Woodification: User‐Controlled Cambial Growth Modeling

We present a botanical simulation of secondary (cambial) tree growth coupled to a physical cracking simulation of its bark. Whereas level set growth would use a fixed resolution voxel grid, our system extends the deformable simplicial complex (DSC), supporting new biological growth functions robustly on any surface polygonal mesh with adaptive subdivision, collision detection and topological control. We extend the DSC with temporally coherent texturing, and surface cracking with a user‐controllable biological model coupled to the stresses introduced by the cambial growth model.     

The effect of piezoresistive microcantilever geometry on cantilever sensitivity during surface stress chemical sensing

We have designed, fabricated, and tested five piezoresistive cantilever configurations to investigate the effect of shape and piezoresistor placement on the sensitivity of microcantilevers under both point loading and surface stress loading. The experimental study reveals that: (1) high aspect ratio cantilevers that are much longer than they are wide are optimal for point-loading applications such as microscopy and force measurements; (2) low aspect ratio cantilevers that are short and wide are optimal for surface stress-loading scenarios such as those that occur in biological and chemical sensor applications. The sensitivity data for both point loads and surface stress are consistent with previously developed finite-element models.     

Practical Interdomain Routing Security

This article reviews risks and vulnerabilities in interdomain routing and best practices that can have near-term benefits for routing security. It includes examples of routing failures and common attacks on routers, and countermeasures to reduce router vulnerabilities.     

The effect of polyethylene thickness in fixed- and mobile-bearing total knee replacements

In this paper fixed- and mobile-bearing implants were simulated using a multibody dynamic model and a finite element model to investigate the contact pressure distribution in the ultra high molecular weight polyethylene tibial bearing component. The thickness of polyethylene varied from 6.8 to 12.3 mm and the polyethylene was modelled as a non-linear material. It was found that the contact pressure on the polyethylene decreased in the fixed-bearing implant when the thickness of polyethylene increased from 6.8 to 8 and 9.6 mm, but there was little further decrease in pressure with the increase of polyethylene thickness from 9.6 to 11.0 and 12.3 mm. In the mobile-bearing implant, no increase in contact pressure on the superior surface was found with the increase in the thickness of the polyethylene; however, the contact pressures on the inferior contact surface of the thicker designs were higher than those in the 6.8 mm design. The numerical results obtained in this paper are in good agreement with published experimental test results. Moreover, the paper presents a detailed pressure distribution on the tibial bearing component during a full gait cycle.     

Domain structure of the Fib-1 and Fib-2 regions of human fibronectin. Thermodynamic properties of the type I finger module

The stability of the Fib-1 (29 kDa) and Fib-2 (19 kDa) fragments of human fibronectin as well as several different subfragments and isolated type I "finger" modules were studied under various solvent conditions by differential scanning calorimetry and fluorescence spectroscopy. It was established that all fibronectin fingers constitute independently folded domains whose melting temperatures range from 54 to 108 degrees C. The difference between heat capacities of the native and denatured states (delta Cp) is low, about 0.03 cal/K-g, which is consistent with the relatively low percentage of hydrophobic amino acids and the consequent small change in non-polar surface area exposed to the solvent upon denaturation. The free energy of unfolding at 25 degrees, as calculated from the calorimetric data or measured directly by titration with GdmSCN is also small, in the range of 2.4 to 6.7 kcal/mol. The small delta G value and its flat dependence on temperature (determined by delta Cp) translates the small variations in delta G between fingers into large variations in tm. The small value of delta G also indicates that finger modules are structurally rather fragile which may account for their sensitivity to proteolysis; almost any cleavage within either of the two disulfide loops destroys the cooperative structure and abolishes the corresponding melting transition. The fact that some fingers exhibit large decreases in tm upon separation from more stable neighbors with which they interact can also be viewed as a consequence of the low values of delta G and delta Cp.     

The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution

The dimer of bovine pancreatic ribonuclease A (RNase A) discovered by Crestfield, Stein, and Moore in 1962 has been crystallized and its structure determined and refined to a 2.1-A resolution. The dimer is 3D domain-swapped. The N-terminal helix (residues 1-15) of each subunit is swapped into the major domain (residues 23-124) of the other subunit. The dimer of bull seminal ribonuclease (BS-RNase) is also known to be domain-swapped, but the relationship of the subunits within the two dimers is strikingly different. In the RNase A dimer, the 3-stranded beta sheets of the two subunits are hydrogen-bonded at their edges to form a continuous 6-stranded sheet across the dimer interface; in the BS-RNase dimer, it is instead the two helices that abut. Whereas the BS-RNase dimer has 2-fold molecular symmetry, the two subunits of the RNase A dimer are related by a rotation of approximately 160 degrees. Taken together, these structures show that intersubunit adhesion comes mainly from the swapped helical domain binding to the other subunit in the "closed interface" but that the overall architecture of the domain-swapped oligomer depends on the interactions in the second type of interface, the "open interface." The RNase A dimer crystals take up the dye Congo Red, but the structure of a Congo Red-stained crystal reveals no bound dye molecule. Dimer formation is inhibited by excess amounts of the swapped helical domain. The possible implications for amyloid formation are discussed.     

Infective endocarditis complicated with rapidly progressive glomerulonephritis: a case report

Despite a general national decline in criminal activities in the 1990s, juvenile criminal offenses continue to increase, (including violent, property, and delinquency acts). In addition increased numbers of children are being held in juvenile jails. It is all but impossible for pediatric health providers to think that "their patients" and "their practices" are immune from the epidemic of crime that affects and is caused by "just kids."     

Automated generation of lattice QCD Feynman rules

The derivation of the Feynman rules for lattice perturbation theory from actions and operators is complicated, especially for highly improved actions such as HISQ. This task is, however, both important and particularly suitable for automation. We describe a suite of software to generate and evaluate Feynman rules for a wide range of lattice field theories with gluons and (relativistic and/or heavy) quarks. Our programs are capable of dealing with actions as complicated as (m)NRQCD and HISQ. Automated differentiation methods are used to calculate also the derivatives of Feynman diagrams.

Program summary

Program title: HiPPY, HPsrcCatalogue identifier: AEDX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GPLv2 (see Additional comments below)No. of lines in distributed program, including test data, etc.: 513 426No. of bytes in distributed program, including test data, etc.: 4 893 707Distribution format: tar.gzProgramming language: Python, Fortran95Computer: HiPPy: Single-processor workstations. HPsrc: Single-processor workstations and MPI-enabled multi-processor systemsOperating system: HiPPy: Any for which Python v2.5.x is available. HPsrc: Any for which a standards-compliant Fortran95 compiler is availableHas the code been vectorised or parallelised?: YesRAM: Problem specific, typically less than 1 GB for either codeClassification: 4.4, 11.5Nature of problem: Derivation and use of perturbative Feynman rules for complicated lattice QCD actions.Solution method: An automated expansion method implemented in Python (HiPPy) and code to use expansions to generate Feynman rules in Fortran95 (HPsrc).Restrictions: No general restrictions. Specific restrictions are discussed in the text.Additional comments: The HiPPy and HPsrc codes are released under the second version of the GNU General Public Licence (GPL v2). Therefore anyone is free to use or modify the code for their own calculations. As part of the licensing, we ask that any publications including results from the use of this code or of modifications of it cite Refs. [1,2] as well as this paper. Finally, we also ask that details of these publications, as well as of any bugs or required or useful improvements of this core code, would be communicated to us.Running time: Very problem specific, depending on the complexity of the Feynman rules and the number of integration points. Typically between a few minutes and several weeks. The installation tests provided with the program code take only a few seconds to run.References:

• [1] 

  A. Hart, G.M. von Hippel, R.R. Horgan, L.C. Storoni, Automatically generating Feynman rules for improved lattice eld theories, J. Comput. Phys. 209 (2005) 340–353, doi:10.1016/j.jcp.2005.03.010, arXiv:hep-lat/0411026.

• [2] 

  M. Lüscher, P. Weisz, Efficient Numerical Techniques for Perturbative Lattice Gauge Theory Computations, Nucl. Phys. B 266 (1986) 309, doi:10.1016/0550-3213(86)90094-5.

     

CRT and LCD monitor and process materials evaluated for environmental improvement

Decision rules have been developed and applied to the bills of materials of a color cathode‐ray tube (CRT) and a liquid‐crystal‐display (LCD) desktop monitor to determine which product and process materials will be evaluated in an environmental life‐cycle assessment. Materials of significant mass, of technological importance, and of potential environmental impact are targeted. The list of materials identified are those for which life‐cycle inventory data will be obtained for the materials extraction and materials processing life‐cycle stages of a CRT and an LCD. Additionally, materials identified will also be used to represent life‐cycle impact in terms of resource consumption, as well as surrogates for occupational health impacts.     

Evolutionary pattern search algorithms for unconstrained andlinearly constrained optimization

We describe a convergence theory for evolutionary pattern search algorithms (EPSA) on a broad class of unconstrained and linearly constrained problems. EPSA adaptively modify the step size of the mutation operator in response to the success of previous optimization steps. The design of EPSA is inspired by recent analyzes of pattern search methods. Our analysis significantly extends the previous convergence theory for EPSA. Our analysis applies to a broader class of EPSA and it applies to problems that are nonsmooth, have unbounded objective functions, and are linearly constrained. Further, we describe a modest change to the algorithmic framework of EPSA for which a nonprobabilistic convergence theory applies. These analyses are also noteworthy because they are considerably simpler than previous analyses of EPSA