bluuebunny/crossref_metadata_2025 huggingface dataset:
The latitudinal gradient of beta diversity in relation to climate and topography for mammals in North America
Authors: Qian Hong , Badgley Catherine , Fox David L.
Published: August 2008

Aim  Spatial turnover of species, or beta diversity, varies in relation to geographical distance and environmental conditions, as well as spatial scale. We evaluated the explanatory power of distance, climate and topography on beta diversity of mammalian faunas of North America in relation to latitude.

Location  North America north of Mexico.

Methods  The study area was divided into 313 equal‐area quadrats (241 × 241 km). Faunal data for all continental mammals were compiled for these quadrats, which were divided among five latitudinal zones. These zones were comparable in terms of latitudinal and longitudinal span, climatic gradients and elevational gradients. We used the natural logarithm of the Jaccard index (lnJ) to measure species turnover between pairs of quadrats within each latitudinal zone. The slope of lnJ in relation to distance was compared among latitudinal zones. We used partial regression to partition the variance in lnJ into the components uniquely explained by distance and by environmental differences, as well as jointly by distance and environmental differences.

Results  Mammalian faunas of North America differ more from each other at lower latitudes than at higher latitudes. Regression models of lnJ in relation to distance, climatic difference and topographic difference for each zone demonstrated that these variables have high explanatory power that diminishes with latitude. Beta diversity is higher for zones with higher mean annual temperature, lower seasonality of temperature and greater topographic complexity. For each latitudinal zone, distance and environmental differences explain a greater proportion of the variance in lnJ than distance, climate or topography does separately.

Main conclusions  The latitudinal gradient in beta diversity of North American mammals corresponds to a macroclimatic gradient of decreasing mean annual temperature and increasing seasonality of temperature from south to north. Most of the variance in spatial turnover is explained by distance and environmental differences jointly rather than distance, climate or topography separately. The high predictive power of geographical distance, climatic conditions and topography on spatial turnover could result from the direct effects of physical limiting factors or from ecological and evolutionary processes that are also influenced by the geographical template.
Stoma obstruction after laparoscopic adjustable gastric banding for morbid obesity: report of two cases and treatment options
Authors: Louri N. , Darwish B. , Alkhalifa K.
Published: August 2008

Laparoscopic adjustable gastric band is one of the surgical options available for morbid obesity in the current century. Its popularity is gained by its proven efficacy with a reported low incidence of the intraoperative as well as the postoperative complications. Stomal obstruction post‐laparoscopic adjustable gastric band (LAGB) has been under reported in the English literature. We report this complication in two patients and discuss two different simple modalities of treatment. Post‐LAGB complications are numerous, dealing with their complications have a steeping curve. Educating the patients postoperatively in regard to food ingestion manner is a must and should prevent such complication.
What's in a War? (Politics as War, War as Politics)
Authors: BALIBAR ETIENNE
Published: August 2008

Abstract.  This paper combines reflections on the current “state of war” in the Middle East with an epistemological discussion of the meaning and implications of the category “war” itself, in order to dissipate the confusions arising from the idea of a “War on Terror.” The first part illustrates the insufficiency of the ideal type involved in dichotomies which are implicit in the naming and classifications of wars. They point nevertheless to a deeper problem which concerns the antinomic character of a collective institution of violence. The second part discusses the extent to which, in spite of the historical transformations in the means and political objectives of wars, the contemporary confrontation still obeys the rules of warfare described by Clausewitz, particularly with respect to temporality (“friction”). The third part discusses “non‐clausewitzian” aspects of the “new wars” defined by Martin Van Creveld and Mary Kaldor, while suggesting that they have left aside the most salient contradiction illustrated by the US interventions, which results from the combination of a claim to universal sovereignty and a reduction of war to generalized police operations.
METHODOLOGICAL INVENTION AS A CONSTRUCTIVE PROJECT: Exploring the Production of Ethical Knowledge through the Interaction of Discursive Logics
Authors: Bucar Elizabeth M.
Published: August 2008

This article reflects one scholar's attempt to locate herself within emerging ethical methodologies given a specific concern with cross‐cultural women's moral praxis. The field of comparative ethics's debt to past debates over methodology is considered through a typology of three waves of methodological invention. The article goes on to describe a specific research focus on U.S. Catholic and Iranian Shii women that initiated a search for a distinct method. This method of comparative ethics, which focuses on the production of ethical knowledge through the interaction of discursive logics of various moral agents, is described. The conclusion turns to how methodological invention can itself become a constructive project through the way it (1) locates the scholar in relation to her subject of study and (2) allows for isolation of tactics within specific moral discourses.
APPROACHING ISLAM: Comparative Ethics through Human Rights
Authors: Oh Irene
Published: August 2008

A dialogical approach to understanding Islamic ethics rejects objectivist methods in favor of a conversational model in which participants accept each other as rational moral agents. Hans‐Georg Gadamer asserts the importance of agreement upon a subject matter through conversation as a means to gaining insight into other persons and cultures, and Jürgen Habermas stresses the importance of fairness in dialogue. Using human rights as a subject matter for engaging in dialogue with Islamic scholars, Muslim perspectives on issues such as democracy, toleration, and freedom of conscience emerge. A capabilities approach to human rights, such as that developed by Martha Nussbaum, enables the coexistence of multiple religious ethical visions while insisting upon the need to protect and nurture essential human abilities.
HAUERWAS AND POLITICAL THEOLOGY: The Next Generation
Authors: Pinches Charles
Published: August 2008

In this review essay, I consider the recent work of students of Stanley Hauerwas on matters related to political theology. Eight books (and scattered articles) are treated in two groups: one more theoretical, the other more practically oriented. Of special interest is whether and how Jeffrey Stout's concerns about Hauerwas's negative political “influence” apply. I suggest that while sometimes narratives of decline dominate overmuch, these works rightly and creatively seek to expand our political imagination beyond the narrowness of modern nation‐state politics and its attending capitalist assumptions. Moreover, in all cases, Hauerwas's students stress a kind of political embodiment of Christ in the practices of particular communities, beginning with the Christian Church, but including also medicine, economy, and family. Spread out, this embodiment combats a pervasive modern Gnosticism, trains us in patience and hope, and gives room for a more truthful description of Church and world.
THE TWO‐DIMENSIONALIST REDUCTIO
Authors: HOWELL ROBERT J.
Published: August 2008

Abstract: In recent years two‐dimensional semantics has become one of the most serious alternatives to Millianism for the proper interpretation of modal discourse. It has origins in the works of a diverse group of philosophers, and it has proven popular as an interpretation of both language and thought. It has probably received most of its attention, however, because of its use by David Chalmers in his arguments against materialism. It is this more metaphysical application of two‐dimensionalism that is the concern in this paper. For though there is probably something salvageable from two‐dimensionalism as a way to explain the content of thought, as a metaphysical tool it should be abandoned. In this paper I aim to establish this point by reductio: if ‘metaphysical’ two‐dimensionalism is assumed, it can be shown to be false.
Law Applicable in the Absence of Choice – The New Article 4 of the Rome I Regulation
Authors: Tang Zheng
Published: August 2008

The applicable law to a contract in the absence of the parties' choice is governed by Article 4 of the Rome Convention, which has been implemented in the UK by the Contracts (Applicable Law) Act 1990. This rule adopts the ‘closest connection principle’ as a basic principle to decide the applicable law, but also introduces specific presumptions to simplify the process. The current rule has been criticised for its uncertainty. As a result, a substantive change has been provided in the Rome I Regulation, which aims to modernise the current choice of law rules in contractual obligations and convert the Rome Convention into a Council Regulation. The new Article 4 aims to enhance certainty and to overcome the difficulties of the current rules of the Rome Convention. However, a close scrutiny of the new Article 4 shows that it does not properly achieve its aim. The article aims to critically analyse Article 4 of the Rome I Regulation and to provide suggestions for its interpretation and understanding.
Protective nesting associations in birds
Authors: QUINN JOHN L. , UETA MUTSUYUKI
Published: August 2008

Exploiting the nest defence behaviour of another relatively aggressive species is one of the most unusual amongst a great diversity of strategies used by animals to evade predation. Here we review 62 studies that have looked at protective nesting associations in which at least one species is a bird. Most ‘protected’ associates are found in the Anseriformes, the Charadriiformes and the Passeriformes, while most ‘protective’ associates come from the Charadriiformes and the Falconiformes. Protected associates primarily benefit from a reduced predation rate when nesting near protective species although a variety of other, often unusual benefits have been described, including early warning of predators, lower parasitism, lower brood‐parasitism, nest stability and higher mating success. Protected associates sometimes also pay costs when they or their young are killed by their aggressive associate, or when they are forced to abandon their nest. Two studies demonstrate that protected species manipulate the trade‐off between the costs and benefits of nesting near an aggressive associate, while only a handful of studies have found specific adaptations to help avoid costs. In contrast, there is little evidence to suggest that the protective associates pay costs or gain benefits. This is probably because few researchers set out to test this hypothesis specifically, but we tentatively conclude that the majority of nesting associations are commensal in nature, and that only a few are parasitic or mutualistic. Many studies show that nesting associations occur by active choice and not because the associate species choose similar habitat, but only one study does so experimentally. In two cases the nesting association is obligatory for one of the species but there was also evidence for significant local adaptation to nesting near protective species, sometimes across a broad geographical range. Finally, we identify potential pathways that may have led to the evolution of nesting associations, discuss some possible implications for the populations involved and argue that nesting associations provide many novel research opportunities.
Cats and seabirds: effects of feral Domestic Cat Felis silvestris catus eradication on the population of Sooty Terns Onychoprion fuscata on Ascension Island, South Atlantic
Authors: HUGHES B. JOHN , MARTIN GRAHAM R. , REYNOLDS S. JAMES
Published: August 2008

The population of Sooty Terns Onychoprion fuscata breeding on Ascension Island in the Atlantic Ocean was monitored over 17 years (1990–2007). This period spanned the programme of feral Domestic Cat Felis silvestris catus eradication from the island, which commenced in 2001 with the last Cat recorded in 2004. We report on the abundance of Sooty Terns and Black Rats Rattus rattus before and after Cat eradication. The Sooty Tern breeding population in the 1990s averaged 368 000 and Cats were killing Terns at an average rate of 33 adults per night. Following Cat eradication, adult Terns are no longer predated. However, egg predation by both Rats and Common Mynas Acridotheres tristis has continued with Mynas destroying more eggs than Rats. Unexpectedly, we observed a change in Rat predatory behaviour. Following Cat eradication, Rats have become a major predator of Sooty Tern chicks. Despite this change, the Tern population has shown a season‐on‐season increase since Cat eradication, 48.8% in 2005, 8.2% in 2006 and 6.1% in 2007, and the breeding population increased to 420 000 birds in 2007. Incubation success improved from 66.0 to 84.4% during Cat eradication, before dropping down again to 67.9% after Cats were eradicated and Rat control measures were introduced. Index traplines were set for Rats and Rat numbers fluctuated widely immediately after Cats were eradicated but there were no significant differences that could be attributed to changes in Cat numbers. Ascension Island Sooty Terns breed every 9.6 months and juveniles defer breeding for seven seasons. Hence 2008 is the first year in which an increase in the breeding Sooty Tern population directly attributable to Cat eradication is likely to be detected. We conclude that long‐term monitoring is essential to guide conservation practice even in this relatively simple predator–prey system.
The direct and indirect effects of predation by Hen Harriers Circus cyaneus on trends in breeding birds on a Scottish grouse moor
Authors: BAINES DAVID , REDPATH STEPHEN , RICHARDSON MICHAEL , THIRGOOD SIMON
Published: August 2008

Two phases of an experimental reduction in management at Langholm Moor in southwest Scotland provided an insight into factors that determined trends in the abundance of moorland birds. In 1992 the historical control of breeding Hen Harriers Circus cyaneus stopped and in 2000 grouse moor management was discontinued. Golden Plover Pluvialis apricaria, Lapwing Vanellus vanellus, Curlew Numenius arquata and Red Grouse Lagopus lagopus scoticus declined, whilst Carrion Crow Corvus corone and Snipe Gallinago gallinago increased. Hen Harriers increased from two to 20 breeding females, then declined back to two. Lapwing abundance was positively associated with that of Hen Harriers, and moorland passerines (Skylark Alauda arvensis, Meadow Pipit Anthus pratensis and Stonechat Saxicola torquata) were negatively associated. Golden Plover, Lapwing, Curlew, Red Grouse, Skylark and Hen Harrier were more abundant when the moor was managed for grouse, whilst Carrion Crow, a common predator of clutches of ground‐nesting birds, increased during the second half when management ceased. Increased Crow numbers, together with an increase in Red Foxes Vulpes vulpes, probably contributed to the observed bird declines.
Detection of Pseudomonas aeruginosa quorum sensing signals in an infected ischemic wound: An experimental study in rats
Authors: Nakagami Gojiro , Sanada Hiromi , Sugama Junko , Morohoshi Tomohiro , Ikeda Tsukasa , Ohta Yasunori
Published: August 2008

Quorum sensing is a cell‐to‐cell communication that occurs via autoinducers, regulating a number of bacterial virulence factors including the opportunistic wound pathogen Pseudomonas aeruginosa, which uses the N‐(3‐oxododecanoyl)‐homoserine lactone as one of the two main autoinducers; however, little is known about its role in chronic wound infection. This study was designed to quantify this autoinducer from P. aeruginosa‐infected wounds with the aim of examining the possible use of autoinducers as an indicator of chronic wound infection. Pressure‐induced ischemic wounds were infected with P. aeruginosa (N=12) or uninfected as a control (N=12). The autoinducer was quantified by bioassay method employing Escherichia coli DH5α (pJN105L, pSC11) or Agrobacterium tumefaciens NTL4 (pZLR4) reporter, which expresses β‐galactosidase when exposed to P. aeruginosa quorum sensing signals. The average concentration of autoinducer was 0.33 pmol/g at day 3 and 0.49 pmol/g at day 7 in the infected wounds, as detected from tissue samples. A linear correlation between autoinducer concentration and bacterial counts was observed. No autoinducer was detected in tissue samples from the uninfected control group. Our findings indicate that the quantification of autoinducers is possible and quorum sensing system could play a role in in vivo wound infection models, and also suggest possible clinical implications of autoinducer signal quantification in diagnosis of chronic wound infection.
MDI 301, a nonirritating retinoid, improves abrasion wound healing in damaged/atrophic skin
Authors: Warner Roscoe L. , Bhagavathula Narasimharao , Nerusu Kamalakar , Hanosh Andrew , McClintock Shannon D. , Naik Madhav K. , Johnson Kent J. , Ginsburg Isaac , Varani James
Published: August 2008

MDI 301 is a picolinic acid‐substituted ester of 9‐cis retinoic acid. It has been shown in the past that MDI 301 increases epidermal thickness, decreases matrix metalloproteinase (MMP) activity, and increases procollagen synthesis in organ‐cultured human skin. Unlike all‐trans retinoic acid (RA), MDI 301 does not induce expression of proinflammatory cytokines or induce expression of leukocyte adhesion molecules in human skin. In the present study we examined topical MDI 301 treatment for ability to improve the structure and function of skin in three models of skin damage in rodents and for ability to improve abrasion wound healing in these models. MDI 301 was applied daily to the skin of rats treated with the potent corticosteroid, clobetasol propionate, to the skin of diabetic rats (8 weeks posttreatment with streptozotocin) and to the skin of aged (14–16‐month‐old) rats. In all three models, subsequently induced abrasion wounds healed more rapidly in the retinoid‐treated animals than in vehicle‐treated controls. Immediately after complete wound closure, tissue from the wound site (as well as from a control site) was put into organ culture and maintained for 3 days. At the end of the incubation period, culture fluids were assessed for soluble type I collagen and for MMPs‐2 and ‐9. In all three models, the level of type I collagen was increased and MMP levels were decreased by MDI 301. In all three models, skin irritation during the retinoid‐treatment phase was virtually nonexistent.
Controlled delivery of bFGF to recipient bed enhances the vascularization and viability of an ischemic skin flap
Authors: Fujihara Yuko , Koyama Hiroyuki , Ohba Makoto , Tabata Yasuhiko , Fujihara Hisako , Yonehara Yoshiyuki , Takato Tsuyoshi
Published: August 2008

Therapeutic angiogenesis is a promising approach to treat ischemic skin flaps. We delivered basic fibroblast growth factor (bFGF) to the recipient bed of a rat dorsal skin flap by a drug delivery system with acidic gelatin hydrogel microspheres (AGHMs), and assessed augmentation of neovascularization and flap viability. An axial skin flap was elevated on the back of male Sprague–Dawley rats, and bFGF solution or bFGF‐impregnated AGHMs were injected into the recipient bed. The dose of bFGF in the bFGF solution was set to 15 (Sol‐15 group), 50 (Sol‐50 group), or 150 μg (Sol‐150 group). Correspondingly, 2 mg AGHMs were impregnated with 15 (AGHM‐15 group), 50 (AGHM‐50 group), or 150 μg (AGHM‐150 group) bFGF. Other groups of animals received phosphate‐buffered saline (Sol‐Cont group) or phosphate‐buffered saline‐impregnated AGHMs (AGHM‐Cont group) as controls. Seven days later, analyses of the area of necrosis, microangiographic findings, and histological findings in the flap were carried out. The area of necrosis in the AGHM‐150 group was significantly smaller than that in the other groups. Microangiographic and histological analyses showed that neovascularization of the ischemic skin flap significantly increased in the AGHM‐150 group as compared with the Sol‐150 group and the AGHM‐Cont group. These findings suggest that continuous delivery of bFGF to the recipient bed by bFGF‐impregnated AGHMs enhances the viability of an ischemic skin flap.
Dermal fibroblasts from red Duroc and Yorkshire pigs exhibit intrinsic differences in the contraction of collagen gels
Authors: De Hemptinne Isabelle , Gallant‐Behm Corrie L. , Noack Cassandra L. , Parreno Justin , Hart David A.
Published: August 2008

Previous studies have shown that the Yorkshire (Y) pig is a model for normal skin wound healing, while red Duroc (RD) pigs form hypercontracted scars similar to human hypertrophic scars. In order to determine potential intrinsic differences in fibroblast phenotypes, the ability of normal dorsal and ventral dermal fibroblasts from Y and RD pigs to contract collagen gels was assessed. Cells plated in gels were cultured in media supplemented with 2% or 10% FBS ± 1 or 10 ng/mL transfroming growth factor β1. The degree of contraction of the gels was quantified at defined time‐points postrelease. Final contraction levels were dependent on cell density and serum concentration for all cell types. The rates of contraction of RD dorsal fibroblasts were significantly greater than those for Y dorsal fibroblasts. Immunocytochemical analysis revealed the presence of α‐smooth muscle actin in contracted cells. Furthermore, mRNA levels for matrix metalloproteinase‐2 and decorin showed specific increases for the RD cells during contraction. These findings have revealed intrinsically different, location‐specific in vitro responses with normal dermal fibroblasts from the two breeds of pig, suggesting that the abnormal skin healing phenotype of RD pigs may be attributable in part to intrinsic genetic differences in fibroblasts between the breeds.
Effect of root surface treatment with propolis and fluoride in delayed tooth replantation in rats
Authors: Gulinelli Jéssica Lemos , Panzarini Sônia Regina , Fattah Cristiane Mara Ruiz de Sousa , Poi Wilson Roberto , Sonoda Celso Koogi , Negri Márcia Regina , Saito Célia Tomiko Matida Hamata
Published: August 2008

Abstract –  Replantation is an acceptable option for treatment of an avulsed permanent tooth. Nevertheless, an extended extraoral period damages the periodontal ligament and results in external root resorption. The purpose of this study was to assess by histologic and histometric analysis, the influence of propolis 15% (natural resinous substance collected by Apis mellifera bees from various plants) and the fluoride solution used as root surface treatment on the healing process after delayed tooth replantation. Thirty Wistar (Rattus norvegicus albinus) rats were submitted to extraction of their upper right incisor. The teeth were maintained in a dry environment for 60 min. After this, the pulp was extirpated and the papilla, enamel organ and periodontal ligament were removed with scalpel. The teeth were divided into three experimental groups: Group I – teeth immersed in 20 ml of physiologic saline; Group II – teeth immersed in 20 ml of 2% acidulated phosphate sodium fluoride; Group III – teeth immersed in 20 ml of 15% propolis. After 10 min of immersion in the solutions, the root canals were dried and filled with calcium hydroxide paste and the teeth were replanted. The animals were euthanized 60 days after replantation. The results showed that similar external root resorption was seen in the propolis and fluoride groups. Teeth treated with physiologic saline tended to have more inflammatory root resorption compared with those treated with fluoride or propolis. However, the comparative analysis did not reveal statistically significant differences (P > 0.05) between the treatment modalities when used for delayed tooth replantation.
LRP‐associated protein gene (LRPAP1) and susceptibility to degenerative dementia
Authors: Pandey P. , Pradhan S. , Mittal B.
Published: August 2008

Difference in genetic makeup of lipid metabolizing proteins may increase susceptibility to dementia. The aim of this study was to investigate variations in two lipid metabolizing genes, low‐density lipoprotein receptor‐related protein‐associated protein gene (LRPAP) and apolipoprotein E (APOE), in vascular and degenerative dementias. This hospital‐based association study included 147 patients with dementia and 163 age‐matched controls. Genotyping for LRPAP1 intron 5 insertion/deletion and APOEHhaI polymorphism was carried out by polymerase chain reaction (PCR)/PCR–restriction fragment length polymorphism method. The frequency of DD genotype and *D allele of LRPAP gene was high in degenerative dementias compared with controls (76.6% vs. 44.8% and 86.4% vs. 69.3%, respectively) suggesting increased susceptibility [P < 0.0001, odds ratio (OR) =3.76 for DD genotype and P < 0.0001, OR = 2.80 for D allele]. Vascular dementia patients showed statistically insignificant but increasing trend for allele I (40.0% vs. 30.7%). We also observed significant association of APOEɛ4 allele with degenerative dementias (P < 0.0001, OR =5.35). Our study suggests that LRPAP1‐D and APOE E4 alleles significantly increase the susceptibility to degenerative dementias.
Deciphering the key residues in Plasmodium falciparumβ‐ketoacyl acyl carrier protein reductase responsible for interactions with Plasmodium falciparum acyl carrier protein
Authors: Karmodiya Krishanpal , Modak Rahul , Sahoo Nirakar , Sajad Syed , Surolia Namita
Published: August 2008

The type II fatty acid synthase (FAS) pathway of Plasmodium falciparum is a validated unique target for developing novel antimalarials, due to its intrinsic differences from the type I pathway operating in humans. β‐Ketoacyl acyl carrier protein (ACP) reductase (FabG) performs the NADPH‐dependent reduction of β‐ketoacyl‐ACP to β‐hydroxyacyl‐ACP, the first reductive step in the elongation cycle of fatty acid biosynthesis. In this article, we report intensive studies on the direct interactions of Plasmodium FabG and Plasmodium ACP in solution, in the presence and absence of its cofactor, NADPH, by monitoring the change in intrinsic fluorescence of P. falciparum FabG (PfFabG) and by surface plasmon resonance. To address the issue of the importance of the residues involved in strong, specific and stoichiometric binding of PfFabG to P. falciparum ACP (PfACP), we mutated Arg187, Arg190 and Arg230 of PfFabG. The activities of the mutants were assessed using both an ACP‐dependent and an ACP‐independent assay. The affinities of all the PfFabG mutants for acetoacetyl‐ACP (the physiological substrate) were reduced to different extents as compared to wild‐type PfFabG, but were equally active in biochemical assays with the substrate analog acetoacetyl‐CoA. Kinetic analysis and studies of direct binding between PfFabG and PfACP confirmed the identification of Arg187 and Arg230 as critical residues for the PfFabG–PfACP interactions. Our studies thus reveal the significance of the positively charged/hydrophobic patch located adjacent to the active site cavities of PfFabG for interactions with PfACP.
Characterization of mutations in crucial residues around the Qo binding site of the cytochrome bc1 complex from Paracoccus denitrificans
Authors: Kleinschroth Thomas , Anderka Oliver , Ritter Michaela , Stocker Andreas , Link Thomas A. , Ludwig Bernd , Hellwig Petra
Published: August 2008

The protonation state of residues around the Qo binding site of the cytochrome bc1 complex from Paracoccus denitrificans and their interaction with bound quinone(s) was studied by a combined electrochemical and FTIR difference spectroscopic approach. Site‐directed mutations of two groups of conserved residues were investigated: (a) acidic side chains located close to the surface and thought to participate in a water chain leading up to the heme bL edge, and (b) residues located in the vicinity of this site. Interestingly, most of the mutants retain a high degree of catalytic activity. E295Q, E81Q and Y297F showed reduced stigmatellin affinity. On the basis of electrochemically induced FTIR difference spectra, we suggest that E295 and D278 are protonated in the oxidized form or that their mutation perturbs protonated residues. Mutations Y302, Y297, E81 and E295, directly perturb signals from the oxidized quinone and of the protein backbone. By monitoring the interaction with the inhibitor stigmatellin for the wild‐type enzyme at various redox states, interactions of the bound stigmatellin with amino acid side chains such as protonated acidic residues and the backbone were observed, as well as difference signals arising from the redox active inhibitor itself and the replaced quinone. The infrared difference spectra of the above Qo site mutations in the presence of stigmatellin confirm the previously established role of E295 as a direct interaction partner in the enzyme from P. denitrificans as well. The protonated residue E295 is proposed to change the hydrogen‐bonding environment upon stigmatellin binding in the oxidized form, and is deprotonated in the reduced form. Of the residues located close to the surface, D278 remains protonated and unperturbed in the oxidized form but its frequency shifts in the reduced form. The mechanistic implications of our observations are discussed, together with previous inhibitor binding data, and referred to the published X‐ray structures.
SURREPLY
Authors: Edwards Hon. Leonard , Baron Steve , Ferrick George
Published: August 2008

This is a follow‐up to our previous “Comment” responding to an article by William How and Hugh McIsaac.
Exploring the species diversity of Trichoderma in Norwegian drinking water systems by DNA barcoding
Authors: HAGESKAL GUNHILD , VRÅLSTAD TRUDE , KNUTSEN ANN KRISTIN , SKAAR IDA
Published: August 2008

A total of 123 Trichoderma strains were isolated from Norwegian surface‐sourced drinking water. The water samples included raw water, treated water, and water from private homes and hospital installations. Trichoderma species are difficult to differentiate morphologically, but recent molecular identification tools, including DNA barcoding, successfully distinguish between closely related species. The diversity of Trichoderma spp. was explored by DNA sequencing of internal transcribed spacer (ITS) and translation elongation factor 1 alpha (TEF‐1α). Sequence identification was performed in the TrichOKEY version 2.0 barcode program and in the multilocus similarity search database TrichoBLAST, combined with traditional blast searches in the EMBL/GenBank. A total of 11 known Trichoderma/Hypocrea species were identified. In addition, one group of unidentified Trichoderma strains was found to represent a separate, strongly supported subclade within the Pachybasium‘A’/Hamatum clade, based on their TEF‐1α haplotypes. Trichoderma viride comprised 49% of the identified strains, and was represented by four and eight slightly different ITS and TEF‐1α haplotypes, respectively. Approximately 22% of the surface‐derived water samples were positive for T. viride, and the species was frequently isolated throughout the surface‐sourced drinking water distribution system. The results indicate that a broad range of Trichoderma species are present in Norwegian surface‐sourced drinking. Water treatment has minor effect in removing Trichoderma from raw water, and active growth in the water distribution system is likely to occur.
Pathological role of CD44 on NKT cells in carbon tetrachloride‐mediated liver injury
Authors: Kimura Kiminori , Nagaki Masahito , Matsuura Tomokazu , Moriwaki Hisataka , Kakimi Kazuhiro
Published: August 2008

Aim:  CD44 has a variety of functions in immune regulation and signal transduction. Although CD44 is involved in the induction of several inflammatory diseases, it remains unknown whether CD44‐targeting therapies are useful for liver diseases. Here, we examined whether CD44 blockade is effective in a chemical‐induced liver injury model.

Methods:  We injected CD44 knock out (KO) or wild type mice with carbon tetrachloride (CCl4) and examined the difference of liver injury by immunological or histological analysis.

Results:  Although CD44KO mice exhibited suppressed liver injury at 6 h after CCl4 injection with decreased inflammatory cell numbers and cytokine production, these mice showed severe liver injury at 24 h. We found that NKT cells played an important role in liver injury with increased infiltration of theliver after migration, which was independent of the CD44 pathway. In CD44NKT double‐KO mice, liver injury was suppressed with reduced cytokine production and macrophage infiltration compared with CD44KO mice. Furthermore, MIP‐2 derived from NKT cells or tumor necrosis factor alpha from macrophages contributed to exacerbation of the liver injury, since neutralization of MIP‐2 provided significant protection against liver injury in CD44KO mice. Finally, we found that CD44KO mice exhibited excessive liver fibrosis compared with wild‐type mice after repeated CCl4 injections.

Conclusion:  We found that CD44 has unique characteristics for inflammatory liver diseases associated with NKT cell infiltration and activation. Furthermore, CD44‐targeting therapies may need to be viewed with caution for liver diseases due to the actions of the liver immune system.
Mechanisms of Self-Sustained Oscillations Induced by a Flow Over a
Cavity
Authors: Massenzio Michel , Blaise Alain , Lesueur Claude
Published: August 2008

This paper discusses the phenomena of flow-acoustic coupling between an unstable shear layer across a slot covering a cavity, thereby forming a Helmholtz resonator. The flow was caused by a turbulent boundary layer flowing over the slot. The physical phenomena implicated were responsible for the generation of high-amplitude sound level that occurred at the resonant frequencies of the system. It concerns a wide variety of applications, especially in the transport industry. Cavity oscillations have been studied steadily for some 50years and there is by now a vast and conflicting literature on the measured tonal frequencies, the physical explanations, and the predictive models for them. A theory was presented to predict the onset of the instability. It was based on the identification of the main parameters that played a role in the shear layer. Particularly it was suggested to use the frequency dependent phase velocity instead of the flow velocity. The theory was then confronted with results obtained from an experimental study carried out in a wind tunnel on several models. This validation underlined the sturdiness and the efficiency of the model, which made it useful for engineering applications.
Analytical Solutions for DVA Optimization Based on the Lyapunov Equation
Authors: Du Dong
Published: August 2008

A novel method is proposed to obtain the optimum configuration of dynamic vibration absorber (i.e., DVA) attached to an undamped or damped primary structure. The performance index, i.e., the quadratic integration, includes two types of controls, i.e., velocity and displacement controls of the primary mass. Based on the Lyapunov equation, the performance indices are simplified into matrix quadratic forms. With the help of the Kronecker product and matrix column expansion, the closed-form solutions of optimum parameters for undamped primary structure are finally presented. Moreover, in some cases, the method can produce perturbation solutions in simple forms for damped primary structure. Especially, from these solutions, the classical optimum H2 designs under external force or base acceleration excitation can be derived out.
Stochastic Averaging of Strongly Nonlinear Oscillators Under Combined Harmonic and Wide-Band Noise Excitations
Authors: Wu Y. J. , Zhu W. Q.
Published: August 2008

Physical and engineering systems are often subjected to combined harmonic and random excitations. The random excitation is often modeled as Gaussian white noise for mathematical tractability. However, in practice, the random excitation is nonwhite. This paper investigates the stationary response probability density of strongly nonlinear oscillators under combined harmonic and wide-band noise excitations. By using generalized harmonic functions, a new stochastic averaging procedure for estimating stationary response probability density of strongly nonlinear oscillators under combined harmonic and wide-band noise excitations is developed. The damping can be linear and (or) nonlinear and the excitations can be external and (or) parametric. After stochastic averaging, the system state is represented by two-dimensional time-homogeneous diffusive Markov processes. The method of reduced Fokker–Planck–Kolmogorov equation is used to investigate the stationary response of the vibration system. A nonlinearly damped Duffing oscillator is taken as an example to show the application and validity of the method. In the case of primary external resonance, based on the stationary joint probability density of amplitude and phase difference, the stochastic jump of the Duffing oscillator and P-bifurcation as the system parameters change are examined for the first time. The agreement between the analytical results and those from Monte Carlo simulation of original system shows that the proposed procedure works quite well.
Inversion-Based Feedforward Approach to Broadband Acoustic Noise Reduction
Authors: Waite Tom C. , Zou Qingze , Kelkar Atul
Published: August 2008

In this article, an inversion-based feedforward control approach to achieve broadband active-noise control is investigated. Broadband active-noise control is needed in many areas, from heating, ventilation and air conditioning (HVAC) ducts to aircraft cabins. Achieving broadband active-noise control, however, is very challenging due to issues such as the complexity of acoustic dynamics (which has no natural roll-off at high frequency, and is often nonminimum phase), the wide frequency spectrum of the acoustic noise, and the critical requirement to overcome the delay of the control input relative to the noise signal. These issues have limited the success of existing feedforward control techniques to the low-frequency range of [0,1]kHz. The modeling issues in capturing the complex acoustic dynamics coupled with its nonminimum-phase characteristic also prevent the use of high-gain feedback methods, making the design of an effective controller to combat broadband noises challenging. In this article, we explore, through experiments, the potential of inversion-based feedforward control approach for noise control over the 1kHz low-frequency range limit. Then we account for the effect of modeling errors on the feedforward input by a recently developed inversion-based iterative control technique. Experimental results presented show that noise reduction of over 10–15dB can be achieved in a broad frequency range of 5kHz by using the inversion-based feedforward control technique.
Stability Analysis of a Three-Ball Automatic Balancer
Authors: Lu Chung-Jen , Hung Chia-Hsing
Published: August 2008

Ball-type automatic balancers can effectively reduce the vibrations of optical disk drives due to the inherent imbalance of the disk. Although the ball-type automatic balancer used in practice consists of several balls moving along a circular orbit, few studies have investigated the dynamic characteristics of ball-type balancers with more than two balls. The aim of this paper is to study the dynamic characteristics of a three-ball automatic balancer. Emphasis is put on the effects of the number of balls on the stability of the perfect balancing positions—the equilibrium positions where the disk is perfectly balanced. A theoretical model of an optical disk drive packed with a three-ball automatic balancer is constructed first. The governing equations of the theoretical model are derived using Lagrange’s equations. Closed-form formulas for the equilibrium positions are presented. The stability of the perfect balancing positions is checked with the variations for a pair of design parameters. Stable regions of the perfect balancing positions in the parameter plane of a three-ball balancer are identified and compared with those of a two-ball balancer.
Algorithms for Generating Adaptive Projection Patterns for 3D Shape Measurement
Authors: Peng Tao , Gupta Satyandra K.
Published: August 2008

Point cloud construction using digital fringe projection (PCCDFP) is a noncontact technique for acquiring dense point clouds to represent the 3D shapes of objects. Most existing PCCDFP systems use projection patterns consisting of straight fringes with fixed fringe pitches. In certain situations, such patterns do not give the best results. In our earlier work, we have shown that for surfaces with large range of normal directions, patterns that use curved fringes with spatial pitch variation can significantly improve the process of constructing point clouds. This paper describes algorithms for automatically generating adaptive projection patterns that use curved fringes with spatial pitch variation to provide improved results for an object being measured. We also describe the supporting algorithms that are needed for utilizing adaptive projection patterns. Both simulation and physical experiments show that adaptive patterns are able to achieve improved performance, in terms of measurement accuracy and coverage, as compared to fixed-pitch straight fringe patterns.
Description Logic Representation of Finite Element Analysis Models for Automated Retrieval
Authors: Udoyen Nsikan , Rosen David
Published: August 2008

Adaptive reuse of archived parametric finite element analysis (FEA) models involves integration of new information into archived models to model similar new problems. Retrieval of relevant archived models and supporting documents from electronic repositories is difficult when a modeler is unable to describe information needs precisely in a query using keywords. The use of description logic (DL) concepts to describe archived models and build expandable classification hierarchies to facilitate retrieval is proposed and illustrated. A domain-independent retrieval algorithm based on the traversal of description logic concept hierarchies is introduced. The usefulness of the approach is asserted by showing that precise classifications of FEA models can be automatically computed from semantically rich representations in a fairly inexpressive DL using subsumption. The usefulness of subsumption hierarchies for efficient retrieval of FEA models illustrates the benefits of DL for their automated management.
Applications of Software Engineering to Manufacturing Process Planning
Authors: Sundararajan V. , Wright Paul K.
Published: August 2008

Agile methods of software development promote the use of flexible architectures that can be rapidly refactored and rebuilt as necessary for the project. In the mechanical engineering domain, software tends to be very complex and requires the integration of several modules that result from the efforts of large numbers of programmers over several years. Such software needs to be extensible, modular, and adaptable so that a variety of algorithms can be quickly tested and deployed. This paper presents an application of the unified process (UP) to the development of a research process planning system called CyberCut. UP is used to (1) analyze and critique early versions of CyberCut and (2) to guide current and future developments of the CyberCut system. CyberCut is an integrated process planning system that converts user designs to instructions for a computer numerical control (CNC) milling machine. The conversion process involves algorithms to perform tasks such as feature extraction, fixture planning, tool selection, and tool-path planning. The UP-driven approach to the development of CyberCut involves two phases. The inception phase outlines a clear but incomplete description of the user needs. The elaboration phase involves iterative design, development, and testing using short cycles. The software makes substantial use of design patterns to promote clean and well-defined separation between and within components to enable independent development and testing. The overall development of the software tool took about two months with five programmers. It was later possible to easily integrate or substitute new algorithms into the system so that programming resources were more productively used to develop new algorithms. The experience with UP shows that methodologies such as UP are important for engineering software development where research goals, technology, algorithms, and implementations show dramatic and frequent changes.
Atomic force microscopy and scanning tunneling microscopy-spectroscopy characterization of ZnO nanobelts
Authors: Maffeïs T. G. G. , Penny M. W. , Brown M. R. , Liew K. W. , Fu D. , Tsolakoglou N. , Wright C. J. , Wilks S. P.
Published: August 2008

The surface properties of ZnO nanobelts grown by chemical vapor deposition were investigated by tapping mode atomic force microscopy (AFM) and scanning tunneling microscopy (STM). AFM images showed a type 1 (high aspect ratio) nanobelt lying across a type 2 (low aspect ratio) nanobelt, bending at an angle of 20.9° without breaking. Step defects were also observed on the surface for the first time, with step edges running along the [−1−120] direction. These surface defects are also observed by STM while scanning tunneling spectroscopy measurements yield a band gap of 3.3eV and near flatband conditions.
Surface bound organic nanowires
Authors: Balzer Frank , Schiek Manuela , Rubahn Horst-Günter , Al-Shamery Katharina , Lützen Arne
Published: August 2008

The results of a comparative study of nanowires grown on single crystalline substrates from para-hexaphenylene, α-sexithiophene, and 5,5′-Di-4-biphenyl-2,2′-bithiophene are presented. Due to their interesting optical properties such nanowires are of importance for future integrated optoelectronic devices. From atomic force microscopy and polarized far-field optical microscopy data, it is deduced that epitaxy and electrostatic interactions determine the microscopic growth mechanism, whereas kinetics ascertains the macroscopic habit. Understanding such basic growth principles for these systems allows one to predict qualitatively nanowire surface growth from other conjugated molecules and thus allows for a sophisticated design of new devices.
Impact of near-surface native point defects, chemical reactions, and surface morphology on ZnO interfaces
Authors: Doutt D. R. , Zgrabik C. , Mosbacker H. L. , Brillson L. J.
Published: August 2008

The authors used a complement of depth-resolved cathodoluminescence spectroscopy (DRCLS), atomic force microscopy (AFM), and Kelvin probe force microscopy (KPFM) to correlate the formation of native point defects with interface chemical reactions as well as surface morphology. A wide array of ZnO crystals grown by both melt and hydrothermal growth methods display orders-of-magnitude variation in 2.1, 2.5, and 3.0eV native point defect optical transitions at their free surface and as a function of depth on a nanometer scale. AFM surface morphology scans taken simultaneously with KPFM potential maps reveal large variations in surface morphology related to the growth method and subsequent processing. Notably, when DRCLS defect emissions are low, the surface roughness is low and the morphology matches its respective KPFM potential map. When DRCLS emissions vary with depth, the morphology and potential maps do not correlate. Indeed, the latter can vary by hundreds of meV across micron square areas. These subsurface electrical changes are consistent with DRCLS features and emphasize the contribution of surface morphology to electrically active interface defects. The relative strength of near band edge to deep level defect emissions exhibit a threshold dependence on surface roughness.