Comparing circadian dynamics in primary derived stem cells from different sources of human adult tissue

Optimising cell/tissue constructs so that they can be successfully accepted and integrated within a host body is essential in modern tissue engineering. To do this, adult stem cells are frequently utilised, but there are many aspects of their environment in vivo that are not completely understood. There is evidence to suggest that circadian rhythms and daily circadian temporal cues have substantial effects on stem cell activation, cell cycle, and differentiation. It was hypothesised that the circadian rhythm in human adult stem cells differs depending on the source of tissue and that different entraining signals exert differential effects depending on the anatomical source. Dexamethasone and rhythmic mechanical stretch were used to synchronise stem cells derived from the bone marrow, tooth dental pulp, and abdominal subcutaneous adipose tissue, and it was experimentally evidenced that these different stem cells differed in their circadian clock properties in response to different synchronisation mechanisms. The more primitive dental pulp-derived stem cells did not respond as well to the chemical synchronisation but showed temporal clock gene oscillations following rhythmic mechanical stretch, suggesting that incorporating temporal circadian information of different human adult stem cells will have profound implications in optimising tissue engineering approaches and stem cell therapies

A microRNA focus on acne

Acne (syn. acne vulgaris) is a common inflammatory skin disorder associated with puberty and adolescence. Driven by complex interactions between the pilosebaceous unit and Cutibacterium acnes (C. acnes) bacteria, the disease is characterised by comedonal lesions, papules, pustules and nodules that appear predominantly on the face. Acne and sequelae such as scarring and pigment changes affect health-related quality of life negatively. Approvals for nucleic acid therapies (NATs) such as short-interfering RNA (siRNA) drugs and antisense oligonucleotides (ASOs) have surged in recent years, for rare disorders with little or no effective treatments. These advances, along with clinical trials for microRNA (miRNA) modulation in skin contexts, raise the possibility that NATs may have potential for future acne treatment regimens. In this review, we highlight potential miRNA targets for anti-acne therapy. We provide a brief overview of acne pathophysiology and highlight roles of C. acnes. We then focus on recently discovered differential effects of planktonic and biofilm C. acnes on a Toll-like receptor 2 (TLR2) axis spanning miR-146a-5p. We appraise miR-146a-5p in sebocytes before addressing the putative contributions of miR-21-5p, miR-233-3p and miR-150-5p to inflammatory axes in acne. We conclude with translational perspectives and considerations of patient involvement in miRNA-related research for acne

Prediction of lethal and synthetically lethal knock-outs in regulatory networks

The complex interactions involved in regulation of a cell's function are captured by its interaction graph. More often than not, detailed knowledge about enhancing or suppressive regulatory influences and cooperative effects is lacking and merely the presence or absence of directed interactions is known. Here we investigate to which extent such reduced information allows to forecast the effect of a knock-out or a combination of knock-outs. Specifically we ask in how far the lethality of eliminating nodes may be predicted by their network centrality, such as degree and betweenness, without knowing the function of the system. The function is taken as the ability to reproduce a fixed point under a discrete Boolean dynamics. We investigate two types of stochastically generated networks: fully random networks and structures grown with a mechanism of node duplication and subsequent divergence of interactions. On all networks we find that the out-degree is a good predictor of the lethality of a single node knock-out. For knock-outs of node pairs, the fraction of successors shared between the two knocked-out nodes (out-overlap) is a good predictor of synthetic lethality. Out-degree and out-overlap are locally defined and computationally simple centrality measures that provide a predictive power close to the optimal predictor.Comment: published version, 10 pages, 6 figures, 2 tables; supplement at http://www.bioinf.uni-leipzig.de/publications/supplements/11-01

A Time to Heal: MicroRNA and Circadian Dynamics in Cutaneous Wound Repair

Many biological systems have evolved circadian rhythms based on the daily cycles of daylight and darkness on Earth. Such rhythms are synchronised or entrained to 24-hour cycles, predominantly by light, and disruption of the normal circadian rhythms has been linked to elevation of multiple health risks. The skin serves as a protective barrier to prevent microbial infection and maintain homeostasis of the underlying tissue and the whole organism. However, in chronic non-healing wounds such as diabetic foot ulcers, pressures sores, venous and arterial ulcers, a variety of factors conspire to prevent wound repair. On the other hand, keloids and hypertrophic scars arise from over-active repair mechanisms that fail to cease in a timely fashion, leading to excessive production of extracellular matrix components such as such as collagen. Recent years have seen huge increases in our understanding of the functions of microRNAs (miRNA) in wound repair. Concomitantly, there has been growing recognition of miRNA roles in circadian processes, either as regulators or targets of clock activity or direct responders to external circadian stimuli. In addition, miRNAs are now known to function as intercellular signalling mediators through extracellular vesicles. In this review, we explore the intersection of mechanisms by which circadian and miRNA responses interact with each other in relation to wound repair in the skin, using keratinocytes, macrophages and fibroblasts as exemplars. We highlight areas for further investigation to support the development of translational insights to support circadian medicine in the context of these cells

Defining the Properties of an Array of -NH2-Modified Substrates for the Induction of a Mature Osteoblast/Osteocyte Phenotype from a Primary Human Osteoblast Population Using Controlled Nanotopography and Surface Chemistry

Accelerating the integration of a joint replacement or the healing of a bone fracture, particularly a complicated non-union fracture, would improve patient welfare and decrease healthcare costs. Currently, an autologous bone graft is the gold standard method for the treatment of complicated non-union fractures, but it is not always possible to harvest such a graft. A proactive highly inductive so-called smart material approach is pertinent in these cases. In this study, the surface chemistry of a previously approved material with desirable bulk material properties was modified to investigate its potential as an economical and effective alternative. The objective was to create stable synthetic chemical coatings that could guide cells along the osteogenic lineage required to generate mineralised tissue that would induce and accelerate bone healing. Primary human osteoblast-like cells were cultured in vitro for 7, 14 and 28 days on amine-terminated (chain length in the range 3–11) silane-modified glass surfaces with controlled nanotopography, to determine how surface chemistry and nanotopography change osteoblast function. The materials were characterised using atomic force microscopy (AFM), scanning electron microscopy (SEM), water contact angle (WCA) and a novel ninhydrin assay. The cells were analysed using qRT-PCR, von Kossa tinctural staining for mineralisation, and visualised using both transmitted white light and electron microscopy. Bone-like nodules, quantified using microscopy, only formed on the short-chain (chain length 3 and 4) amines after 7 days, as did the up-regulation of sclerostin, suggestive of a more mature osteoblast phenotype. In this paper, we report more rapid nodule formation than has previously been observed, without the addition of exogenous factors in the culture medium. This suggests that the coating would improve the integration of implants with bone or be the basis of a smart biomaterial that would accelerate the bone regeneration process

Magnesium hydroxide addition reduces aqueous carbon dioxide in wastewater discharged to the ocean

Ocean alkalinity enhancement (OAE) reduces the concentration of dissolved carbon dioxide (CO2) in seawater, leading to atmospheric carbon dioxide removal (CDR). Here we report laboratory experiments and a field-trial of alkalinity enhancement through addition of magnesium hydroxide to wastewater and its subsequent discharge to the coastal ocean. In wastewater, a 10% increase of average alkalinity (+0.56 mmol/kg) led to a 74% reduction in aqueous CO2 (−0.41 mmol/kg) and pH increase of 0.4 units to 7.78 (efficiency 0.73 molCO2/mol alkalinity). The alkalinization signal was limited to within a few metres of the ocean discharge, evident as 27.2 μatm reduction in CO2 partial pressure and 0.017 unit pH increase, and was consistent with rapid dilution of the alkali-treated wastewater. While this proof of concept field trial did not achieve CDR due to its small scale, it demonstrated the potential of magnesium hydroxide addition to wastewater as a CDR solution

Selecting cash management models from a multiobjective perspective

[EN] This paper addresses the problem of selecting cash management models under different operating conditions from a multiobjective perspective considering not only cost but also risk. A number of models have been proposed to optimize corporate cash management policies. The impact on model performance of different operating conditions becomes an important issue. Here, we provide a range of visual and quantitative tools imported from Receiver Operating Characteristic (ROC) analysis. More precisely, we show the utility of ROC analysis from a triple perspective as a tool for: (1) showing model performance; (2) choosingmodels; and (3) assessing the impact of operating conditions on model performance. We illustrate the selection of cash management models by means of a numerical example.Work partially funded by projects Collectiveware TIN2015-66863-C2-1-R (MINECO/FEDER) and 2014 SGR 118.Salas-Molina, F.; Rodríguez-Aguilar, JA.; Díaz-García, P. (2018). Selecting cash management models from a multiobjective perspective. Annals of Operations Research. 261(1-2):275-288. https://doi.org/10.1007/s10479-017-2634-9S2752882611-2Ballestero, E. (2007). Compromise programming: A utility-based linear-quadratic composite metric from the trade-off between achievement and balanced (non-corner) solutions. European Journal of Operational Research, 182(3), 1369–1382.Ballestero, E., & Romero, C. (1998). Multiple criteria decision making and its applications to economic problems. Berlin: Springer.Bi, J., & Bennett, K. P. (2003). Regression error characteristic curves. In Proceedings of the 20th international conference on machine learning (ICML-03), pp. 43–50.Bradley, A. P. (1997). The use of the area under the roc curve in the evaluation of machine learning algorithms. Pattern Recognition, 30(7), 1145–1159.da Costa Moraes, M. B., Nagano, M. S., & Sobreiro, V. A. (2015). Stochastic cash flow management models: A literature review since the 1980s. In Decision models in engineering and management (pp. 11–28). New York: Springer.Doumpos, M., & Zopounidis, C. (2007). Model combination for credit risk assessment: A stacked generalization approach. Annals of Operations Research, 151(1), 289–306.Drummond, C., & Holte, R. C. (2000). Explicitly representing expected cost: An alternative to roc representation. In Proceedings of the sixth ACM SIGKDD international conference on Knowledge discovery and data mining (pp. 98–207). New York: ACM.Drummond, C., & Holte, R. C. (2006). Cost curves: An improved method for visualizing classifier performance. Machine Learning, 65(1), 95–130.Elkan, C. (2001). The foundations of cost-sensitive learning. In International joint conference on artificial intelligence (Vol. 17, pp. 973–978). Lawrence Erlbaum associates Ltd.Fawcett, T. (2006). An introduction to roc analysis. Pattern Recognition Letters, 27(8), 861–874.Flach, P. A. (2003). The geometry of roc space: understanding machine learning metrics through roc isometrics. In Proceedings of the 20th international conference on machine learning (ICML-03), pp. 194–201.Garcia-Bernabeu, A., Benito, A., Bravo, M., & Pla-Santamaria, D. (2016). Photovoltaic power plants: a multicriteria approach to investment decisions and a case study in western spain. Annals of Operations Research, 245(1–2), 163–175.Glasserman, P. (2003). Monte Carlo methods in financial engineering (Vol. 53). New York: Springer.Gregory, G. (1976). Cash flow models: a review. Omega, 4(6), 643–656.Hernández-Orallo, J. (2013). Roc curves for regression. Pattern Recognition, 46(12), 3395–3411.Hernández-Orallo, J., Flach, P., & Ferri, C. (2013). Roc curves in cost space. Machine Learning, 93(1), 71–91.Hernández-Orallo, J., Lachiche, N., & Martınez-Usó, A. (2014). Predictive models for multidimensional data when the resolution context changes. In Workshop on learning over multiple contexts at ECML, volume 2014.Metz, C. E. (1978). Basic principles of roc analysis. In Seminars in nuclear medicine (Vol. 8, pp. 283–298). Amsterdam: Elsevier.Miettinen, K. (2012). Nonlinear multiobjective optimization (Vol. 12). Berlin: Springer.Ringuest, J. L. (2012). Multiobjective optimization: Behavioral and computational considerations. Berlin: Springer.Ross, S. A., Westerfield, R., & Jordan, B. D. (2002). Fundamentals of corporate finance (sixth ed.). New York: McGraw-Hill.Salas-Molina, F., Pla-Santamaria, D., & Rodriguez-Aguilar, J. A. (2016). A multi-objective approach to the cash management problem. Annals of Operations Research, pp. 1–15.Srinivasan, V., & Kim, Y. H. (1986). Deterministic cash flow management: State of the art and research directions. Omega, 14(2), 145–166.Steuer, R. E., Qi, Y., & Hirschberger, M. (2007). Suitable-portfolio investors, nondominated frontier sensitivity, and the effect of multiple objectives on standard portfolio selection. Annals of Operations Research, 152(1), 297–317.Stone, B. K. (1972). The use of forecasts and smoothing in control limit models for cash management. Financial Management, 1(1), 72.Torgo, L. (2005). Regression error characteristic surfaces. In Proceedings of the eleventh ACM SIGKDD international conference on Knowledge discovery in data mining (pp. 697–702). ACM.Yu, P.-L. (1985). Multiple criteria decision making: concepts, techniques and extensions. New York: Plenum Press.Zeleny, M. (1982). Multiple criteria decision making. New York: McGraw-Hill

Practice Nurses' views of their role in the management of Chronic Fatigue Syndrome/Myalagic Encephalitis: a qualitative study

<p>Abstract</p> <p>Background</p> <p>NICE guidelines suggest that patients with Chronic Fatigue Syndrome/Myalgic Encephalitis (CFS/ME) should be managed in Primary Care. Practice Nurses are increasingly being involved in the management of long-term conditions, so are likely to also have a growing role in managing CFS/ME. However their attitudes to, and experiences of patients with CFS/ME and its management must be explored to understand what barriers may exist in developing their role for this group of patients. The aim of this study was to explore Practice Nurses' understanding and beliefs about CFS/ME and its management.</p> <p>Methods</p> <p>Semi-structured interviews with 29 Practice Nurses. Interviews were transcribed verbatim and an iterative approach used to develop themes from the dataset.</p> <p>Results</p> <p>Practice nurses had limited understanding about CFS/ME which had been largely gained through contact with patients, friends, personal experiences and the media rather than formal training. They had difficulty seeing CFS/ME as a long term condition. They did identify a potential role they could have in management of CFS/ME but devalued their own skills in psychological intervention, and suggested counselling would be an appropriate therapeutic option. They recognised a need for further training and on going supervision from both medical and psychological colleagues. Some viewed the condition as contentious and held pejorative views about CFS/ME. Such scepticism and negative attitudes will be a significant barrier to the management of patients with CFS/ME in primary care.</p> <p>Conclusion</p> <p>The current role of Practice Nurses in the ongoing management of patients with CFS/ME is limited. Practice Nurses have little understanding of the evidence-base for treatment of CFS/ME, particularly psychological therapies, describing management options in terms of advice giving, self-help or counselling. Practice Nurses largely welcomed the potential development of their role in this area, but identified barriers and training needs which must be addressed to enable them to feel confident managing of patients with this condition. Training must begin by addressing negative attitudes to patients with CFS/ME.</p

Cyclic AMP Control Measured in Two Compartments in HEK293 Cells: Phosphodiesterase KM Is More Important than Phosphodiesterase Localization

The intracellular second messenger cyclic AMP (cAMP) is degraded by phosphodiesterases (PDE). The knowledge of individual families and subtypes of PDEs is considerable, but how the different PDEs collaborate in the cell to control a cAMP signal is still not fully understood. In order to investigate compartmentalized cAMP signaling, we have generated a membrane-targeted variant of the cAMP Bioluminiscence Resonance Energy Transfer (BRET) sensor CAMYEL and have compared intracellular cAMP measurements with it to measurements with the cytosolic BRET sensor CAMYEL in HEK293 cells. With these sensors we observed a slightly higher cAMP response to adenylyl cyclase activation at the plasma membrane compared to the cytosol, which is in accordance with earlier results from Fluorescence Resonance Energy Transfer (FRET) sensors. We have analyzed PDE activity in fractionated lysates from HEK293 cells using selective PDE inhibitors and have identified PDE3 and PDE10A as the major membrane-bound PDEs and PDE4 as the major cytosolic PDE. Inhibition of membrane-bound or cytosolic PDEs can potentiate the cAMP response to adenylyl cyclase activation, but we see no significant difference between the potentiation of the cAMP response at the plasma membrane and in cytosol when membrane-bound and cytosolic PDEs are inhibited. When different levels of stimulation were tested, we found that PDEs 3 and 10 are mainly responsible for cAMP degradation at low intracellular cAMP concentrations, whereas PDE4 is more important for control of cAMP at higher concentrations