3,595 research outputs found
Letters to Andrew Inglis Clark, Tasmania, from George B. Edwards - 17 Nov 1879 - 1 Oct 1907 and one from J.G. Witton to G. B. Edwards, 23 Apr 1883
No full textLetters to Andrew Inglis Clark, Tasmania, from George B. Edwards 17 Nov 1879 - 1 Oct 1907, containing reminiscences of the Minerva Club; life in Sydney; personal, literary and religious matters, including Conway's visit; Tasmanian politics and newspapers, life and politics in Launceston and one from J.G. Witton to G. B. Edwards, 23 Apr 1883, about life in Melbourne.
C4/C54-7
Conserving idealized landscapes: past history, public perception and future management in the New Forest (UK)
No full textThe New Forest is one of the most visited regions of Britain. It has recently been designated a National Park in recognition of its unique wood pasture ecosystems, a traditional land-use system, its magnificent scenery and recreational potential, and its biodiversity importance. The Forest's highly prized Ancient and Ornamental (A&O) woodlands are a result of complex interactions among human activities of several kinds and the ecology of the dominant species-beech and oak-under the climate conditions of the last one to two millennia. Major changes in management practices over the 20th century, combined with the historical imprint of previous centuries of use, have set the A&O woodlands on a trajectory that means their nature and appearance will inevitably change over the coming decades. When the potential stresses that will be imposed by 21st century climate change are also considered, it will be challenging to find a management strategy to maintain A&O woodlands in their present form. Beech, which owes its current dominance largely to human disturbances of the woodland ecosystem, will be particularly stressed under future conditions. Future conservation policies, and hence management strategies, must be flexible as to the species composition and structure of future woodlands. However, the wide range of users and their different values add further complexity to forest management, and managers must also focus on issues of public perception. For example visitors idealize current landscapes, and this exerts a pressure to maintain the status quo as far as appearance is concerned that will be hard to achieve in practice. Management strategies will be greatly constrained unless conflicts about values and uses are resolved
slimsuite/depthsizer: DepthSizer v1.4.0 (IndelRatio)
No full textThis release features an extensive reworking under the hood, which moves the main calculation into R and smooths the read depth modal density calculation. Some of the older, less accurate, approaches have been dropped in favour of some additional mapping adjustments that aim to frame the upper and lower bounds of genome size.
Current citation:
Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, Sauquet H, Bourke G, Bragg JG & Edwards RJ (preprint): Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C. bioRxiv 2021.06.02.444084; doi: 10.1101/2021.06.02.444084
Letter to Andrew Inglis Clark, Tasmania, from George B. Edwards, 23 May 1885
No full textLetter to Andrew Inglis Clark, Tasmania, dated 23 May 1885. C4/C6
Letter to Andrew Inglis Clark, Tasmania, from George B. Edwards, 21 May 1884
No full textLetter to Andrew Inglis Clark, Tasmania, dated 21 May 1884. C4/C6
Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach
No full textBackground: Previously it has been shown that insulin-mediated tyrosine phosphorylation of myosin heavy chain is concomitant with enhanced association of C-terminal SRC kinase during skeletal muscle differentiation. We sought to identify putative site(s) for this phosphorylation event.Results: A combined bioinformatics approach of motif prediction and evolutionary and structural analyses identified tyrosines163 and 1856 of the skeletal muscle heavy chain as the leading candidate for the sites of insulin-mediated tyrosine phosphorylation.Conclusion: Our work is suggestive that tyrosine phosphorylation of myosin heavy chain, whether in skeletal muscle or in platelets, is a significant event that may initiate cytoskeletal reorganization of muscle cells and platelets. Our studies provide a good starting point for further functional analysis of MHC phosphor-signalling events within different cells.<br/
slimsuite/depthsizer: DepthSizer v1.6.2 (MapRatio)
No full text<p>This release features some more reworking under the hood with an improved R script shared by <a href="https://github.com/slimsuite/depthkopy">DepthKopy</a>. A couple of additional mapping adjustments have been added. This version should be consistent with the version used for the final waratah genome publication, which is the citation for DepthSizer:</p>
<blockquote><p>Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, Sauquet H, Bourke G, Amos TG, Bragg JG & Edwards RJ (2022).
Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads,
linked-reads and Hi-C. Molecular Ecology Resources doi: <a href="https://doi.org/10.1111/1755-0998.13574">10.1111/1755-0998.13574</a></p>
</blockquote>
<p>Please contact the author if you have trouble getting the full text version, or read the bioRxiv preprint version:</p>
<blockquote><p>Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads,
linked-reads and Hi-C. <a href="https://www.biorxiv.org/content/10.1101/2021.06.02.444084v2.full">bioRxiv 2021.06.02.444084</a>;
doi: 10.1101/2021.06.02.444084.</p>
</blockquote>
slimsuite/diploidocus: Diploidocus v1.1.2 (Tidy)
No full text<p>This is an updated release, with a few bug fixes and some re-engineered elements to be more consistent with <a href="https://github.com/slimsuite/depthsizer">DepthSizer</a> and <a href="https://github.com/slimsuite/depthkopy">DepthKopy</a>.</p>
<p>The main Diploidocus tidy mode has been published as part of the Waratah genome paper:</p>
<blockquote><p>Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, Sauquet H, Bourke G, Amos TG, Bragg JG & Edwards RJ (2022).
Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads,
linked-reads and Hi-C. <em>Molecular Ecology Resources</em> doi: <a href="https://doi.org/10.1111/1755-0998.13574">10.1111/1755-0998.13574</a></p>
</blockquote>
<p>Note that the genome size prediction and copy number estimation modes are now available through <a href="https://github.com/slimsuite/depthsizer">DepthSizer</a>
and <a href="https://github.com/slimsuite/depthkopy">DepthKopy</a>, which should cite the same article.
Please contact the author if you have trouble getting the full text version, or read the bioRxiv preprint version:</p>
<blockquote><p>Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads,
linked-reads and Hi-C. <a href="https://www.biorxiv.org/content/10.1101/2021.06.02.444084v2.full"><em>bioRxiv</em> 2021.06.02.444084</a>;
doi: 10.1101/2021.06.02.444084.</p>
</blockquote>
<p>If using the simplified Nala version of the tidy algorithm, please cite: Edwards RJ et al. (2021), BMC Genomics [PMID: 33726677].</p>
<p>If using the 10x genomics non-redundancy pipeline, cite the Starling genome paper:</p>
<blockquote><p>Stuart KC<em>, Edwards RJ</em>, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M,
Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL & Rollins LA (preprint):
Transcript- and annotation-guided genome assembly of the European starling.
<a href="https://www.biorxiv.org/content/10.1101/2021.04.07.438753v1.full"><em>bioRxiv</em> 2021.04.07.438753</a>; doi: 10.1101/2021.04.07.438753. [*Joint first authors]</p>
</blockquote>
Computational identification and analysis of protein short linear motifs
No full textShort linear motifs (SLiMs) in proteins can act as targets for proteolytic cleavage, sites of post-translational modification, determinants of sub-cellular localization, and mediators of protein-protein interactions. Computational discovery of SLiMs involves assembling a group of proteins postulated to share a potential motif, masking out residues less likely to contain such a motif, down-weighting shared motifs arising through common evolutionary descent, and calculation of statistical probabilities allowing for the multiple testing of all possible motifs. Much of the challenge for motif discovery lies in the assembly and masking of datasets of proteins likely to share motifs, since the motifs are typically short (between 3 and 10 amino acids in length), so that potential signals can be easily swamped by the noise of stochastically recurring motifs. Focusing on disordered regions of proteins, where SLiMs are predominantly found, and masking out non-conserved residues can reduce the level of noise but more work is required to improve the quality of high-throughput experimental datasets (e.g. of physical protein interactions) as input for computational discovery
Invariant tori and Lagrange stability of pendulum-type equations
No full textAbstractIn this paper we prove that the pendulum-type equation x″ + g(t, x) = 0 possesses infinitely many invariant tori whenever g(t, x) has zero mean value on the torus T2, where g(t, x) belongs to C∞(T2). This yields the boundedness for solutions of the considered pendulum-type equation and thus leads to an answer to J. Moser's boundedness problem (1973, Ann. of Math. Stud. 77)
- …
