Collision free region determination by modified polygonal Boolean operations

Cutting and packing problems are found in numerous industries such as garment, wood and shipbuilding. The collision free region concept is presented, as it represents all the translations possible for an item to be inserted into a container with already placed items. The often adopted nofit polygon concept and its analogous concept inner fit polygon are used to determine the collision free region. Boolean operations involving nofit polygons and inner fit polygons are used to determine the collision free region. New robust non-regularized Boolean operations algorithm is proposed to determine the collision free region. The algorithm is capable of dealing with degenerated boundaries. This capability is important because degenerated boundaries often represent local optimal placements. A parallelized version of the algorithm is also proposed and tests are performed in order to determine the execution times of both the serial and parallel versions of the algorithm.

Demonstration of pelvic anatomy by modified midline transection that maintains intact internal pelvic organs

Gross dissection for demonstrating anatomy of the human pelvis has traditionally involved one of two approaches, each with advantages and disadvantages. Classic hemisection in the median plane through the pelvic ring transects the visceral organs but maintains two symmetric pelvic halves. An alternative paramedial transection compromises one side of the bony pelvis but leaves the internal organs intact. The authors propose a modified technique that combines advantages of both classical dissections. This novel approach involves dividing the pubic symphysis and sacrum in the median plane after shifting all internal organs to one side. The hemipelvis without internal organs is immediately available for further dissection of the lower limb. The hemipelvis with intact internal organs is ideal for showing the complex spatial relationships of the pelvic organs and vessels relative to the intact pelvic floor.

Stable alteration of pre-mRNA splicing patterns by modified U7 small nuclear RNAs.

In several forms of beta-thalassemia, mutations in the second intron of the beta-globin gene create aberrant 5' splice sites and activate a common cryptic 3' splice site upstream. As a result, the thalassemic beta-globin pre-mRNAs are spliced almost exclusively via the aberrant splice sites leading to a deficiency of correctly spliced beta-globin mRNA and, consequently, beta-globin. We have designed a series of vectors that express modified U7 snRNAs containing sequences antisense to either the aberrant 5' or 3' splice sites in the IVS2-705 thalassemic pre-mRNA. Transient expression of modified U7 snRNAs in a HeLa cell line stably expressing the IVS2-705 beta-globin gene restored up to 65% of correct splicing in a sequence-specific and dose-dependent manner. Cell lines that stably coexpressed IVS2-705 pre-mRNA and appropriately modified U7 snRNA exhibited up to 55% of permanent restoration of correct splicing and expression of full-length beta-globin protein. This novel approach provides a potential alternative to gene replacement therapies.

Use of intrinsic binding energy for catalysis by an RNA enzyme

The contribution of several individual ribozyme⋅substrate base pairs to binding and catalysis has been investigated using hammerhead ribozyme substrates that were truncated at their 3′ or 5′ ends. The base pairs at positions 1.1–2.1 and 15.2–16.2, which flank the conserved core, each contribute 104-fold in the chemical step, without affecting substrate binding. In contrast, base pairs distal to the core contribute to substrate binding but have no effect on the chemical step. These results suggest a “fraying model” in which each ribozyme⋅substrate helix can exist in either an unpaired (“open”) state or a helical (“closed”) state, with the closed state required for catalysis. The base pairs directly adjacent to the conserved core contribute to catalysis by allowing the closed state to form. Once the number of base pairs is sufficient to ensure that the closed helical state predominates, additional residues provide stabilization of the helix, and therefore increase binding, but have no further effect on the chemical step. Remarkably, the >5 kcal/mol free energy contribution to catalysis from each of the internal base pairs is considerably greater than the free energy expected for formation of a base pair. It is suggested that this unusually large energetic contribution arises because free energy that is typically lost in constraining residues within a base pair is expressed in the transition state, where it is used for positioning. This extends the concept of “intrinsic binding energy” from protein to RNA enzymes, suggesting that intrinsic binding energy is a fundamental feature of biological catalysis.

Rotation of subunits during catalysis by Escherichia coli F1-ATPase.

During oxidative and photo-phosphorylation, F0F1-ATP synthases couple the movement of protons down an electrochemical gradient to the synthesis of ATP. One proposed mechanistic feature that has remained speculative is that this coupling process requires the rotation of subunits within F0F1. Guided by a recent, high-resolution structure for bovine F1 [Abrahams, J. P., Leslie, A. G., Lutter, R. & Walker, J. E. (1994) Nature (London) 370, 621-628], we have developed a critical test for rotation of the central gamma subunit relative to the three catalytic beta subunits in soluble F1 from Escherichia coli. In the bovine F1 structure, a specific point of contact between the gamma subunit and one of the three catalytic beta subunits includes positioning of the homolog of E. coli gamma-subunit C87 (gamma C87) close to the beta-subunit 380DELSEED386 sequence. A beta D380C mutation allowed us to induce formation of a specific disulfide bond between beta and gamma C87 in soluble E. coli F1. Formation of the crosslink inactivated beta D380C-F1, and reduction restored full activity. Using a dissociation/reassembly approach with crosslinked beta D380C-F1, we incorporated radiolabeled beta subunits into the two noncrosslinked beta-subunit positions of F1. After reduction of the initial nonradioactive beta-gamma crosslink, only exposure to conditions for catalytic turnover results in similar reactivities of unlabeled and radiolabeled beta subunits with gamma C87 upon reoxidation. The results demonstrate that gamma subunit rotates relative to the beta subunits during catalysis.

Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization.

A fundamental catalytic principle for protein enzymes in the use of binding interactions away from the site of chemical transformation for catalysis. We have compared the binding and reactivity of a series of oligonucleotide substrates and products of the Tetrahymena ribozyme, which catalyzes a site-specific phosphodiester cleavage reaction: CCCUCUpA+G<-->CCCUCU-OH+GpA. The results suggest that this RNA enzyme, like protein enzymes, can utilize binding interactions to achieve substantial catalysis via entropic fixation and substrate destabilization. The stronger binding of the all-ribose oligonucleotide product compared to an analog with a terminal 3' deoxyribose residue gives an effective concentration of 2200 M for the 3' hydroxyl group, a value approaching those obtained with protein enzymes and suggesting the presence of a structurally well defined active site capable of precise positioning. The stabilization from tertiary binding interactions is 40-fold less for the oligonucleotide substrate than the oligonucleotide product, despite the presence of the reactive phosphoryl group in the substrate. This destabilization is accounted for by a model in which tertiary interactions away from the site of bond cleavage position the electron-deficient 3' bridging phosphoryl oxygen of the oligonucleotide substrate next to an electropositive Mg ion. As the phosphodiester bond breaks and this 3' oxygen atom develops a negative charge in the transition state, the weak interaction of the substrate with Mg2+ becomes strong. These strategies of "substrate destabilization" and "transition state stabilization" provide estimated rate enhancements of approximately 280- and approximately 60-fold, respectively. Analogous substrate destabilization by a metal ion or hydrogen bond donor may be used more generally by RNA and protein enzymes catalyzing reactions of phosphate esters.

Microwave-assisted catalysis by iron oxide nanoparticles on MCM-41: Effect of the support morphology

Catalytically active heterogeneous catalysts have been prepared via microwave deposition of iron oxide nanoparticles (0.5–1.2 wt%) on MCM-41 type silica materials with different morphologies (particles, helical and spheres). This methodology leads to iron oxide nanoparticles composed by a mixture of FeO and Fe2O3 species, being the Fe(II)/Fe(III) peak ratio near to 1.11 by XPS. DRUV spectroscopy indicates the presence of tetrahedral coordinated Fe3+ in the silica framework of the three catalysts as well as some extraframework iron species in the catalysts with particle and sphere-like morphologies. The loading of the nanoparticles does neither affect the mesopore arrangement nor the textural properties of the silica supports, as indicated by SAXS and nitrogen adsorption/desorption isotherms. A detailed investigation of the morphology of the supports in various microwave-assisted catalyzed processes shows that helical mesostructures provide optimum catalytic activities and improved reusabilities in the microwave-assisted redox (selective oxidation of benzyl alcohol) catalyzed process probably due to a combination of lower particle size and higher acidity in comparison with the supports with particle and sphere morphology.

Calculated atomic photoeffect cross sections by modified Stobbe theory for atomic number from Z=2 through Z=50, add photon energies between 0.5 keV and 40.0 keV.

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Fire retardant viscosity measured by modified marsh funnel /

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Effects of lycopene on the induction of foam cell formation by modified LDL.

The effect of lycopene on macrophage foam cell formation induced by modified low-density lipoprotein (LDL) was studied. Human monocyte-derived macrophages (HMDM) were incubated with lycopene in the presence or absence of native LDL (nLDL) or LDL modified by oxidation (oxLDL), aggregation (aggLDL), or acetylation (acLDL). The cholesterol content, lipid synthesis, scavenger receptor activity, and the secretion of inflammatory [interleukin (IL)-1β and tumor necrosis factor (TNF)-α] and anti-inflammatory (IL-10) cytokines was determined. Lycopene was found to decrease the synthesis of cholesterol ester in incubations without LDL or with oxLDL while triacylglycerol synthesis was reduced in the presence of oxLDL and aggLDL. Scavenger receptor activity as assessed by the uptake of acLDL was decreased by ∼30% by lycopene. In addition, lycopene inhibited IL-10 secretion by up to 74% regardless of the presence of nLDL or aggLDL but did not affect IL-1β or TNF-α release. Lycopene also reduced the relative abundance of mRNA transcripts for scavenger receptor A (SR-A) in THP-1 macrophages treated with aggLDL. These findings suggest that lycopene may reduce macrophage foam cell formation induced by modified LDL by decreasing lipid synthesis and downregulating the activity and expression of SR-A. However, these effects are accompanied by impaired secretion of the anti-inflammatory cytokine IL-10, suggesting that lycopene may also exert a concomitant proinflammatory effect.

Porous solids from layered clays by combined pillaring and templating approaches

The pore structure formation in bentonite, pillared with a mixed sol of silicon and titanium hydroxides and treated subsequently with quaternary ammonium surfactants, is investigated. The surfactant micelles act as a template, similar to their role in MCM41 synthesis. Because both the surfactant micelles and the sol particles are positively charged, it is greatly favorable for them to form meso-phase assembles in the galleries between the clay layers that bear negative charges. Besides, the sol particles do not bond the clay layers strongly as other kinds of pillar precursors do, so that the treatment with surfactants can result in radical structure changes in sol-pillared clays. This allows us to tailor the pore structure of these porous clays by choice of surfactant. The surfactant treatment also results in profound increases in porosity and improvement in thermal stability. Therefore, the product porous clays have great potential to be Used to deal with large molecules or at high operating temperatures. We also found that titanium in these samples is highly dispersed in the silica matrix rather than existing in the form of small particles of pure titania. Such highly dispersed Ti active centers may offer excellent activities for catalytic oxidation reactions such as alkanes into alcohols and ketones.

Characterisation of the acid-base properties of pillared montmorillonites

Iron and mixed iron aluminium pillared montrnorillonites prepared by partial hydrolysis method were subjected to room temperature exchange with transition metals of the first series. The resulting materials were characterised by different spectroscopic techniques and surface area measurements. About 1-3% transition metals were incorporated into the porous network. The structural stability of the porous network was not affected by exchange. XRD and AI NMR spectroscopy evidenced the presence of iron substituted Al13 like polymers in FeAl pillared systems. Acidity and basicity benefited much as a result of metal exchange. Acidity and basicity were quantified by model reactions, viz., cumene cracking and cyclohexanol decomposition respectively. The presence of basic sites in otherwise acidic pillared clays, though diminutive in amount can be of much importance in acid base catalysed reactions.