bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel Brucella isolate in association with two cases of stillbirth in non‐human primates – first report
Authors: Schlabritz‐Loutsevitch Natalia E. , Whatmore Adrian M. , Quance Christine R. , Koylass Mark S. , Cummins L. Bill , Dick Jr Edward J. , Snider Cathy L. , Cappelli David , Ebersole Jeffrey L. , Nathanielsz Peter W. , Hubbard Gene B.
Published: January 2009

Background  Brucellosis is veterinary and human health problem.

Methods  A 13‐year‐old wild caught multiparous and an 8‐year‐old colony‐born nulliparous baboon had stillbirths in the second trimester of pregnancy. Culture isolates from both postpartum uteruses were characterized using traditional biochemical analysis, PCR, and multilocus sequencing.

Results  The isolates morphologically resembled Brucella although their phenotypic characteristics were not consistent with any currently described species. The isolates represent a novel lineage within the genus with unique alleles, not previously seen in surveys of greater than 300 isolates representing the known diversity of the genus, present at 5/9 loci examined.

Conclusions  The described cases are to the best of our knowledge the first presentation of a naturally acquired Brucella infection in non‐human primates associated with stillbirths from the same colony where Brucella seropositivity in the baboons was described 45 years ago. The organism appears to represent a previously undescribed Brucella species.
The relationship between environmental complexity, species diversity and productivity in a natural reconstructed yeast community
Authors: Replansky Taissa , Bell Graham
Published: January 2009

Diversity, whether ecological or genetic, is widely believed to be beneficial to the functioning of ecosystems. Although many studies have investigated relationships between environmental complexity, species diversity and ecosystem function, few have examined these factors simultaneously. We propagated combinations of three naturally coexisting yeast species for 200 generations, in environments of increasing complexity represented by combinations of up to eight different carbon sources. We found that competitive ability was transitive, and not related to productivity, which was equal among the species. Species diversity had a positive effect on productivity and overyielding in mixtures was caused primarily by complementation. Environmental complexity and species diversity were positively correlated, though not significantly, and the sole case of coexistence of all three yeasts after 200 generations occurred on a single carbon source, melezitose. Environmental complexity also enhanced productivity, although this relationship failed, for unknown reasons, at the highest level of complexity. Our results suggest that maintaining species diversity contributes to ecosystem productivity, but that the mechanisms responsible for maintaining diversity may not be straightforward.
African sunbirds hover to pollinate an invasive hummingbird‐pollinated plant
Authors: Geerts Sjirk , Pauw Anton
Published: January 2009

Why do hummingbirds hover while Old World nectar‐feeding birds perch? A unique opportunity to explore this question is presented by the invasion into Africa of a plant adapted for pollination by hovering hummingbirds. Like other hover‐pollinated plants of the New World, the flowers of the tree tobacco Nicotiana glauca lack perches and are oriented towards open space. We find that Old World nectarivores, especially the malachite sunbird, Nectarinia famosa, hover 80% of the time when taking nectar from these flowers. They hover for up to 30 s, and are able to sustain this hovering lifestyle in an area where native nectar plants are absent. Nicotiana glauca greatly increases the local abundance of sunbirds compared with uninvaded areas. In turn, flowers visited by sunbirds formed significantly more capsules and set significantly more seed than sunbird‐excluded flowers, possibly facilitating the invasion. The results suggest a prominent role for plant, rather than bird traits in determining the occurrence of hover‐pollination, begging the question of why plants adapted for hover pollination do not occur outside the New World.
Effects of urbanisation on disease prevalence and age structure in blackbirdTurdus merulapopulations
Authors: Evans Karl L. , Gaston Kevin J. , Sharp Stuart P. , McGowan Andrew , Simeoni Michelle , Hatchwell Ben J.
Published: January 2009

Despite increasing interest in urban ecology most attention has focussed on describing changes in assemblage composition and structure along urbanisation gradients, whilst relatively little research has focussed on the mechanisms behind these changes. Ecological theory predicts that alterations in biotic interactions are particularly likely to arise, especially with regard to disease risk. Here, we report on differences in prevalence of avian malaria and tick infection and intensity in 11 paired urban and rural blackbirdTurdus merulapopulations from across the western Palearctic. We find large and consistent reductions in tick prevalence and intensity in urban areas. There are also large reductions in the prevalence of avian malaria in many, but not all, urban areas. The proportion of first year birds in urban populations is significantly lower than that in rural ones, and across the more natural rural sites southerly populations contain fewer first years than northern ones. These patterns are expected to arise if survival rates are higher in urban areas, and are negatively correlated with latitude.
Benthic algae support zooplankton growth during winter in a clear‐water lake
Authors: Karlsson Jan , Säwström Christin
Published: January 2009

We used stable carbon (δ13C) and nitrogen (δ15N) isotopes to assess the importance of benthic algae for the zooplankton individual growth in winter in a shallow, clear subarctic lake. The δ13C values of calanoid (Eudiaptomus graciloides) and cyclopoid (Cyclops scutifer) zooplankton in autumn suggest a food resource of pelagic origin during the ice‐free period. The zooplankton δ13C values were high in spring compared to autumn. E. graciloides did not grow over winter and the change in δ13C was attributed to a decrease in lipid content during the winter. In contrast, the increase in δ13C values of C. scutifer over the winter was explained by their growth on organic carbon generated by benthic algae. The δ15N of the C. scutifer food resource during winter was low compared to δ15N of the benthic community, suggesting that organic matter generated by benthic algae was mainly channelled to zooplankton via 15N‐depleted heterotrophic bacteria. The results demonstrate that benthic algae can sustain zooplankton metabolic demands and growth during long winters, which, in turn, may promote zooplankton growth on pelagic resources during the summer. Such multi‐chain omnivory challenges the view of zooplankton as mainly dependent on internal primary production and stresses the importance of benthic resources for the productivity of plankton food webs in shallow lakes.
Retention of dead leaves by grasses as a defense against herbivores. A test on the palatable grass Paspalum dilatatum
Authors: Mingo Antonio , Oesterheld Martín
Published: January 2009

The vast majority of grass species retain their leaves as they become senescent, inducing an accumulation of dead biomass that may limit plant productivity. In this research, we tested the hypothesis that dead leaf retention by grasses act as a defense against large herbivores. In a natural grassland of the Flooding Pampa, we carried out a factorial experiment with dead‐leaf removal and grazing as main factors. Dead leaves were removed from the palatable grass Paspalum dilatatum, and growth was measured either in the absence or in the presence of large grazers. In the absence of grazers, dead‐leaf removal promoted plant growth. In the presence of grazers, dead‐leaf removal increased consumption by cattle, particularly among the largest plants. As a result, in the presence of grazers, plants with dead leaves removed grew less than intact plants. The results indicate that retaining dead leaves is costly for grass species in the absence of grazers, but, as proposed by our hypothesis, that cost is compensated by a corresponding reduction of grazing consumption.
Tissue viability imaging: mapping skin erythema
Authors: Zhai Hongbo , Chan Heidi P. , Farahmand Sara , Nilsson Gert E. , Maibach Howard I.
Published: January 2009

Background: Tissue Viability Imaging (TiVi) is an emerging bioengineering technology intended for two‐dimensional mapping of skin erythema and blanching. Before TiVi can be effectively used in studies of diseased or damaged skin, the variability in normal skin red blood cell concentration (RBCconc) requires evaluation.

Objective: To demonstrate how TiVi maps spatial and temporal variations in normal skin RBCconc at the dorsal side of the hand at rest and during post‐occlusive hyperemia.

Methods: Short‐term and day‐to‐day variations in skin RBCconc were quantified at the dorsal side of the hand in four healthy volunteers at rest. In a separate study, the increase in skin RBCconc was recorded during post‐occlusive hyperemia.

Results: A lower skin RBCconc (179–184 TiVi units) was observed at the back of the hand and base of the thumb compared with areas adjacent to the nailfoldfold region of the fingers (190–213 TiVi units). The short‐term variation (within 70 s) was <2% in all areas of the dorsal side of the hand, while day‐to‐day variations were in the range 5–7% in the back of the hand and up to 10% in areas adjacent to the nailfold region. In the post‐occlusive hyperemia phase, up to a 60% increase in skin RBCconc was observed in the early part of the reactive hyperemia phase. This increase in skin RBCconc successively decreased but remained about 18% above the pre‐occlusion level after 30 min.

Conclusion: Establishment of healthy skin RBCconc reference values is important for the design of versatile test procedures for assessment of skin damage caused by vibration tools, chemical exposure or peripheral vascular disease.
Bone density at interradicular sites: implications for orthodontic mini‐implant placement
Authors: Chun YS , Lim WH
Published: January 2009

Structured Abstract

Authors –  Chun YS, Lim WH

Objectives –  Implant stability is primarily related to local bone density; Few studies have evaluated interradicular bone density related to mini‐implant placement for orthodontic anchorage. Therefore, this study evaluated bone density differences between interradicular sites.

Setting and Sample Population –  Computed tomographic (CT) images were obtained from 14 males and 14 females (mean age 27 years, range 23–35 years). Bone density in Hounsfield units (HU) was measured at 13 interradicular sites and four bone levels.

Results –  Bone densities in most areas were higher than 850 HU. Statistically significant differences in bone density were detected at different levels and sites. Bone densities in both maxilla and mandible significantly increased from the alveolar crest toward basal bone in posterior areas, while the opposite was observed in anterior areas. There were statistically significant differences in bone densities between the maxilla and mandible in posterior areas. Bone densities progressively increased from anterior to posterior areas in the mandible.

Conclusion –  The results suggest that mini‐implants for orthodontic anchorage may be effective when placed in most areas with equivalent bone density up to 6 mm apical to the alveolar crest. Site selection should be adjusted according to bone density assessment.
Reproducibility of facial soft tissue landmarks on 3D laser‐scanned facial images
Authors: Toma AM , Zhurov A , Playle R , Ong E , Richmond S
Published: January 2009

Structured Abstract

Authors –  Toma AM, Zhurov A, Playle R, Ong E, Richmond S

Background –  The three‐dimensional (3D) measuring technology is useful to inspect facial shape in three planes of space (X, Y, and Z). Recent work has been directed to analyse craniofacial morphology using facial soft tissue landmarks to identify facial differences among population. The reproducibility of facial landmarks is almost necessary to ensure accurate 3D facial measurements.

Objective –  The aim of this study is to assess the reproducibility of facial soft tissue landmarks using laser‐scan 3D imaging technology.

Subjects and Methods –  Facial landmarks were assessed for 30 15½‐year‐old British‐Caucasian children (15 males and 15 females). The sample was recruited from the Avon Longitudinal Study of Parents and Children (ALSPAC). The 3D facial images were acquired for each subject using two high‐resolution Konica/Minolta laser scanners. Twenty‐one facial landmarks (63 X, Y, and Z coordinates) were identified and recorded on each 3D facial image by two examiners. The reproducibility of landmarks identification at 2‐week interval was assessed for one of the examiners (intra‐examiner). In addition, the reproducibility of landmarks was assessed between the two examiners (inter‐examiner). Using Bland‐Altman plots, both intra‐ and inter‐examiner assessments had evaluated landmarks reproducibility in three dimensions for the sample divided by gender. The reproducibility of the 3D‐coordinates for each landmark was considered under three categories (< 0.5 mm, < 1 mm, and >1 mm) for both intra‐ and inter‐examiner reproducibility assessments.

Results –  The distribution of coordinates at the three levels of reproducibility show the following percentages: intra‐examiner: < 0.5 mm (38%), < 1 mm (51%), >1 mm (11%); inter‐examiner: < 0.5 mm (35%), < 1 mm (48%), >1 mm (17%). Generally, 10 landmarks were reproducible to less than 1 mm for both intra‐ and inter‐examiner reproducibility assessments. The Labiale Superius was the most reproducible and Palebrale Superius was the least reproducible landmark. Some landmarks showed greater reliability in certain planes of space; the Glabella was more reliable in the Z than the Y axis. Gender differences were found; Subnasale was more reproducible in the Y‐axis in males compared with females.

Conclusions –  The reproducibility of facial landmarks should be considered in the three planes of space. The majority of X‐Y‐Z coordinates taken to the 21 facial landmarks were reproducible to < 1 mm which is clinically acceptable. The accuracy of landmarks identification ranged from 0.39 to 1.49 mm. The reliability in identification depends on the clarity and definition of each landmark as well as gender characteristics. The different landmarks reproducibility should be considered when evaluating changes related to growth and healthcare interventions.
Intolerance reactions to knee arthroplasty in patients with nickel/cobalt allergy and disappearance of symptoms after revision surgery with titanium‐based endoprostheses
Authors: Dietrich Karin‐Almut , Mazoochian Farhad , Summer Burkhard , Reinert Mark , Ruzicka Thomas , Thomas Peter
Published: January 2009

Intolerance reactions to metal implants may present as dermatitis, impaired wound healing, effusions, pain or loosening. The clinical relevance of metal allergy in the differential diagnosis is often unclear and patients may even tolerate implants containing metals to which they are allergic. We present four patients with knee arthroplasty in whom after exclusion of infection or mechanical causes, a nickel/cobalt allergy led to replacement surgery with titanium‐based prostheses. The subsequent alleviation of symptoms underlined the relevance and usefulness of allergological diagnostics in selected cases of complicated arthroplasty.
High prevalence of cardio‐metabolic risk factors among adolescents with intellectual disability
Authors: Wallén Eva Flygare , Müllersdorf Maria , Christensson Kyllike , Malm Gunilla , Ekblom Örjan , Marcus Claude
Published: January 2009

Adults with intellectual disabilities (IDs) have poor lifestyle‐related health compared with the general population. Our aim was to study whether such differences are present already in adolescents.

Aim: To compare the prevalence and severity of cardio‐metabolic risk factors and cardio‐vascular fitness in adolescents with and without IDs.

Methods: Intellectual disability (ID) students (n = 66) and non‐intellectual disability (non‐ID) students from practical (non‐ID‐p) (n = 34) and theoretical (non‐ID‐t) (n = 56) programmes were recruited from three upper secondary schools. Anthropometric data, blood pressure, body composition, fasting‐insulin, fasting‐glucose, fasting‐lipids and cardio‐vascular fitness were measured.

Results: Participants with and without ID differed significantly in the prevalence of cardio‐metabolic risk factors with participants with ID having a higher percentage of total fat mass, wider waist circumferences (WCs), lower levels of fat‐free mass (FFM), lower bone mineral density (BMD) and higher insulin and homeostasis model assessment of insulin resistance (HOMA) levels and poorer cardio‐vascular fitness. The healthiest levels were found in the non‐ID‐t group compared to the group with ID and the group with non‐ID‐p in between.

Conclusion: The prevalence of cardio‐metabolic risk factors and poor cardio‐vascular fitness was found to be high in this young population with intellectual disabilities. Measures should be taken to improve the health messages directed towards children and adolescents with intellectual disabilities.
Immunolocalization of Fascin, an Actin‐Bundling Protein and Glial Fibrillary Acidic Protein in Human Astrocytoma Cells
Authors: Mondal Soma , Dirks Peter , Rutka James T.
Published: January 2009

Fascin is a 55‐kDa globular protein that functions to organize filamentous‐actin into parallel bundles. A role for fascin in cell migration has led to its study in many tumor types. In this report, we investigate fascin in astrocytomas. We show that fascin is expressed in astrocytes and in a panel of human astrocytoma cell lines. Immunofluorescence analysis demonstrates that fascin and the intermediate filament protein, glial fibrillary acidic protein (GFAP), are both expressed in the perinuclear region and within cytoplasmic processes of astrocytes and astrocytoma cells. Amino acid residues within the NH2 terminus of GFAP can undergo phosphorylation; these modifications regulate intermediate filament disassembly and occur during cytokinesis. We show that fascin and specific phosphorylated species of GFAP colocalize within dividing cells. Finally, we demonstrate that fascin co‐immunoprecipitates with GFAP and that immunocomplex formation is preferential for GFAP phosphorylated at serine residues 8 and 13. These data show that fascin and GFAP are immunolocalized regionally within cells and tumors of astrocytic origin and suggest that their binding may occur during dynamic reorganization of intermediate filaments.
Price discrimination in input markets
Authors: Inderst Roman , Valletti Tommaso
Published: January 2009

We analyze the short‐ and long‐run implications of third‐degree price discrimination in input markets. In contrast to the extant literature, which typically assumes that the supplier is an unconstrained monopolist, in our model input prices are constrained by the threat of demand‐side substitution. In our model, the more efficient buyer receives a discount. A ban on price discrimination thus benefits smaller but hurts more efficient, larger firms. It also stifles incentives to invest and innovate. With linear demand, a ban on price discrimination benefits consumers in the short run but reduces consumer surplus in the long run, which is once again the opposite of what is found without the threat of demand‐side substitution.
Market participation in delegated and intrinsic common‐agency games
Authors: Martimort David , Stole Lars
Published: January 2009

We study how competition in nonlinear pricing between two principals (sellers) affects market participation by a privately informed agent (consumer). When participation is restricted to all or nothing (“intrinsic” agency), the agent must choose between both principals' contracts and selecting her outside option. When the agent is afforded the additional possibilities of choosing only one contract (“delegated” agency), competition is more intense. The two games have distinct predictions for participation. Intrinsic agency always induces more distortion in participation relative to the monopoly outcome, and equilibrium allocations are discontinuous for the marginal consumer. Under delegated agency, relative to monopoly, market participation increases (respectively, decreases) when contracting variables are substitutes (respectively, complements) on the intensive margin. Equilibrium allocations are continuous for the marginal consumer and the range of product offerings is identical to both the first‐best and the monopoly outcome.
Characteristics and Control of the Draft-Tube Flow in Part-Load Francis Turbine
Authors: Zhang Ri-kui , Mao Feng , Wu Jie-Zhi , Chen Shi-Yi , Wu Yu-Lin , Liu Shu-Hong
Published: January 2009

Under part-load conditions, a Francis turbine often suffers from very severe low-frequency and large-amplitude pressure fluctuation, which is caused by the unsteady motion of vortices (known as “vortex ropes”) in the draft tube. This paper first reports our numerical investigation of relevant complex flow phenomena in the entire draft tube, based on the Reynolds-averaged Navier–Stokes (RANS) equations. We then focus on the physical mechanisms underlying these complex and somewhat chaotic flow phenomena of the draft-tube flow under a part-load condition. The flow stability and robustness are our special concern, since they determine what kind of control methodology will be effective for eliminating or alleviating those adverse phenomena. Our main findings about the flow behavior in the three segments of the draft tube, i.e., the cone inlet, the elbow segment, and the outlet segment with three exits, are as follows. (1) In the cone segment, we reconfirmed a previous finding of our research group based on the turbine’s whole-flow RANS computation that the harmful vortex rope is an inevitable consequence of the global instability of the swirling flow. We further identified that this instability is caused crucially by the reversed axial flow at the inlet of the draft tube. (2) In the elbow segment, we found a reversed flow continued from the inlet cone, which evolves to slow and chaotic motion. There is also a fast forward stream driven by a localized favorable axial pressure gradient, which carries the whole mass flux downstream. The forward stream and reversed flow coexist side-by-side in the elbow, with a complex and unstable shear layer in between. (3) In the outlet segment with three exits, the forward stream always goes through a fixed exit, leaving the other two exits with a chaotic and low-speed fluid motion. Based on these findings, we propose a few control principles to suppress the reversed flow and to eliminate the harmful helical vortex ropes. Of the methods we tested numerically, a simple jet injection in the inlet is proven successful.
Abdominal Aortic Aneurysm Risk of Rupture: Patient-Specific FSI Simulations Using Anisotropic Model
Authors: Rissland Peter , Alemu Yared , Einav Shmuel , Ricotta John , Bluestein Danny
Published: January 2009

Abdominal aortic aneurysm (AAA) rupture represents a major cardiovascular risk, combining complex vascular mechanisms weakening the abdominal artery wall coupled with hemodynamic forces exerted on the arterial wall. At present, a reliable method to predict AAA rupture is not available. Recent studies have introduced fluid structure interaction (FSI) simulations using isotropic wall properties to map regions of stress concentrations developing in the aneurismal wall as a much better alternative to the current clinical criterion, which is based on the AAA diameter alone. A new anisotropic material model of AAA that closely matches observed biomechanical AAA material properties was applied to FSI simulations of patient-specific AAA geometries in order to develop a more reliable predictor for its risk of rupture. Each patient-specific geometry was studied with and without an intraluminal thrombus (ILT) using two material models—the more commonly used isotropic material model and an anisotropic material model—to delineate the ILT contribution and the dependence of stress distribution developing within the aneurismal wall on the material model employed. Our results clearly indicate larger stress values for the anisotropic material model and a broader range of stress values as compared to the isotropic material, indicating that the latter may underestimate the risk of rupture. While the locations of high and low stresses are consistent in both material models, the differences between the anisotropic and isotropic models become pronounced at large values of strain—a range that becomes critical when the AAA risk of rupture is imminent. As the anisotropic model more closely matches the biomechanical behavior of the AAA wall and resolves directional strength ambiguities, we conclude that it offers a more reliable predictor of AAA risk of rupture.
Fibril Microstructure Affects Strain Transmission Within Collagen Extracellular Matrices
Authors: Roeder Blayne A. , Kokini Klod , Voytik-Harbin Sherry L.
Published: January 2009

The next generation of medical devices and engineered tissues will require development of scaffolds that mimic the structural and functional properties of the extracellular matrix (ECM) component of tissues. Unfortunately, little is known regarding how ECM microstructure participates in the transmission of mechanical load information from a global (tissue or construct) level to a level local to the resident cells ultimately initiating relevant mechanotransduction pathways. In this study, the transmission of mechanical strains at various functional levels was determined for three-dimensional (3D) collagen ECMs that differed in fibril microstructure. Microstructural properties of collagen ECMs (e.g., fibril density, fibril length, and fibril diameter) were systematically varied by altering in vitro polymerization conditions. Multiscale images of the 3D ECM macro- and microstructure were acquired during uniaxial tensile loading. These images provided the basis for quantification and correlation of strains at global and local levels. Results showed that collagen fibril microstructure was a critical determinant of the 3D global and local strain behaviors. Specifically, an increase in collagen fibril density reduced transverse strains in both width and thickness directions at both global and local levels. Similarly, collagen ECMs characterized by increased fibril length and decreased fibril diameter exhibited increased strain in width and thickness directions in response to loading. While extensional strains measured globally were equivalent to applied strains, extensional strains measured locally consistently underpredicted applied strain levels. These studies demonstrate that regulation of collagen fibril microstructure provides a means to control the 3D strain response and strain transfer properties of collagen-based ECMs.
Prosthetic Ankle-Foot Mechanism Capable of Automatic Adaptation to the Walking Surface
Authors: Williams Ryan J. , Hansen Andrew H. , Gard Steven A.
Published: January 2009

A conceptual design has been generated for a prosthetic ankle-foot mechanism that can automatically adapt to the slope of the walking surface. To help prove this concept, a prototype ankle-foot mechanism was designed, developed, and tested on three subjects with unilateral transtibial amputations walking on level and ramped surfaces. The mechanism is capable of automatically adapting to the walking surface by switching impedance modes at key points of the gait cycle. The mechanism simulates the behavior of the physiologic foot and ankle complex by having a low impedance in the early stance phase and then switching to a higher impedance once foot-flat is reached. The “set-point” at which these changes in impedance occur gets reset on every step in order to reach the proper alignment for the walking surface. The mechanism utilizes the user’s bodyweight to help switch impedance modes and does not require any active control. It was hypothesized that the ankle-foot mechanism would cause the equilibrium point of the ankle moment versus the ankle dorsiflexion angle curves to shift to accommodate the walking surface. For two of the three subjects tested, this behavior was confirmed, supporting the contention that the design provides automatic adaptation for different walking slopes. Further work is needed to develop the prototype into a commercial product, but the mechanism was sufficient for illustrating proof-of-concept.
Viscoelasticity and Preconditioning of Rat Skin Under Uniaxial Stretch: Microstructural Constitutive Characterization
Authors: Lokshin Olga , Lanir Yoram
Published: January 2009

In spite of impressive progress in developing general constitutive laws for soft tissues, there exists still no comprehensive model valid for any general deformation scheme. The present study focuses on the uniaxial response of the skin as a model for other multifibrous soft tissues. While the skin’s nonlinear viscoelastic constitutive response has been extensively studied and modeled, the phenomena associated with mechanical preconditioning have so far not been dealt with. Yet preconditioning is an inherent response feature in the skin, both in vitro and in vivo. It is hypothesized that by considering the structure of the elastic and collagen fibers and their individual rheological properties, it is possible to develop a reliable general constitutive law for the skin’s uniaxial response. A stochastic hybrid constitutive model was developed based on the collagen and elastic fiber morphologies and their rheological properties. The multiple protocol uniaxial data of Eshel and Lanir (“Effects of Strain Level and Proteoglycan Depletion on Preconditioning and Viscoelastic Responses of Rat Dorsal Skin,” 2001, Ann. Biomed. Eng., 29, pp. 164–172) served to estimate the model’s parameters and to validate its reliability. Parametric investigation was then used to test model parsimony (minimal form) and to elucidate the roles of response mechanism and the relative contribution of each constituent. The model predictions show a very close fit to the data and good predictive capability. The results are consistent with the quasilinear viscoelastic response of both elastic and collagen fibers and are likewise consistent with the notion (supported by published experimental observations) that preconditioning in collagen is probably due to an increase in the fiber reference length and is due to strain softening (Mullins effect) in elastic fibers. The predictions also agree with the observed predominance of elastic fibers at low strains and suggest that as strain increases, collagen becomes predominant, but the effect of elastic fibers is still significant. The parsimony analysis of the 22 model parameters (18 are nonlinear in the model) points to the predominant role of viscoelasticity and preconditioning in both fibers, followed in order of importance by collagen waviness and elastic fiber nonlinearity. A reliable and comprehensive uniaxial constitutive law for the rat skin was developed based on the tissue microstructure and on its constituents’ rheological properties.
Correlation Between Angiographic and Particle Image Velocimetry Quantifications of Flow Diverters in an In Vitro Model of Elastase-Induced Rabbit Aneurysms
Authors: Trager Asher L. , Sadasivan Chander , Seong Jaehoon , Lieber Baruch B.
Published: January 2009

The rupture of a cerebral aneurysm can result in a hemorrhagic stroke. A flow diverter, which is a porous tubular mesh, can be placed across the neck of a cerebral aneurysm to induce the cessation of flow and initiate the formation of an intra-aneurysmal thrombus. By finding a correlation between particle image velocimetry (PIV) and digital subtraction angiography, a better assessment of how well an aneurysm is excluded from the parent artery can be made in the clinical setting. A model of a rabbit elastase-induced aneurysm was connected to a mock circulation loop. The model was then placed under angiography. Recorded angiograms were analyzed so that a contrast concentration-time curve based on the average grayscale intensity inside the aneurysm could be determined. That curve was then fitted to a mathematical model that quantifies the influence of convection and diffusion on contrast transport. Optimized parameters were correlated with the intraneurysmal mean kinetic energy measured by PIV in the same aneurysm model. A strong correlation was observed between the convection and diffusion time constants and the mean kinetic energy inside the aneurysm. Analyzing the flow of angiographic contrast into and out of the aneurysm after implantation of a flow diverter allows for prediction of the efficacy of the device in excluding the aneurysm. Correlating hydrodynamic measures obtained by angiography to those obtained by detailed techniques such as PIV increases confidence in such predictions.
Axial Development of Flow Regime in Adiabatic Upward Two-Phase Flow in a Vertical Annulus
Authors: Julia J. Enrique , Ozar Basar , Dixit Abhinav , Jeong Jae-Jun , Hibiki Takashi , Ishii Mamoru
Published: January 2009

This study has investigated the axial development of flow regime of adiabatic upward air-water two-phase flow in a vertical annulus. The inner and outer diameters of the annulus are 19.1 mm and 38.1 mm, respectively. The hydraulic diameter of the flow channel, DH, is 19.0 mm and the total length is 4.37 m. The flow regime map includes 72 flow conditions within a range of 0.01 m/s<⟨jg⟩<30 m/s and 0.2 m/s<⟨jf⟩<3.5 m/s, where ⟨jg⟩ and ⟨jf⟩ are, respectively, superficial gas and liquid velocities. The flow regime has been classified into four categories: bubbly, cap-slug, churn, and annular flows. In order to study the axial development of flow regime, area-averaged void fraction measurements have been performed using impedance void meters at three axial positions corresponding to z/DH=52, 149, and 230 simultaneously, where z represents the axial position. The flow regime indicator has been chosen to be statistical parameters from the probability distribution function of the area-averaged void fraction signals from the impedance meters, and self-organized neural networks have been used as the mapping system. This information has been used to analyze the axial development of flow regime as well as to check the predictions given by the existing flow regime transition models. The axial development of flow regime is quantified using the superficial gas velocity and void fraction values where the flow regime transition takes place. The predictions of the models are compared for each flow regime transition. In the current test conditions, the axial development of flow regime occurs in the bubbly to cap-slug (low superficial liquid velocities) and cap-slug to churn (high superficial liquid velocities) flow regime transition zones.
Contribution of Fish to the Marine Inorganic Carbon Cycle
Authors: Wilson R. W. , Millero F. J. , Taylor J. R. , Walsh P. J. , Christensen V. , Jennings S. , Grosell M.
Published: January 2009

Oceanic production of calcium carbonate is conventionally attributed to marine plankton (coccolithophores and foraminifera). Here we report that marine fish produce precipitated carbonates within their intestines and excrete these at high rates. When combined with estimates of global fish biomass, this suggests that marine fish contribute 3 to 15% of total oceanic carbonate production. Fish carbonates have a higher magnesium content and solubility than traditional sources, yielding faster dissolution with depth. This may explain up to a quarter of the increase in titratable alkalinity within 1000 meters of the ocean surface, a controversial phenomenon that has puzzled oceanographers for decades. We also predict that fish carbonate production may rise in response to future environmental changes in carbon dioxide, and thus become an increasingly important component of the inorganic carbon cycle.
Programmed Assembly of DNA-Coated Nanowire Devices
Authors: Morrow Thomas J. , Li Mingwei , Kim Jaekyun , Mayer Theresa S. , Keating Christine D.
Published: January 2009

Combining biomolecular function with integrated circuit technology could usher in a new era of biologically enabled electronics. A key challenge has been coupling different molecular functions to specific chip locations for communication with the circuit. We used spatially confined electric fields to assemble different populations of DNA-coated nanowires to desired positions with an accuracy that enabled postassembly fabrication of contacts to each individual nanowire, with high yield and without loss of DNA function. This combination of off-chip synthesis and biofunctionalization with high-density, heterogeneous assembly and integration at the individual nanowire level points to new ways of incorporating biological functionality with silicon electronics.
The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria
Authors: Moran Nancy A. , McLaughlin Heather J. , Sorek Rotem
Published: January 2009

Among cellular organisms, symbiotic bacteria provide the extreme examples of genome degradation and reduction. However, only isolated snapshots of eroding symbiont genomes have previously been available. We documented the dynamics of symbiont genome evolution by sequencing seven strains of
Buchnera aphidicola
from pea aphid hosts. We estimated a spontaneous mutation rate of at least 4 × 10
–9
substitutions per site per replication, which is more than 10 times as high as the rates previously estimated for any bacteria. We observed a high rate of small insertions and deletions associated with abundant DNA homopolymers, and occasional larger deletions. Although purifying selection eliminates many mutations, some persist, resulting in ongoing loss of genes and DNA from this already tiny genome. Our results provide a general model for the stepwise process leading to genome reduction.
Genomic Comparison of PE and PPE Genes in theMycobacterium aviumComplex
Authors: Mackenzie Nick , Alexander David C. , Turenne Christine Y. , Behr Marcel A. , De Buck Jeroen M.
Published: January 2009

TheMycobacterium aviumcomplex (MAC) comprises genomically similar but phenotypically divergent bacteria that inhabit diverse environments and that cause disease in different hosts. In this study, a whole-genome approach was used to examine the polymorphic PE (Pro-Glu) and PPE (Pro-Pro-Glu) gene families, implicated in immunostimulation and virulence. The four major groups of MAC organisms were examined, including the newly sequenced type strains ofM. intracellulareandM. aviumsubsp.avium, plusM. aviumsubsp.paratuberculosisandM. aviumsubsp.hominissuis, for the purpose of finding genetic differences that could be exploited to design diagnostic tests specific to these groups and that could help explain their divergence in pathogenesis and host specificity. Unique and missing PPE genes were found in all MAC members exceptM. aviumsubsp.avium. OnlyM. intracellularehad a unique PE gene. Apart from this, most PE and PPE sequences were conserved, with average nucleotide sequence identities of 99.1 and 98.1%, respectively, among theM. aviumsubspecies, but only 82.9 and 79.7% identities with the PE and PPE sequences ofM. intracellulare, respectively. A detailed analysis of the amino acid sequences was performed betweenM. aviumsubsp.paratuberculosisandM. aviumsubsp.hominissuis. Most differences were detected in the PPE proteins, with amino acid substitutions and frame shifts leading to unique amino acid sequences. In conclusion, several unique PPE proteins were identified in MAC organisms next to numerous polymorphisms in both the PE and PPE gene families. These substantial differences could help explain the divergence in phenotypes within the MAC and could lead to diagnostic tests with better discriminatory abilities.
Biofilm Formation by
Staphylococcus haemolyticus
Authors: Fredheim Elizabeth Gladys Aarag , Klingenberg Claus , Rohde Holger , Frankenberger Stephanie , Gaustad Peter , Flægstad Trond , Sollid Johanna Ericson
Published: January 2009

Infections due to coagulase-negative staphylococci (CoNS) most frequently occur after the implantation of medical devices and are attributed to the biofilm-forming potential of CoNS.
Staphylococcus haemolyticus
is the second most frequently isolated CoNS from patients with hospital-acquired infections. There is only limited knowledge of the nature of
S. haemolyticus
biofilms. The aim of this study was to characterize
S. haemolyticus
biofilm formation. We analyzed the biofilm-forming capacities of 72 clinical
S. haemolyticus
isolates. A detachment assay with NaIO
4
, proteinase K, or DNase was used to determine the main biofilm components. Biofilm-associated genes, including the
ica
operon, were analyzed by PCR, and the gene products were sequenced. Confocal laser scanning microscopy (CLSM) was used to elucidate the biofilm structure. Fifty-three isolates (74%) produced biofilms after growth in Trypticase soy broth (TSB) with glucose, but only 22 (31%) produced biofilms after growth in TSB with NaCl. It was necessary to dissolve the biofilm in ethanol-acetone to measure the optical density of the full biofilm mass. DNase, proteinase K, and NaIO
4
caused biofilm detachment for 100%, 98%, and 38% of the isolates, respectively.
icaRADBC
and polysaccharide intercellular adhesin (PIA) production were found in only two isolates. CLSM indicated that the biofilm structure of
S. haemolyticus
clearly differs from that of
S. epidermidis
. We conclude that biofilm formation is a common phenotype in clinical
S. haemolyticus
isolates. In contrast to
S. epidermidis
, proteins and extracellular DNA are of functional relevance for biofilm accumulation, whereas PIA plays only a minor role. The induction of biofilm formation and determination of the biofilm mass also needed to be optimized for
S. haemolyticus
.
Factors Affecting Isolation and Identification ofMycobacterium aviumsubsp.paratuberculosisfrom Fecal and Tissue Samples in a Liquid Culture System
Authors: Whittington Richard J.
Published: January 2009

Culture ofMycobacterium aviumsubsp.paratuberculosisis the definitive diagnostic test for Johne's disease, a chronic granulomatous enteropathy of animals. Compared to solid media, the identification of all strains of the organism in liquid media can be more difficult because the appearance of colonies and mycobactin dependence are not observable, and the growth of other organisms needs to be distinguished, commonly by PCR. Factors affecting the isolation rate of S strains and the contamination rate in modified Middlebrook 7H9 broth (Bactec 12B) and 7H10 agar were studied using 11,598 fecal samples and 2,577 tissue samples from sheep from 1,421 farms over 10 years. Minimization of contamination in Bactec cultures required the avoidance of the carryover of fecal particles from the first sedimentation step in the double-incubation centrifugation method, and contamination was reduced significantly by incubating the sample in a solution containing vancomycin, amphotericin B, and nalidixic acid for 3 days compared to 2 days. The growth of irrelevant microorganisms confounded the identification ofM. aviumsubsp.paratuberculosisin liquid culture by inhibiting IS900PCR and in solid medium culture by inhibiting the growth ofM. aviumsubsp.paratuberculosisor obscuring colonies. The contamination of samples was clustered in certain laboratory submissions and was reduced by including ampicillin in Bactec medium without affecting the odds of isolation ofM. aviumsubsp.paratuberculosis. The long-term contamination rate for fecal cultures was about 7%, and that for tissue cultures was <0.2%. Liquid medium was more sensitive than solid medium culture forM. aviumsubsp.paratuberculosis. The applicability of these findings for C strains is discussed.
Modified General Primer PCR System for Sensitive Detection of Multiple Types of Oncogenic Human Papillomavirus
Authors: Söderlund-Strand Anna , Carlson Joyce , Dillner Joakim
Published: January 2009

Human papillomavirus (HPV) infection is a necessary cause of cervical cancer and cervical dysplasia. Accurate and sensitive genotyping of multiple oncogenic HPVs is essential for a multitude of both clinical and research uses. We developed a modified general primer (MGP) PCR system with five forward and five reverse consensus primers. The MGP system was compared to the classical HPV general primer system GP5+/6+ using a proficiency panel with HPV plasmid dilutions as well as cervical samples from 592 women with low-grade cytological abnormalities. The reference method (GP5+/6+) had the desirable high sensitivity (five copies/PCR) for five oncogenic HPV types (HPV type 16 [HPV-16], HPV-18, HPV-56, HPV-59, and HPV-66). The MGP system was able to detect all 14 oncogenic HPV types at five copies/PCR. In the clinical samples, the MGP system detected a significantly higher proportion of women with more than two concomitant HPV infections than did the GP5+/6+ system (102/592 women compared to 42/592 women). MGP detected a significantly greater number of infections with HPV-16, -18, -31, -33, -35, -39, -42, -43, -45, -51, -52, -56, -58, and -70 than did GP5+/6+. In summary, the MGP system primers allow a more sensitive amplification of most of the HPV types that are established as oncogenic and had an improved ability to detect multiple concomitant HPV infections.
Specificity of Ertapenem Susceptibility Screening for Detection of
Klebsiella pneumoniae
Carbapenemases
Authors: McGettigan Shannon E. , Andreacchio Kathleen , Edelstein Paul H.
Published: January 2009

Detection of
Klebsiella pneumoniae
carbapenemases (KPCs) can be nonspecific, especially when KPCs are uncommon. We determined the positive predictive value and specificity of ertapenem resistance for KPC detection in 2,696
Enterobacteriaceae
isolates. The positive predictive value and specificity of ertapenem resistance for KPC detection were 74% and 99.2%, respectively.
MDM2-Dependent Inhibition of p53 Is Required for Epstein-Barr Virus B-Cell Growth Transformation and Infected-Cell Survival
Authors: Forte Eleonora , Luftig Micah A.
Published: January 2009

Epstein-Barr virus (EBV) growth transformation of primary B lymphocytes into indefinitely proliferating lymphoblastoid cell lines (LCLs) depends on the concerted activities of a subset of viral proteins expressed during latency. EBV drives quiescent B cells into S phase, and consequently, a host response is activated that includes expression of p53 and its target genes. Since LCLs retain wild-type p53, it was of interest to determine what contribution the p53 pathway may have in controlling established LCL growth and EBV-mediated transformation of primary B cells. We found that liberation of p53 through chemical antagonism of one of its major ubiquitin ligases, MDM2, using the small-molecule Nutlin-3 led to apoptosis of established LCLs and suppressed EBV-mediated transformation of primary B cells. The activation of latent p53 induced target genes associated with apoptosis. Furthermore, MDM2 antagonism synergized with NF-κB inhibition in killing LCLs. NF-κB was important to increase steady-state MDM2 protein levels rather than in affecting p53-dependent transcription, suggesting a unique mechanism by which LCLs survive in the presence of a primed p53 pathway. Nutlin sensitivity of EBV-infected cells provides a novel system for studying the pathways that dictate LCL survival and regulate EBV transformation. Finally, MDM2 antagonists may be considered for therapeutic intervention in EBV-associated malignancies expressing wild-type p53.