Limitation of finite element analysis of poroelastic behavior of biological tissues undergoing rapid loading

The finite element method is used in biomechanics to provide numerical solutions to simulations of structures having complex geometry and spatially differing material properties. Time-varying load deformation behaviors can result from solid viscoelasticity as well as viscous fluid flow through porous materials. Finite element poroelastic analysis of rapidly loaded slow-draining materials may be ill-conditioned, but this problem is not widely known in the biomechanics field. It appears as instabilities in the calculation of interstitial fluid pressures, especially near boundaries and between different materials. Accurate solutions can require impractical compromises between mesh size and time steps. This article investigates the constraints imposed by this problem on tissues representative of the intervertebral disc, subjected to moderate physiological rates of deformation. Two test cylindrical structures were found to require over 10(4) linear displacement-constant pressure elements to avoid serious oscillations in calculated fluid pressure. Fewer Taylor–Hood (quadratic displacement–linear pressure elements) were required, but with complementary increases in computational costs. The Vermeer–Verruijt criterion for 1D mesh size provided guidelines for 3D mesh sizes for given time steps. Pressure instabilities may impose limitations on the use of the finite element method for simulating fluid transport behaviors of biological soft tissues at moderately rapid physiological loading rates

Measuring environmental contamination in critical care using dilute hydrogen peroxide (DHP) technology: An observational cross-over study

BackgroundThe environment has an important role in the transmission of healthcare associated infections. This has encouraged interest in novel methods to improve hygiene in hospitals. One such technology is the use of hydrogen peroxide to decontaminate rooms and equipment; there are, however, few studies that have investigated the effect of continuous dilute hydrogen peroxide (DHP) in the clinical environment. The aim of this study was to examine the use of dilute hydrogen peroxide (DHP) in a critical care unit and measure the microbiological impact on surface contamination.MethodsWe conducted a prospective observational cross-over study in a ten-bed critical care unit in one rural Australian hospital. Selected high-touch sites were screened using dipslides across three study phases: baseline; continuous DHP; and no DHP (control). Quantitative aerobic colony counts (ACC) were assessed against a benchmark standard of ACC >2.5 cfu/cm 2 to indicate hygiene failure.ResultsThere were low levels of microbial contamination in the unit for baseline; DHP; and no DHP phases: 2.2% (95% CI 0.7–5.4%) vs 7.7% (95% CI 4.3–13.0%) vs 6% (95% CI 3.2–10.4%) hygiene failures, respectively. Significant reduction in ACCs did not occur when the DHP was operating compared with baseline and control phases.ConclusionFurther work is needed to determine whether continuous DHP technology has a role in decontamination for healthcare settings

Analysis of factor V in zebrafish demonstrates minimal levels needed for early hemostasis

In humans, coagulation factor V (FV) deficiency is a rare, clinically heterogeneous bleeding disorder, suggesting that genetic modifiers may contribute to disease expressivity. Zebrafish possess many distinct advantages including high fecundity, optical clarity, external development, and homology with the mammalian hemostatic system, features that make it ideal for genetic studies. Our aim was to study the role of FV in zebrafish through targeted mutagenesis and apply the model to the study of human F5 variants. CRISPR-mediated genome editing of the zebrafish f5 locus was performed, generating mutants homozygous for a 49 base pair deletion in exon 4. Thrombus formation secondary to vascular endothelial injury was absent in f52/2 mutant embryos and larvae. Despite this severe hemostatic defect, homozygous mutants survived before succumbing to severe hemorrhage in adulthood. Human F5 variants of uncertain significance from patients with FV deficiency were evaluated, and the causative mutations identified and stratified by their ability to restore thrombus formation in larvae. Analysis of these novel mutations demonstrates variable residual FV function, with minimal activity being required to restore hemostasis in response to laser-induced endothelial injury. This in vivo evaluation may be beneficial for patients whose factor activity levels lack correlation with bleeding symptomatology, although limitations exist. Furthermore, homozygous mutant embryos tolerate what is a severe and lethal defect in mammals, suggesting the possibility of species-specific factors enabling survival, and allowing further study not possible in the mouse. Identification of these factors or other genetic modifiers could lead to novel therapeutic modalities

Challenges and strategies in the repair of ruptured annulus fibrosus

Lumbar discectomy is the surgical procedure most frequently performed for patients suffering from low back pain and sciatica. Disc herniation as a consequence of degenerative or traumatic processes is commonly encountered as the underlying cause for the painful condition. While discectomy provides favourable outcome in a majority of cases, there are conditions where unmet requirements exist in terms of treatment, such as large disc protrusions with minimal disc degeneration; in these cases, the high rate of recurrent disc herniation after discectomy is a prevalent problem. An effective biological annular repair could improve the surgical outcome in patients with contained disc herniations but otherwise minor degenerative changes. An attractive approach is a tissue-engineered implant that will enable/stimulate the repair of the ruptured annulus. The strategy is to develop three-dimensional scaffolds and activate them by seeding cells or by incorporating molecular signals that enable new matrix synthesis at the defect site, while the biomaterial provides immediate closure of the defect and maintains the mechanical properties of the disc. This review is structured into (1) introduction, (2) clinical problems, current treatment options and needs, (3) biomechanical demands, (4) cellular and extracellular components, (5) biomaterials for delivery, scaffolding and support, (6) pre-clinical models for evaluation of newly developed cell- and material-based therapies, and (7) conclusions. This article highlights that an interdisciplinary approach is necessary for successful development of new clinical methods for annulus fibrosus repair. This will benefit from a close collaboration between research groups with expertise in all areas addressed in this review

Meeting Report: Application of Genotyping Methods to Assess Risks from Cryptosporidium in Watersheds

A workshop titled "Application of Genotyping Methods to Assess Pathogen Risks from Cryptosporidium in Drinking Water Catchments" was held at the International Water Association biennial conference, Marrakech, Morocco, 23 September 2004. The workshop presented and discussed the findings of an interlaboratory trial that compared methods for genotyping Cryptosporidium oocysts isolated from feces. The primary goal of the trial and workshop was to assess the utility of current Cryptosporidium genotyping methods for determining the public health significance of oocysts isolated from feces in potable-water-supply watersheds. An expert panel of 16 watershed managers, public health practitioners, and molecular parasitologists was assembled for the workshop. A subordinate goal of the workshop was to educate watershed management and public health practitioners. An open invitation was extended to all conference delegates to attend the workshop, which drew approximately 50 interested delegates. In this report we summarize the peer consensus emerging from the workshop. Recommendations on the use of current methods by watershed managers and public health practitioners were proposed. Importantly, all the methods that were reported in the trial were mutually supporting and found to be valuable and worthy of further utility and development. Where there were choices as to which method to apply, the small-subunit ribosomal RNA gene was considered to be the optimum genetic locus to target. The single-strand conformational polymorphism method was considered potentially the most valuable for discriminating to the subtype level and where a large number of samples were to be analyzed. A research agenda for protozoan geneticists was proposed to improve the utility of methods into the future. Standardization of methods and nomenclature was promoted

The CcmC-CcmE interaction during cytochrome c maturation by System I is driven by protein-protein and not protein-heme contacts.

Cytochromes c are ubiquitous proteins, essential for life in most organisms. Their distinctive characteristic is the covalent attachment of heme to their polypeptide chain. This post-translational modification is performed by a dedicated protein system, which in many Gram-negative bacteria and plant mitochondria is a nine-protein apparatus (CcmA-I) called System I. Despite decades of study, mechanistic understanding of the protein-protein interactions in this highly complex maturation machinery is still lacking. Here, we focused on the interaction of CcmC, the protein that sources the heme cofactor, with CcmE, the pivotal component of System I responsible for the transfer of the heme to the apocytochrome. Using in silico analyses, we identified a putative interaction site between these two proteins (residues Asp <sup>47</sup> , Gln <sup>50</sup> , and Arg <sup>55</sup> on CcmC; Arg <sup>73</sup> , Asp <sup>101</sup> , and Glu <sup>105</sup> on CcmE), and we validated our findings by in vivo experiments in Escherichia coli Moreover, employing NMR spectroscopy, we examined whether a heme-binding site on CcmE contributes to this interaction and found that CcmC and CcmE associate via protein-protein rather than protein-heme contacts. The combination of in vivo site-directed mutagenesis studies and high-resolution structural techniques enabled us to determine at the residue level the mechanism for the formation of one of the key protein complexes for cytochrome c maturation by System I

Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins

Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we describe computer simulations of a few related model systems. The dynamics of collapse of eicosane shows that upon expulsion of water the linear hydrocarbon chain adopts an ordered helical hairpin structure with 1.5 turns. The structure of dimer of eicosane molecules has two well ordered helical hairpins that are stacked perpendicular to each other. As a prelude to studying folding in confined spaces we used simulations to understand changes in hydrophobic and ionic interactions in nano droplets. Solvation of hydrophobic and charged species change drastically in nano water droplets. Hydrophobic species are localized at the boundary. The tendency of ions to be at the boundary where water density is low increases as the charge density decreases. Interaction between hydrophobic, polar, and charged residue are also profoundly altered in confined spaces. Using the results of computer simulations and accounting for loss of chain entropy upon confinement we argue and then demonstrate, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores

The UDF05 follow-up of the Hubble Ultra Deep Field. I. The faint-end slope of the Lyman Break Galaxy Population at z ~ 5

We present the UDF05 HST program, which consists of three disjoint fields—NICP12, NICP34, plus the HUDF—with deep ACS (F606W, F775W, and F850LP) and NICMOS (F110W and F160W) imaging. Here we use the ACS data for the NICP12 and HUDF fields to implement a (V − i) − (i − z) selection criterion that allows us to identify a sample of 101 (133) z ~ 5 Lyman break galaxies (LBGs) down to z850 = 28.5 (29.25) mag in NICP12 (HUDF). We construct the rest-frame 1400 Å LBG luminosity function (LF) over the range M1400 = [ − 21.4, − 17.1] , i.e. down to ~0.04L* at z ~ 5, and use Subaru Deep Field results (Yoshida et al. 2006) to constrain our LF at the bright end (M1400 ≥ − 22.2). We show that (1) different assumptions regarding the LBG SED distribution, dust properties, and intergalactic absorption result in a 25% variation in the number density of LBGs at z ~ 5; (2) under consistent assumptions for dust properties and intergalactic absorption, the HUDF is ~30% underdense in z ~ 5 LBGs relative to the NICP12 field, a variation which is well explained by cosmic variance; and (3) the faint-end slope of the LF does not depend on the input parameters, and has a value of α ~ − 1.6, similar to the faint-end slope of the LF of z ~ 3 and z ~ 6 LBGs. Our study therefore supports no variation in the faint end of the LBG LF over the whole redshift range z ~ 3 to z ~ 6. Based on a comparison with semianalytical models, we speculate that the z ~ 5 LBGs might have a top-heavy IMF