Flow Residence Time and Regions of Intraluminal Thrombus Deposition in Intracranial Aneurysms

Thrombus formation in intracranial aneurysms, while sometimes stabilizing lesion growth, can present additional risk of thrombo-embolism. The role of hemodynamics in the progression of aneurysmal disease can be elucidated by patient-specific computational modeling. In our previous work, patient-specific computational fluid dynamics (CFD) models were constructed from MRI data for three patients who had fusiform basilar aneurysms that were thrombus-free and then proceeded to develop intraluminal thrombus. In this study, we investigated the effect of increased flow residence time (RT) by modeling passive scalar advection in the same aneurysmal geometries. Non-Newtonian pulsatile flow simulations were carried out in base-line geometries and a new postprocessing technique, referred to as “virtual ink” and based on the passive scalar distribution maps, was used to visualize the flow and estimate the flow RT. The virtual ink technique clearly depicted regions of flow separation. The flow RT at different locations adjacent to aneurysmal walls was calculated as the time the virtual ink scalar remained above a threshold value. The RT values obtained in different areas were then correlated with the location of intra-aneurysmal thrombus observed at a follow-up MR study. For each patient, the wall shear stress (WSS) distribution was also obtained from CFD simulations and correlated with thrombus location. The correlation analysis determined a significant relationship between regions where CFD predicted either an increased RT or low WSS and the regions where thrombus deposition was observed to occur in vivo. A model including both low WSS and increased RT predicted thrombus-prone regions significantly better than the models with RT or WSS alone

“Bibliostory—Educational Comic Stories.” A Social Constructivist Approach to Media and Information Literacy Education for Children and Adolescents

Our paper presents a theoretical background for a Polish comic book “Bibliostory—educational comic stories” (Pl. Bibliostory—edukacyjne historie komiksowe). The comic targets children between 9 and 12 years of age and youths from 13 to 16 years of age. Each story illustrates one issue, such as information searching, organization of information, plagiarism, and information problem solving strategy. Bibliostory is based on two constructivist pedagogical concepts: the zone of proximal development (ZPD) and case-based learning/teaching. These concepts, on application level, are first of all associated with designing educational situations and relationships between teachers and students (educators and learners). The aim of our paper is to present the possibilities of application of these concepts in the educational comic books. We describe the general assumptions of two concepts, then we focus on elements applied in Bibliostory project. We also provide a review of literature on the educational potential of comic books.Zuza Wiorogórska’s work was carried out during her stay as the visiting scholar at the University of California, Berkeley, thanks to a scholarship from the Kosciuszko Foundation. Ewa Rozkosz’s work was carried out thanks to the grant awarded by the Faculty of Education of the University of Lower Silesia for the project “Społeczno-kulturowe podejście w projektowaniu materiałów edukacyjnych na potrzeby edukacji medialnej I inforamacyjnej dzieci i młodzieży na przykładzie »Bibliostory«” (nr 05/ WGW/dok/2016)

Visualization of Early Events in Acetic Acid Denaturation of HIV-1 Protease: A Molecular Dynamics Study

Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR) was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH) solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH reveal that the PR denaturation begins by separation of dimer into intact monomers and it is only after this separation that the monomer units start denaturing. The denaturation of the monomers is flagged off by the loss of crucial interactions between the α-helix at C-terminal and surrounding β-strands. This causes the structure to transit from the equilibrium dynamics to random non-equilibrating dynamics. Residence time calculations indicate that denaturation occurs via direct interaction of the acetic acid molecules with certain regions of the protein in 9 M AcOH. All these observations have helped to decipher a picture of the early events in acetic acid denaturation of PR and have illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function

Scaling behaviour for the water transport in nanoconfined geometries

The transport of water in nanoconfined geometries is different from bulk phase and has tremendous implications in nanotechnology and biotechnology. Here molecular dynamics is used to compute the self-diffusion coefficient D of water within nanopores, around nanoparticles, carbon nanotubes and proteins. For almost 60 different cases, D is found to scale linearly with the sole parameter theta as D(theta)=DB[1+(DC/DB-1)theta], with DB and DC the bulk and totally confined diffusion of water, respectively. The parameter theta is primarily influenced by geometry and represents the ratio between the confined and total water volumes. The D(theta) relationship is interpreted within the thermodynamics of supercooled water. As an example, such relationship is shown to accurately predict the relaxometric response of contrast agents for magnetic resonance imaging. The D(theta) relationship can help in interpreting the transport of water molecules under nanoconfined conditions and tailoring nanostructures with precise modulation of water mobility

How Sensory Experiences Affect Adolescents with an Autistic Spectrum Condition within the Classroom

Sensory processing difficulties are consistently reported amongst individuals with an autistic spectrum condition (ASC); these have a significant impact on daily functioning. Evidence in this area comes from observer reports and first-hand accounts; both have limitations. The current study used the Adolescent/Adult Sensory Profile (AASP; Brown and Dunn in The Adolescent/Adult Sensory Profile: self questionnaire. Pearson, 2002a), and a qualitative questionnaire to investigate sensory issues in school children with ASC. The AASP found that the participants’ mean scores were outside normal parameters. Participants reported difficulties in at least one sensory domain, with hearing affecting them the most. Content analysis revealed sensory sensitivity to affect the participant’s learning and that sensory experiences were largely negative. Results suggest that schools need to create sensory profiles for each individual with ASC

Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites

Apicomplexan parasites rely on a novel form of actin-based motility called gliding, which depends on parasite actin polymerization, to migrate through their hosts and invade cells. However, parasite actins are divergent both in sequence and function and only form short, unstable filaments in contrast to the stability of conventional actin filaments. The molecular basis for parasite actin filament instability and its relationship to gliding motility remain unresolved. We demonstrate that recombinant Toxoplasma (TgACTI) and Plasmodium (PfACTI and PfACTII) actins polymerized into very short filaments in vitro but were induced to form long, stable filaments by addition of equimolar levels of phalloidin. Parasite actins contain a conserved phalloidin-binding site as determined by molecular modeling and computational docking, yet vary in several residues that are predicted to impact filament stability. In particular, two residues were identified that form intermolecular contacts between different protomers in conventional actin filaments and these residues showed non-conservative differences in apicomplexan parasites. Substitution of divergent residues found in TgACTI with those from mammalian actin resulted in formation of longer, more stable filaments in vitro. Expression of these stabilized actins in T. gondii increased sensitivity to the actin-stabilizing compound jasplakinolide and disrupted normal gliding motility in the absence of treatment. These results identify the molecular basis for short, dynamic filaments in apicomplexan parasites and demonstrate that inherent instability of parasite actin filaments is a critical adaptation for gliding motility

The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures

Repeat-proteins are made up of near repetitions of 20– to 40–amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi–one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete “domain” (the stability and cooperativity of the repeating array) can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (ΔGwater) and the cooperativity of denaturation (m-value), which do not ordinarily apply for globular proteins. We show how the parameters for the “coarse-grained” description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR) repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are “poised” at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions