando and Yajaira Suárez. Copyright © 2016 Elsevier B.V. All rights reserved.

Bayesian Recovery of Clipped OFDM Signals: A Receiver-based Approach

KAUST Repository

Al-Rabah, Abdullatif R.

2013-01-01

recovery algorithm to reconstruct the clipping signal at the receiver side by measuring part of subcarriers, iii) perform well in the absence of statistical information about the signal (e.g. clipping level) and the noise (e.g. noise variance

Computational Investigations of Post-Transcriptional Regulation

DEFF Research Database (Denmark)

Rasmussen, Simon Horskjær

and miRNA regulation was studied by cross-linking immunoprecipitation (CLIP) and RBP double knockdown experiments. A comprehensive analysis of 107 CLIP datasets of 49 RBPs demonstrated that RBPs modulate miRNA regulation. Results suggest it is mediated by RBP-binding hotspots that likely...... investigated using high-throughput data. Analysis of IMP RIP-seq, iCLIP and RNA-seq datasets identified transcripts associated with cytoplasmic IMP ribonucleoproteins. Many of these transcripts were functionally involved in actin cytoskeletal remodeling. Further analyses of this data permitted estimation...... of a bipartite motif, composed of an AU-rich and a CA-rich domain. In addition, a regulatory motif discovery method was developed and applied to identify motifs using differential expression data and CLIP-data in the above investigations. This thesis increased the understanding of the role of RBPs in mi...

Association of MiRNA-146a, MiRNA-499, IRAK1 and PADI4 Polymorphisms with Rheumatoid Arthritis in Egyptian Population

Directory of Open Access Journals (Sweden)

Olfat Gamil Shaker

2018-05-01

Full Text Available Background/Aims: Rheumatoid arthritis (RA is a systemic autoimmune disease affecting up to 1% of the population worldwide. The aim of the present study was to investigate whether miRNA-146a rs2910164, miRNA-499 rs3746444, IRAK1 rs3027898 and PADI4 rs1748033 polymorphisms are associated with susceptibility to RA in Egyptians and whether they influence disease severity and activity. Methods: The study was performed on 104 unrelated RA patients and 112 healthy subjects. RA patients were further subdivided into active and inactive RA groups. Polymorphisms were genotyped by using real-time polymerase chain reaction with TaqMan allelic discrimination assay. Results: Significant differences in the frequency of miRNA-146a rs2910164, miRNA-499 rs3746444, IRAK1 rs3027898 and PADI4 rs1748033 alleles and genotypes were observed between RA patients and controls. Only CA and AA genotypes of IRAK1 rs3027898 shows a significant difference between active and inactive subgroups. MiRNA-146a rs2910164 and IRAK1 rs3027898 polymorphisms were a risk factor for predisposition to RA in codominant and dominant tested inheritance models, while, the miRNA-499 rs3746444 and PADI4 rs1748033 polymorphisms were a risk factor in codominant and recessive one. CG and GG genotypes of miRNA-146a rs2910164 were associated with positive erosions. CA genotype of IRAK1 rs3027898 was associated with low disease activity and negative erosions, while, the AA genotype was associated with high disease activity. CC genotype of PADI4 rs1748033 was associated with negative rheumatoid factor. Conclusion: The 4 studied SNPs were likely to play an important role in the susceptibility to RA and can influence disease severity and activity in Egyptian population.

Equation-Method for correcting clipping errors in OFDM signals.

Science.gov (United States)

Bibi, Nargis; Kleerekoper, Anthony; Muhammad, Nazeer; Cheetham, Barry

2016-01-01

Orthogonal frequency division multiplexing (OFDM) is the digital modulation technique used by 4G and many other wireless communication systems. OFDM signals have significant amplitude fluctuations resulting in high peak to average power ratios which can make an OFDM transmitter susceptible to non-linear distortion produced by its high power amplifiers (HPA). A simple and popular solution to this problem is to clip the peaks before an OFDM signal is applied to the HPA but this causes in-band distortion and introduces bit-errors at the receiver. In this paper we discuss a novel technique, which we call the Equation-Method, for correcting these errors. The Equation-Method uses the Fast Fourier Transform to create a set of simultaneous equations which, when solved, return the amplitudes of the peaks before they were clipped. We show analytically and through simulations that this method can, correct all clipping errors over a wide range of clipping thresholds. We show that numerical instability can be avoided and new techniques are needed to enable the receiver to differentiate between correctly and incorrectly received frequency-domain constellation symbols.

Epigenetic regulation of normal human mammary cell type-specific miRNAs

Energy Technology Data Exchange (ETDEWEB)

Vrba, Lukas [Univ. of Arizona, Tucson, AZ (United States). Arizona Cancer Center; Inst. of Plant Molecular Biology, Ceske Budejovice (Czech Republic). Biology Centre ASCR; Garbe, James C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Center; Stampfer, Martha R. [Univ. of Arizona, Tucson, AZ (United States). Arizona Cancer Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Center; Futscher, Bernard W. [Univ. of Arizona, Tucson, AZ (United States). Arizona Cancer Center and Dept. of Pharmacology & Toxicology

2011-08-26

Epigenetic mechanisms are important regulators of cell type–specific genes, including miRNAs. In order to identify cell type-specific miRNAs regulated by epigenetic mechanisms, we undertook a global analysis of miRNA expression and epigenetic states in three isogenic pairs of human mammary epithelial cells (HMEC) and human mammary fibroblasts (HMF), which represent two differentiated cell types typically present within a given organ, each with a distinct phenotype and a distinct epigenotype. While miRNA expression and epigenetic states showed strong interindividual concordance within a given cell type, almost 10% of the expressed miRNA showed a cell type–specific pattern of expression that was linked to the epigenetic state of their promoter. The tissue-specific miRNA genes were epigenetically repressed in nonexpressing cells by DNA methylation (38%) and H3K27me3 (58%), with only a small set of miRNAs (21%) showing a dual epigenetic repression where both DNA methylation and H3K27me3 were present at their promoters, such as MIR10A and MIR10B. Individual miRNA clusters of closely related miRNA gene families can each display cell type–specific repression by the same or complementary epigenetic mechanisms, such as the MIR200 family, and MIR205, where fibroblasts repress MIR200C/141 by DNA methylation, MIR200A/200B/429 by H3K27me3, and MIR205 by both DNA methylation and H3K27me3. Since deregulation of many of the epigenetically regulated miRNAs that we identified have been linked to disease processes such as cancer, it is predicted that compromise of the epigenetic control mechanisms is important for this process. Overall, these results highlight the importance of epigenetic regulation in the control of normal cell type–specific miRNA expression.

TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues

OpenAIRE

Berillo, Olga; Régnier, Mireille; Ivashchenko, Anatoly

2014-01-01

microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents ...

Modeling Timbre Similarity of Short Music Clips.

Science.gov (United States)

Siedenburg, Kai; Müllensiefen, Daniel

2017-01-01

There is evidence from a number of recent studies that most listeners are able to extract information related to song identity, emotion, or genre from music excerpts with durations in the range of tenths of seconds. Because of these very short durations, timbre as a multifaceted auditory attribute appears as a plausible candidate for the type of features that listeners make use of when processing short music excerpts. However, the importance of timbre in listening tasks that involve short excerpts has not yet been demonstrated empirically. Hence, the goal of this study was to develop a method that allows to explore to what degree similarity judgments of short music clips can be modeled with low-level acoustic features related to timbre. We utilized the similarity data from two large samples of participants: Sample I was obtained via an online survey, used 16 clips of 400 ms length, and contained responses of 137,339 participants. Sample II was collected in a lab environment, used 16 clips of 800 ms length, and contained responses from 648 participants. Our model used two sets of audio features which included commonly used timbre descriptors and the well-known Mel-frequency cepstral coefficients as well as their temporal derivates. In order to predict pairwise similarities, the resulting distances between clips in terms of their audio features were used as predictor variables with partial least-squares regression. We found that a sparse selection of three to seven features from both descriptor sets-mainly encoding the coarse shape of the spectrum as well as spectrotemporal variability-best predicted similarities across the two sets of sounds. Notably, the inclusion of non-acoustic predictors of musical genre and record release date allowed much better generalization performance and explained up to 50% of shared variance ( R 2 ) between observations and model predictions. Overall, the results of this study empirically demonstrate that both acoustic features related