Periodic pattern formation in reaction-diffusion systems -an introduction for numerical simulation

The aim of the present review is to provide a comprehensive explanation of Turing reaction–diffusion systems in sufficient detail to allow readers to perform numerical calculations themselves. The reaction–diffusion model is widely studied in the field of mathematical biology, serves as a powerful paradigm model for self-organization and is beginning to be applied to actual experimental systems in developmental biology. Despite the increase in current interest, the model is not well understood among experimental biologists, partly because appropriate introductory texts are lacking. In the present review, we provide a detailed description of the definition of the Turing reaction–diffusion model that is comprehensible without a special mathematical background, then illustrate a method for reproducing numerical calculations with Microsoft Excel. We then show some examples of the patterns generated by the model. Finally, we discuss future prospects for the interdisciplinary field of research involving mathematical approaches in developmental biology

Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells

Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell proliferation and apoptosis, development, immune responses, and pathogenesis. One of the major types of glycans, N-linked glycans, is formed by sequential attachments of monosaccharides to proteins by a limited number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thereby generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigated the large-scale organization of such N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation pathways are extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis. This unique structural property allows the glycan production between modules to be controlled by the upstream region. Although the enzymes act on multiple glycan substrates, indicating cross-talk between modules, the impact of the cross-talk on the module-specific enhancement of glycan synthesis may be confined within a moderate range by transcription-level control. The findings of the present study provide experimentally-testable predictions for glycosylation processes, and may be applicable to therapeutic glycoprotein engineering

Atypical onset of diabetes in a teenage girl: a case report

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Equal Graph Partitioning on Estimated Infection Network as an Effective Epidemic Mitigation Measure

Controlling severe outbreaks remains the most important problem in infectious disease area. With time, this problem will only become more severe as population density in urban centers grows. Social interactions play a very important role in determining how infectious diseases spread, and organization of people along social lines gives rise to non-spatial networks in which the infections spread. Infection networks are different for diseases with different transmission modes, but are likely to be identical or highly similar for diseases that spread the same way. Hence, infection networks estimated from common infections can be useful to contain epidemics of a more severe disease with the same transmission mode. Here we present a proof-of-concept study demonstrating the effectiveness of epidemic mitigation based on such estimated infection networks. We first generate artificial social networks of different sizes and average degrees, but with roughly the same clustering characteristic. We then start SIR epidemics on these networks, censor the simulated incidences, and use them to reconstruct the infection network. We then efficiently fragment the estimated network by removing the smallest number of nodes identified by a graph partitioning algorithm. Finally, we demonstrate the effectiveness of this targeted strategy, by comparing it against traditional untargeted strategies, in slowing down and reducing the size of advancing epidemics

Surgical management of a diabetic calcaneal ulceration and osteomyelitis with a partial calcanectomy and a sural neurofasciocutaneous flap

The treatment of calcaneal osteomyelitis in diabetic patients poses a great challenge to the treating physician and surgeon. The use of a distally based sural neurofasciocutaneous flap after an aggressive debridement of non-viable and poorly vascularized tissue and bone that is combined with a thorough antibiotic regimen provides a great technique for adequate soft tissue coverage of the heel. In this case report, the authors describe the aforementioned flap as a versatile alternative to the use of local or distant muscle flaps for diabetic patients with calcaneal osteomyelitis and concomitant large wounds

Psycho-education programme for temporomandibular disorders: a pilot study

BACKGROUND: Temporomandibular disorders (TMDs) are by far the most predominant condition affecting the temporomandibular joint (TMJ), however many patients have mild self-limiting symptoms and should not be referred for specialist care. The aim of this pilot study was to develop a simple, cost-effective management programme for TMDs using CD-ROM. 41 patients (age 18–70) participated in this study, patients were divided into three groups: the 1st group were involved in an attention placebo CD-ROM (contain anatomical information about the temporomandibular system), the 2nd group received information on CD-ROM designed to increase their control and self efficacy, while the 3rd group received the same programme of the 2nd group added to it an introduction to self-relaxing techniques followed by audio tape of progressive muscle relaxation exercises. Each of the groups was asked to complete a number of questionnaires on the day of initial consultation and six weeks afterwards. RESULTS: The two experimental groups (2nd & 3rd) were equally effective in reducing pain, disability and distress, and both were more effective than the attention placebo group (1st), however the experimental groups appeared to have improved at follow-up relative to the placebo-group in terms of disability, pain and depressed mood. CONCLUSION: This pilot study demonstrates the feasibility and acceptability of the design. A full, randomized, controlled trial is required to confirm the efficacy of the interventions developed here

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale

<p>Abstract</p> <p>Background</p> <p>An important problem in genomics is the automatic inference of groups of homologous proteins from pairwise sequence similarities. Several approaches have been proposed for this task which are "local" in the sense that they assign a protein to a cluster based only on the distances between that protein and the other proteins in the set. It was shown recently that global methods such as spectral clustering have better performance on a wide variety of datasets. However, currently available implementations of spectral clustering methods mostly consist of a few loosely coupled Matlab scripts that assume a fair amount of familiarity with Matlab programming and hence they are inaccessible for large parts of the research community.</p> <p>Results</p> <p>SCPS (Spectral Clustering of Protein Sequences) is an efficient and user-friendly implementation of a spectral method for inferring protein families. The method uses only pairwise sequence similarities, and is therefore practical when only sequence information is available. SCPS was tested on difficult sets of proteins whose relationships were extracted from the SCOP database, and its results were extensively compared with those obtained using other popular protein clustering algorithms such as TribeMCL, hierarchical clustering and connected component analysis. We show that SCPS is able to identify many of the family/superfamily relationships correctly and that the quality of the obtained clusters as indicated by their F-scores is consistently better than all the other methods we compared it with. We also demonstrate the scalability of SCPS by clustering the entire SCOP database (14,183 sequences) and the complete genome of the yeast <it>Saccharomyces cerevisiae </it>(6,690 sequences).</p> <p>Conclusions</p> <p>Besides the spectral method, SCPS also implements connected component analysis and hierarchical clustering, it integrates TribeMCL, it provides different cluster quality tools, it can extract human-readable protein descriptions using GI numbers from NCBI, it interfaces with external tools such as BLAST and Cytoscape, and it can produce publication-quality graphical representations of the clusters obtained, thus constituting a comprehensive and effective tool for practical research in computational biology. Source code and precompiled executables for Windows, Linux and Mac OS X are freely available at <url>http://www.paccanarolab.org/software/scps</url>.</p

PEGylated liposomes associate with Wnt3A protein and expand putative stem cells in human bone marrow populations

Aim: To fabricate PEGylated liposomes which preserve the activity of hydrophobic Wnt3A protein, and to demonstrate their efficacy in promoting expansion of osteoprogenitors from human bone marrow. Methods: PEGylated liposomes composed of several synthetic lipids were tested for their ability to preserve Wnt3A activity in reporter and differentiation assays. Single-molecule microspectroscopy was used to test for direct association of protein with liposomes. Results: Labeled Wnt3A protein directly associated with all tested liposome preparations. However, Wnt3A activity was preserved or enhanced in PEGylated 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes but not in PEGylated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes. PEGylated Wnt3A liposomes associated with skeletal stem cell populations in human bone marrow and promoted osteogenesis. Conclusion: Active Wnt protein-containing PEGylated liposomes may have utility for systemic administration for bone repair.The authors acknowledge funding support from the Medical Research Council, UK (grant number MR/J004103/1), Wessex Medical Research (grant number SO2), UoS Research Management Committee and the Institute for Life Sciences, Southampton. The authors would like to thank the Royal Society for the University Research Fellowship of Steven F Lee (UF120277)

ALMaQUEST. IV. The ALMA-MaNGA QUEnching and STar Formation (ALMaQUEST) Survey

The ALMaQUEST (ALMA-MaNGA QUEnching and STar formation) survey is a program with spatially-resolved $^{12}$CO(1-0) measurements obtained with the Atacama Large Millimeter Array (ALMA) for 46 galaxies selected from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) DR15 optical integral-field spectroscopic survey. The aim of the ALMaQUEST survey is to investigate the dependence of star formation activity on the cold molecular gas content at kpc scales in nearby galaxies. The sample consists of galaxies spanning a wide range in specific star formation rate (sSFR), including starburst (SB), main-sequence (MS), and green valley (GV) galaxies. In this paper, we present the sample selection and characteristics of the ALMA observations, and showcase some of the key results enabled by the combination of spatially-matched stellar populations and gas measurements. Considering the global (aperture-matched) stellar mass, molecular gas mass, and star formation rate of the sample, we find that the sSFR depends on both the star formation efficiency (SFE) and the molecular gas fraction ($f_{\rm H_{2}}$), although the correlation with the latter is slightly weaker. Furthermore, the dependence of sSFR on the molecular gas content (SFE or $f_{\rm H_{2}}$) is stronger than that on either the atomic gas fraction or the molecular-to-atomic gas fraction, albeit with the small HI sample size. On kpc scales, the variations in both SFE and $f_{\rm H_{2}}$ within individual galaxies can be as large as 1-2 dex thereby demonstrating that the availability of spatially-resolved observations is essential to understand the details of both star formation and quenching processes.STFC ER