Deconstructing wound healing: in vitro models and factors affecting stromal tissue repair

Damage to our tissues occurs daily and must be repaired by the body in a timely manner in order to prevent infection and restore tissue integrity. Many cell types are involved in the healing process, but it is the cells of the stroma that are largely responsible for rebuilding fibrous tissue, which provides structure and support for all other cell types during healing. This dissertation focuses on stromal tissue repair, the rebuilding of fibrous tissue by fibroblasts following injury. Specifically, I focus on 1) models to study wound healing in vitro, and the specific biological processes of healing that each model captures, 2) the response of engineered stromal microtissues to different methods of injury, namely laceration and laser ablation, and the subsequent clearance and rebuilding of the extracellular matrix by fibroblasts, and 3) how different types of stromal cells and extracellular matrix proteins contribute to tissue repair in vitro

On the analogy between streamlined magnetic and solid obstacles

Analogies are elaborated in the qualitative description of two systems: the magnetohydrodynamic (MHD) flow moving through a region where an external local magnetic field (magnetic obstacle) is applied, and the ordinary hydrodynamic flow around a solid obstacle. The former problem is of interest both practically and theoretically, and the latter one is a classical problem being well understood in ordinary hydrodynamics. The first analogy is the formation in the MHD flow of an impenetrable region -- core of the magnetic obstacle -- as the interaction parameter $N$, i.e. strength of the applied magnetic field, increases significantly. The core of the magnetic obstacle is streamlined both by the upstream flow and by the induced cross stream electric currents, like a foreign insulated insertion placed inside the ordinary hydrodynamic flow. In the core, closed streamlines of the mass flow resemble contour lines of electric potential, while closed streamlines of the electric current resemble contour lines of pressure. The second analogy is the breaking away of attached vortices from the recirculation pattern produced by the magnetic obstacle when the Reynolds number $Re$, i.e. velocity of the upstream flow, is larger than a critical value. This breaking away of vortices from the magnetic obstacle is similar to that occurring past a real solid obstacle. Depending on the inlet and/or initial conditions, the observed vortex shedding can be either symmetric or asymmetric.Comment: minor changes, accepted for PoF, 26 pages, 7 figure

KESTABILAN SOLUSI NUMERIK SISTEM BERDERAJAT KEBEBASAN TUNGGAL AKIBAT GEMPA DENGAN METODE NEWMARK (Studi Kasus: Menghitung Respons Bangunan Baja Satu Tingkat)

Metode Newmark merupakan salah satu prosedur numerik yang biasa digunakan untuk menganalisa respon struktur terhadap beban gempa. Metode ini mempunyai dua parameter penting yaitu β dan , yang menetapkan variasi dari percepatan terhadap selang waktu dan menentukan karakteristik kestabilan dan akurasi dari metode tersebut. Apabila dipakai nilai γ = dan β = , artinya digunakan prinsip metode percepatan rata-rata. Sedangkan apabila dipakai nilai γ = dan β = , maka digunakan prinsip metode percepatan linear. Dan seperti metode numerik yang lain pada umumnya, kedua prinsip ini masing-masing juga mempunyai tingkat kestabilan dan akurasi yang berbeda-beda. Kestabilan dan ketelitian/akurasi proses numerik akan terjaga apabila dipakai nilai selang waktu (Δt) yang relatif kecil. Tujuan dari penelitian ini adalah mencari seberapa kecil nilai Δt yang harus digunakan untuk mendapatkan respon struktur yang stabil dan akurat. Struktur dimodelkan menjadi sistem berderajat kebebasan tunggal (SDOF) dan dikenakan beban impuls setengah gelombang sinus. Perhitungan respons menggunakan kedua prinsip di atas, masing-masing dilakukan variasi untuk nilai Δt dan periode (T). Prosedur ini dilakukan dengan bantuan program MS Excel. Hasil perhitungan menunjukkan untuk rata-rata prosentase perbedaan nilai hasil simpangan ≤ 1 %, kurang lebih diperlukan rata-rata nilai Δt = 0,007 T bila menggunakan prinsip percepatan linear, dan Δt = 0,005 T bila menggunakan prinsip percepatan rata-rata. Dengan kata lain, metode percepatan linear lebih efisien dalam mendapatkan hasil yang akurat dibandingkan metode percepatan rata-rata. Sebaliknya, metode percepatan linear mempunyai syarat nilai Δt tertentu agar proses numerik dapat dikatakan stabil (conditionally stable). Ketika digunakan Δt > 0,551 T respons yang dihasilkan oleh metode percepatan linear semakin lama semakin besar seiring pertambahan waktu meskipun adanya efek redaman dan ciri khas dari beban impuls dimana respons yang dihasilkan seharusnya semakin lama semakin kecil. Metode ini dapat dikatakan stabil ketika digunakan Δt < 0,551 T. Sedangkan metode percepatan rata-rata tetap stabil untuk berapa pun nilai Δt yang digunakan. Kata kunci : Metode Newmark, SDOF, kestabilan dan akurasi numeri

Core of the Magnetic Obstacle

Rich recirculation patterns have been recently discovered in the electrically conducting flow subject to a local external magnetic termed "the magnetic obstacle" [Phys. Rev. Lett. 98 (2007), 144504]. This paper continues the study of magnetic obstacles and sheds new light on the core of the magnetic obstacle that develops between magnetic poles when the intensity of the external field is very large. A series of both 3D and 2D numerical simulations have been carried out, through which it is shown that the core of the magnetic obstacle is streamlined both by the upstream flow and by the induced cross stream electric currents, like a foreign insulated insertion placed inside the ordinary hydrodynamic flow. The closed streamlines of the mass flow resemble contour lines of electric potential, while closed streamlines of the electric current resemble contour lines of pressure. New recirculation patterns not reported before are found in the series of 2D simulations. These are composed of many (even number) vortices aligned along the spanwise line crossing the magnetic gap. The intensities of these vortices are shown to vanish toward to the center of the magnetic gap, confirming the general conclusion of 3D simulations that the core of the magnetic obstacle is frozen. The implications of these findings for the case of turbulent flow are discussed briefly.Comment: 14 pages, 9 figures, submitted to Journal of Turbulenc

An adaptive numerical method for the Vlasov equation based on a multiresolution analysis.

International audienceIn this paper, we present very first results for the adaptive solution on a grid of the phase space of the Vlasov equation arising in particles accelarator and plasma physics. The numerical algorithm is based on a semi-Lagrangian method while adaptivity is obtained using multiresolution analysis

Kestabilan Solusi Numerik Sistem Berderajat Kebebasan Tunggal Akibat Gempa Dengan Metode Newmark (Studi Kasus: Menghitung Respons Bangunan Baja Satu Tingkat)

Metode Newmark merupakan salah satu prosedur numerik yang biasa digunakan untuk menganalisa respon struktur terhadap beban gempa. Metode ini mempunyai dua parameter penting yaitu β dan , yang menetapkan variasi dari percepatan terhadap selang waktu dan menentukan karakteristik kestabilan dan akurasi dari metode tersebut. Apabila dipakai nilai γ = dan β = , artinya digunakan prinsip metode percepatan rata-rata. Sedangkan apabila dipakai nilai γ = dan β = , maka digunakan prinsip metode percepatan linear. Dan seperti metode numerik yang lain pada umumnya, kedua prinsip ini masing-masing juga mempunyai tingkat kestabilan dan akurasi yang berbeda-beda. Kestabilan dan ketelitian/akurasi proses numerik akan terjaga apabila dipakai nilai selang waktu (Δt) yang relatif kecil. Tujuan dari penelitian ini adalah mencari seberapa kecil nilai Δt yang harus digunakan untuk mendapatkan respon struktur yang stabil dan akurat. Struktur dimodelkan menjadi sistem berderajat kebebasan tunggal (SDOF) dan dikenakan beban impuls setengah gelombang sinus. Perhitungan respons menggunakan kedua prinsip di atas, masing-masing dilakukan variasi untuk nilai Δt dan periode (T). Prosedur ini dilakukan dengan bantuan program MS Excel. Hasil perhitungan menunjukkan untuk rata-rata prosentase perbedaan nilai hasil simpangan ≤ 1 %, kurang lebih diperlukan rata-rata nilai Δt = 0,007 T bila menggunakan prinsip percepatan linear, dan Δt = 0,005 T bila menggunakan prinsip percepatan rata-rata. Dengan kata lain, metode percepatan linear lebih efisien dalam mendapatkan hasil yang akurat dibandingkan metode percepatan rata-rata. Sebaliknya, metode percepatan linear mempunyai syarat nilai Δt tertentu agar proses numerik dapat dikatakan stabil (conditionally stable). Ketika digunakan Δt > 0,551 T respons yang dihasilkan oleh metode percepatan linear semakin lama semakin besar seiring pertambahan waktu meskipun adanya efek redaman dan ciri khas dari beban impuls dimana respons yang dihasilkan seharusnya semakin lama semakin kecil. Metode ini dapat dikatakan stabil ketika digunakan Δt < 0,551 T. Sedangkan metode percepatan rata-rata tetap stabil untuk berapa pun nilai Δt yang digunakan

Interventionsansätze zur Ehescheidung: Systematisierung, Evaluation, Interventionsziele: Einführung in die Thematik

Im folgenden Beitrag wird zum einen der Versuch der Systematisierung verschiedener Interventionsansätze im Bereich Trennung/Scheidung unternommen. Zum anderen befassen sich die Autoren mit dem Stand der Evaluation und den übergreifenden Interventionszielen. (SH

Upside-down fluxes Down Under: CO2 net sink in winter and net source in summer in a temperate evergreen broadleaf forest

Predicting the seasonal dynamics of ecosystem carbon fluxes is challenging in broadleaved evergreen forests because of their moderate climates and subtle changes in canopy phenology. We assessed the climatic and biotic drivers of the seasonality of net ecosystem–atmosphere CO2 exchange (NEE) of a eucalyptus-dominated forest near Sydney, Australia, using the eddy covariance method. The climate is characterised by a mean annual precipitation of 800mm and a mean annual temperature of 18°C, hot summers and mild winters, with highly variable precipitation. In the 4-year study, the ecosystem was a sink each year (−225gCm−2yr−1 on average, with a standard deviation of 108gCm−2yr−1); inter-annual variations were not related to meteorological conditions. Daily net C uptake was always detected during the cooler, drier winter months (June through August), while net C loss occurred during the warmer, wetter summer months (December through February). Gross primary productivity (GPP) seasonality was low, despite longer days with higher light intensity in summer, because vapour pressure deficit (D) and air temperature (Ta) restricted surface conductance during summer while winter temperatures were still high enough to support photosynthesis. Maximum GPP during ideal environmental conditions was significantly correlated with remotely sensed enhanced vegetation index (EVI; r2 = 0.46) and with canopy leaf area index (LAI; r2= 0.29), which increased rapidly after mid-summer rainfall events. Ecosystem respiration (ER) was highest during summer in wet soils and lowest during winter months. ER had larger seasonal amplitude compared to GPP, and therefore drove the seasonal variation of NEE. Because summer carbon uptake may become increasingly limited by atmospheric demand and high temperature, and because ecosystem respiration could be enhanced by rising temperatures, our results suggest the potential for large-scale seasonal shifts in NEE in sclerophyll vegetation under climate change.The Australian Education Investment Fund, Australian Terrestrial Ecosystem Research Network, Australian Research Council and Hawkesbury Institute for the Environment at Western Sydney University supported this work. We thank Jason Beringer, Helen Cleugh, Ray Leuning and Eva van Gorsel for advice and support. Senani Karunaratne provided soil classification details

Arabidopsis Topless-related 1 mitigates physiological damage and growth penalties of induced immunity

Transcriptional corepressors of the Topless (TPL) family regulate plant hormone and immunity signaling. The lack of a genome-wide profile of their chromatin associations limits understanding of the TPL family roles in transcriptional regulation. Chromatin immunoprecipitation with sequencing (ChIP-Seq) was performed on Arabidopsis thaliana lines expressing GFP-tagged Topless-related 1 (TPR1-GFP) with and without constitutive immunity via Enhanced Disease Susceptibility 1 (EDS1). RNA-Seq profiling of the TPR1-GFP lines and pathogen-infected tpl/tpr mutants, combined with measuring immunity, growth, and physiological parameters was employed to investigate TPL/TPR roles in immunity and defense homeostasis. TPR1 was enriched at promoter regions of c. 1400 genes and c. 10% of the detected binding required EDS1 immunity signaling. In a tpr1 tpl tpr4 (t3) mutant, resistance to bacteria was slightly compromised, and defense-related transcriptional reprogramming was weakly reduced or enhanced, respectively, at early (< 1 h) and late 24 h stages of bacterial infection. The t3 plants challenged with bacteria or pathogen-associated molecular pattern nlp24 displayed photosystem II dysfunctions. Also, t3 plants were hypersensitive to phytocytokine pep1 at the level of root growth inhibition. Transgenic expression of TPR1 rescued these t3 physiological defects. We propose that TPR1 and TPL family proteins function in Arabidopsis to reduce detrimental effects associated with activated transcriptional immunity

Numerical Computations with H(div)-Finite Elements for the Brinkman Problem

The H(div)-conforming approach for the Brinkman equation is studied numerically, verifying the theoretical a priori and a posteriori analysis in previous work of the authors. Furthermore, the results are extended to cover a non-constant permeability. A hybridization technique for the problem is presented, complete with a convergence analysis and numerical verification. Finally, the numerical convergence studies are complemented with numerical examples of applications to domain decomposition and adaptive mesh refinement.Comment: Minor clarifications, added references. Reordering of some figures. To appear in Computational Geosciences, final article available at http://www.springerlink.co