Semi-Automatic, Inline and Collaborative Web Page Code Curations

Software developers spend about a quarter of their workday using the web to fulfill various information needs. Searching for relevant information online can be time-consuming, yet acquired information is rarely systematically persisted for later reference. In this work, we introduce SALI, an approach for semi-automated linking web pages to source code locations inline with the source code. SALI helps developers naturally capture high-quality, explicit links between web pages and specific source code locations by suggesting links for curation within the IDE. Through two laboratory studies, we examined the developer’s ability to both curate and consume links between web pages and specific source code locations while performing software development tasks. The studies were performed with 20 subjects working on realistic software change tasks from widely-used open-source projects. Results showed that developers continuously and concisely curate web pages at meaningful locations in the code with little effort. Additionally, we showed that other developers could use these curations while performing new and different change tasks to speed up relevant information gathering within unfamiliar codebases by a factor of 2.4

An Accelerated Conjugate Gradient Algorithm to Compute Low-Lying Eigenvalues --- a Study for the Dirac Operator in SU(2) Lattice QCD

The low-lying eigenvalues of a (sparse) hermitian matrix can be computed with controlled numerical errors by a conjugate gradient (CG) method. This CG algorithm is accelerated by alternating it with exact diagonalisations in the subspace spanned by the numerically computed eigenvectors. We study this combined algorithm in case of the Dirac operator with (dynamical) Wilson fermions in four-dimensional \SUtwo gauge fields. The algorithm is numerically very stable and can be parallelized in an efficient way. On lattices of sizes $4^4-16^4$ an acceleration of the pure CG method by a factor of~$4-8$ is found.Comment: 25 pages, uuencoded tar-compressed .ps-fil

Nanoparticle–cell interaction: a cell mechanics perspective

Progress in the field of nanoparticles has enabled the rapid development of multiple products and technologies; however, some nanoparticles can pose both a threat to the environment and human health. To enable their safe implementation, a comprehensive knowledge of nanoparticles and their biological interactions is needed. In vitro and in vivo toxicity tests have been considered the gold standard to evaluate nanoparticle safety, but it is becoming necessary to understand the impact of nanosystems on cell mechanics. Here, the interaction between particles and cells, from the point of view of cell mechanics (i.e., bionanomechanics), is highlighted and put in perspective. Specifically, the ability of intracellular and extracellular nanoparticles to impair cell adhesion, cytoskeletal organization, stiffness, and migration are discussed. Furthermore, the development of cutting-edge, nanotechnology-driven tools based on the use of particles allowing the determination of cell mechanics is emphasized. These include traction force microscopy, colloidal probe atomic force microscopy, optical tweezers, magnetic manipulation, and particle tracking microrheology

Connexin43 ablation in foetal atrial myocytes decreases electrical coupling, partner connexins, and sodium current

Aims Remodelling and regional gradients in expression of connexins (Cx) are thought to contribute to atrial electrical dysfunction and atrial fibrillation. We assessed the effect of interaction between Cx43, Cx40, and Cx45 on atrial cell-to-cell coupling and inward Na current (INa) in engineered pairs of atrial myocytes derived from wild-type mice (Cx43+/+) and mice with genetic ablation of Cx43 (Cx43−/−). Methods and results Cell pairs were engineered by microcontact printing from atrial Cx43+/+ and Cx43−/− murine myocytes (1 day before birth, 3-5 days in culture). Dual and single voltage clamp were used to measure intercellular electrical conductance, gj, and its dependence on transjunctional voltage, Vj, single gap junction channel conductances, and INa. 3D reconstructions of Cx43, Cx40, and Cx45 immunosignals in gap junctions were made from confocal slices. Full genetic Cx43 ablation produced a decrease in immunosignals of Cx40 to 62 ± 10% (mean ± SE; n= 17) and Cx45 to 66 ± 8% (n= 16). Gj decreased from 80 ± 9 nS (Cx43+/+, n= 17) to 24 ± 2 nS (Cx43−/−, n= 35). Single channel analysis showed a shift in the main peak of the channel histogram from 49 ± 1.7 nS (Cx43+/+) to 67 ± 1.8 nS (Cx43−/−) with a second minor peak appearing at 27 ± 1.5 pS. The dependence of gj on Vj decreased with Cx43 ablation. Importantly, peak INa decreased from −350 ± 44 pA/pF (Cx43+/+) to −154 ± 28 pA/pF (Cx43−/−). Conclusions The dependence of Cx40, Cx45, and INa on Cx43 expression indicates a complex interaction between connexins and INa in the atrial intercalated discs that is likely to be of relevance for arrhythmogenesi

Dynamic and biocompatible thermo-responsive magnetic hydrogels that respond to an alternating magnetic field

Magnetic thermo-responsive hydrogels are a new class of materials that have recently attracted interest in biomedicine due to their ability to change phase upon magnetic stimulation. They have been used for drug release, magnetic hyperthermia treatment, and can potentially be engineered as stimuli-responsive substrates for cell mechanobiology. In this regard, we propose a series of magnetic thermo-responsive nanocomposite substrates that undergo cyclical swelling and de-swelling phases when actuated by an alternating magnetic field in aqueous environment. The synthetized substrates are obtained with a facile and reproducible method from poly-N- isopropylacrylamide and superparamagnetic iron oxide nanoparticles. Their conformation and the temperature-related, magnetic, and biological behaviors were characterized via scanning electron microscopy, swelling ratio analysis, vibrating sample magnetometry, alternating magnetic field stimulation and indirect viability assays. The nanocomposites showed no cytotoxicity with fibroblast cells, and exhibited swelling/de-swelling behavior near physiological temperatures (around 34 °C). Therefore these magnetic thermo-responsive hydrogels are promising materials as stimuli-responsive substrates allowing the study of cell-behavior by changing the hydrogel properties in situ

Taylor dispersion of inorganic nanoparticles and comparison to dynamic light scattering and transmission electron microscopy

Taylor dispersion analysis (TDA) is an analytical method that has so far mainly been utilized to determine the diffusion coefficient of small molecules, and proteins. Due to increasing interest in nanoscience, some research has been done on the applicability of TDA towards characterizing nanoparticles. This work aims to expand this knowledge and give insight into the range for which TDA can be used for nanoparticle characterization, focusing on various materials and sizes. The TDA setup shown in this work was successful in characterizing all engineered metallic, non-metallic nanoparticles, and proteins tested in this work. Results were compared to dynamic light scattering and electron microscopy, and were in good agreement with both methods. Taking into consideration the wide range of nanoparticle sizes that can be characterized, the minimal sample preparation, and sample volume, required and the simplicity of the method, TDA can be considered as a valuable technique for nanoparticle characterization