| 1. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Bradnam, K. R., et al.
(author)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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In: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Journal article (peer-reviewed)abstract
- Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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| 3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Zhuang, C., et al.
(author)
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A neuromuscular electrical stimulation strategy based on muscle synergy for stroke rehabilitation
- 2015
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In: International IEEE/EMBS Conference on Neural Engineering, NER. - : IEEE Computer Society. - 9781467363891 ; , s. 816-819
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Conference paper (peer-reviewed)abstract
- Recent experiments have suggested that the central nervous system (CNS) makes use of muscle synergies as a neural strategy to simplify the control of a variety of movements by using a single pattern of neural command signal. This nature of muscle coordination could have great significance in the treatment and rehabilitation of upper limb impairments for hemiparetic patients post stroke. The use of neuromuscular electrical stimulation (NMES) for neural prosthetics or therapeutic applications has been demonstrated as a promising clinical intervention for stroke patients to recover motor function of the upper extremity. However, the existing NMES systems do not provide control methods for the patient to achieve an individualized and functional rehabilitation training. In this research work, muscle synergies from the flexionextension elbow antagonistic muscles were studied. Using motion information and EMG signals, muscle synergies were extracted using non-negative matrix factorization (NMF) method. Reconstructed signals obtained from the muscle synergies were then applied to the virtual arm (VA) model to test a synergy based NMES strategy. Results show close resemblance to the original elbow trajectory of normal movements and thus the feasibility to control movements in stroke patients for rehabilitation.
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| 5. |
- Nejdl, W, et al.
(author)
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Edutella: A P2P Networking Infrastructure Based on RDF
- 2002
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Conference paper (peer-reviewed)abstract
- Metadata for the World Wide Web is important, but metadata for Peer-to-Peer (P2P) networks is absolutely crucial. In this paper we discuss the open source project Edutella which builds upon metadata standards defined for the WWW and aims to provide an RDFbased metadata infrastructure for P2P applications, building on the recently announced JXTA Framework. We describe the goals and main services this infrastructure will provide and the architecture to connect Edutella Peers based on exchange of RDF metadata. As the query service is one of the core services of Edutella, upon which other services are built, we specify in detail the Edutella Common Data Model (ECDM) as basis for the Edutella query exchange language (RDF-QEL-i) and format implementing distributed queries over the Edutella network. Finally, we shortly discuss registration and mediation services, and introduce the prototype and application scenario for our current Edutella aware peers.
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| 6. |
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| 7. |
- Qu, M., et al.
(author)
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Electrical conductivity and mechanical properties of melt-spun ternary composites comprising PMMA, carbon fibers and carbon black
- 2017
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In: Composites Science And Technology. - : Elsevier. - 0266-3538 .- 1879-1050. ; 150, s. 24-31
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Journal article (peer-reviewed)abstract
- In this study, the electrical conductivity of melt spun composites consisting of PMMA containing both aligned carbon fibers (CF) and carbon black (CB) has been investigated. A broad range of composite compositions (up to 50 vol % CF and 20 vol % CB) was studied. The percolation thresholds of binary PMMA/CF and PMMA/CB composites were determined to 31.8 and 3.9 vol %, respectively. Experimental conductivity contour plots for PMMA/CF/CB ternary composites were presented for the first time. Additionally, based on a model for predicting the percolation threshold of ternary composites, a novel equation was proposed to predict the conductivity of ternary composites, showing results in agreement with corresponding experimental data. Finally, two mechanical contour plots for elastic modulus and tensile strength were presented, showing how the decreasing tensile strength and increasing E-modulus of the PMMA/CF/CB ternary composites was depending on the CB and CF filling fractions. The systematic measurements and novel equations presented in this work are especially valuable when designing ternary conductive polymer composites with two different fillers.
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| 8. |
- Wang, Q., et al.
(author)
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Color-tunable single-fluorophore supramolecular system with assembly-encoded emission
- 2020
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In: Nature Communications. - : Nature Research. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Regulating the fluorescent properties of organic small molecules in a controlled and dynamic manner has been a fundamental research goal. Although several strategies have been exploited, realizing multi-color molecular emission from a single fluorophore remains challenging. Herein, we demonstrate an emissive system by combining pyrene fluorophore and acylhydrazone units, which can generate multi-color switchable fluorescent emissions at different assembled states. Two kinds of supramolecular tools, amphiphilic self-assembly and γ-cyclodextrin mediated host-guest recognition, are used to manipulate the intermolecular aromatic stacking distances, resulting in the tunable fluorescent emission ranging from blue to yellow, including a pure white-light emission. Moreover, an external chemical signal, amylase, is introduced to control the assembly states of the system on a time scale, generating a distinct dynamic emission system. The dynamic properties of this multi-color fluorescent system can be also enabled in a hydrogel network, exhibiting a promising potential for intelligent fluorescent materials.
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