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  • 1
    Publication Date: 2016-09-02
    Description: Motivation: Third generation sequencing methods provide longer reads than second generation methods and have distinct error characteristics. While there exist many read simulators for second generation data, there is a very limited choice for third generation data. Results: We analyzed public data from Pacific Biosciences (PacBio) SMRT sequencing, developed an error model and implemented it in a new read simulator called SimLoRD. It offers options to choose the read length distribution and to model error probabilities depending on the number of passes through the sequencer. The new error model makes SimLoRD the most realistic SMRT read simulator available. Availability and Implementation: SimLoRD is available open source at http://bitbucket.org/genomeinformatics/simlord/ and installable via Bioconda ( http://bioconda.github.io ). Contact: Bianca.Stoecker@uni-due.de or Sven.Rahmann@uni-due.de . Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2015-04-23
    Description: The magnetic composite sheets were designed by using core-shell structured magnetic fillers instead of uncoated magnetic fillers to resolve concurrently the electromagnetic interference and thermal radiation problems. To predict the thermal conductivity of composite sheet, we calculated the thermal conductivity of the uncoated magnetic fillers and core-shell structured fillers. And then, the thermal conductivity of the magnetic composites sheet filled with core-shell structured magnetic fillers was calculated and compared with that of the uncoated magnetic fillers filled in composite sheet. The magnetic core and shell material are employed the typical Fe-Al-Si flake (60  μ m × 60  μ m × 1  μ m) and 250 nm-thick AlN with high thermal conductivity, respectively. The longitudinal thermal conductivity of the core-shell structured magnetic composite sheet (2.45 W/m·K) enhanced about 33.4% in comparison with that of uncoated magnetic fillers (1.83 W/m·K) for the 50 vol. % magnetic filler in polymer matrix.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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  • 3
    Publication Date: 2015-02-11
    Description: Leukocyte common antigen-related receptor protein tyrosine phosphatases—comprising LAR, PTPδ, and PTPσ—are synaptic adhesion molecules that organize synapse development. Here, we identify glypican 4 (GPC-4) as a ligand for PTPσ. GPC-4 showed strong (nanomolar) affinity and heparan sulfate (HS)-dependent interaction with the Ig domains of PTPσ. PTPσ bound only to proteolytically...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 4
    Publication Date: 2014-11-28
    Description: Transcription-coupled DNA repair (TCR) is a subpathway of nucleotide excision repair (NER) dedicated to rapid removal of DNA lesions in the transcribed strand of actively transcribed genes. The precise nature of the TCR signal and how the repair machinery gains access to lesions imbedded in stalled RNA polymerase II (RNAP II) complexes in eukaryotic cells are still enigmatic. RNAP II has an intrinsic capacity for transcription bypass of DNA lesions by incorporation or misincorporation of nucleotides across the lesions. It has been suggested that transcription bypass of lesions, which exposes the lesions, may be required for TCR. Here, we show that E1103G mutation of Rpb1, the largest subunit of RNAP II, which promotes transcription bypass of UV-induced cyclobutane pyrimidine dimers (CPDs), increases survival of UV irradiated yeast cells but attenuates TCR. The increased cell survival is independent of any NER subpathways. In contrast, G730D mutation of Rpb1, which impairs transcription bypass of CPDs, enhances TCR. Our results suggest that transcription bypass of lesions attenuates TCR but enhances cell tolerance to DNA lesions. Efficient stalling of RNAP II is essential for efficient TCR.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2013-02-13
    Description: [1]  Ultraviolet spectra of the extended solar corona have been routinely obtained by SoHO/UVCS since 1996. Sudden variations of spectral parameters are mainly due to the detection of Coronal Mass Ejections (CMEs) crossing the instrumental slit. We present a catalog of CME ultraviolet spectra based upon a systematic search of events in the LASCO CME catalog, and we discuss their statistical properties. Our catalog includes 1059 events through the end of 2005, covering nearly a full solar cycle. It is online available at the URL http://solarweb.oato.inaf.it/UVCS_CME and embedded in the online LASCO CME catalog (http://cdaw.gsfc.nasa.gov/CME_list). The emission lines observed provide diagnostics of CME plasma parameters, such as the light-of-sight velocity, density and temperature and allow to link the CME onset data to the extended corona white-light images. The catalog indicates whether there are clear signatures of features such as shock waves, current sheets, O VI flares, helical motions and which part of the CME structures (front, cavity or prominence material) are detected. The most common detected structure is the cool prominence material (in about 70% of the events). For each event, the catalog also contains movie, images, plots and information relevant to address detailed scientific investigations. The number of events detected in UV is about 1/10 of the LASCO CMEs, and about 1/4 of the halo events. We find that UVCS tends to detect faster, more massive and energetic CME than LASCO and for about 40% of the events events it has been possible to determine the plasma light-of-sight velocity.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
    Publication Date: 2015-12-02
    Description: The 3' untranslated regions (3' UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3' UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu -derived isoforms are often expressed in a tissue-specific manner, and the Alu -derived 3' UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3' UTRs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2008-07-03
    Description: Reprogramming of somatic cells is a valuable tool to understand the mechanisms of regaining pluripotency and further opens up the possibility of generating patient-specific pluripotent stem cells. Reprogramming of mouse and human somatic cells into pluripotent stem cells, designated as induced pluripotent stem (iPS) cells, has been possible with the expression of the transcription factor quartet Oct4 (also known as Pou5f1), Sox2, c-Myc and Klf4 (refs 1-11). Considering that ectopic expression of c-Myc causes tumorigenicity in offspring and that retroviruses themselves can cause insertional mutagenesis, the generation of iPS cells with a minimal number of factors may hasten the clinical application of this approach. Here we show that adult mouse neural stem cells express higher endogenous levels of Sox2 and c-Myc than embryonic stem cells, and that exogenous Oct4 together with either Klf4 or c-Myc is sufficient to generate iPS cells from neural stem cells. These two-factor iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germ line, and form chimaeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jeong Beom -- Zaehres, Holm -- Wu, Guangming -- Gentile, Luca -- Ko, Kinarm -- Sebastiano, Vittorio -- Arauzo-Bravo, Marcos J -- Ruau, David -- Han, Dong Wook -- Zenke, Martin -- Scholer, Hans R -- England -- Nature. 2008 Jul 31;454(7204):646-50. doi: 10.1038/nature07061. Epub 2008 Jun 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Rontgenstrasse 20, 48149 Munster, NRW, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18594515" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/*cytology/metabolism ; Animals ; Cell Differentiation/genetics ; Cells, Cultured ; *Cellular Reprogramming ; Chimera ; DNA-Binding Proteins/genetics/metabolism ; Female ; Gene Expression Profiling ; Genes, myc/genetics ; HMGB Proteins/genetics/metabolism ; Homeodomain Proteins/genetics ; Kruppel-Like Transcription Factors/genetics/metabolism ; Male ; Mice ; Mice, Nude ; Mice, Transgenic ; Neurons/*cytology ; Octamer Transcription Factor-3/genetics/metabolism ; Pluripotent Stem Cells/*cytology/*metabolism ; Proteins/genetics ; Proto-Oncogene Proteins c-myc/metabolism ; RNA, Untranslated ; SOXB1 Transcription Factors ; Transcription Factors/genetics/metabolism ; Transduction, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2003-12-13
    Description: Comet C/2002 X5 (Kudo-Fujikawa) was observed near its perihelion of 0.19 astronomical unit by the Ultraviolet Coronagraph Spectrometer aboard the Solar and Heliospheric Observatory spacecraft. Images of the comet reconstructed from high-resolution spectra reveal a quasi-spherical cloud of neutral hydrogen and a variable tail of C+ and C2+ that disconnects from the comet and subsequently regenerates. The high abundance of C2+ and C+, at least 24% relative to water, cannot be explained by photodissociation of carbon monoxide and is instead attributed to the evaporation and subsequent photoionization of atomic carbon from organic refractory compounds present in the cometary dust grains. This result serves to strengthen the connection between comets and the material from which the Solar System formed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Povich, Matthew S -- Raymond, John C -- Jones, Geraint H -- Uzzo, Michael -- Ko, Yuan-Kuen -- Feldman, Paul D -- Smith, Peter L -- Marsden, Brian G -- Woods, Thomas N -- New York, N.Y. -- Science. 2003 Dec 12;302(5652):1949-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA. mpovich@cfa.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14671299" target="_blank"〉PubMed〈/a〉
    Keywords: *Carbon ; Hydrogen ; Ions ; *Meteoroids ; Spectrum Analysis ; Water
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2016-03-17
    Description: Complex diseases are defined to be determined by multiple genetic and environmental factors alone as well as in interactions. To analyze interactions in genetic data, many statistical methods have been suggested, with most of them relying on statistical regression models. Given the known limitations of classical methods, approaches from the machine-learning community have also become attractive. From this latter family, a fast-growing collection of methods emerged that are based on the Multifactor Dimensionality Reduction (MDR) approach. Since its first introduction, MDR has enjoyed great popularity in applications and has been extended and modified multiple times. Based on a literature search, we here provide a systematic and comprehensive overview of these suggested methods. The methods are described in detail, and the availability of implementations is listed. Most recent approaches offer to deal with large-scale data sets and rare variants, which is why we expect these methods to even gain in popularity.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 10
    Publication Date: 2016-12-02
    Description: The stromal cell-derived factor 1α (CXCL12) belongs to the CXC chemokine family and plays an important role in tissue regeneration and the recruitment of stem cells. Here, a stable chemotactic gradient is essential that is formed by the interaction of CXCL12 with the extracellular matrix. Binding properties of CXCL12 to naturally occurring glycosaminoglycans (GAGs) as well as to the artificial highly sulfated hyaluronic acid (HA) are investigated by using a combination of NMR spectroscopy, molecular modeling and molecular dynamics simulations. Our results demonstrate a preferred protein binding for the sulfated GAGs heparin (HE) and highly sulfated HA. Furthermore, we could demonstrate that the orientation of the sulfate is crucial for binding. All sulfated GAGs interact with the CXCL12 GAG-binding motif (K24-H25-L26-K27-R41-K43-R47), where K27 and R41 represent the anchor points. Furthermore, differences could be observed in the second interaction interface of CXCL12: both HE and highly sulfated HA interfere with the receptor-binding motif, while chondroitin sulfate binds different amino acids in close proximity to this motif. CXCL12 does not interact with HA, which was directly demonstrated by NMR spectroscopy and molecular modeling and explained by the lack of sulfate groups of the HA molecule.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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