bluuebunny/crossref_metadata_2025 huggingface dataset:
Why Do Some Schools Group by Ability?
Authors: VanderHart Peter G.
Published: May 2006

Abstract.  This article explores the reasons that schools choose to group their students by ability. A mathematical model suggests that high diversity of achievement and a large number of students in a school will cause a school to be more likely to group. Less legitimately, some schools may choose to use ability grouping to segregate students by race or class within a school.

The data used in this study come from the 1992 NAEP 8th grade Mathematics Assessment. Cross‐tabulations suggest that ability grouping is correlated with diversity of student achievement, the number of students, racial diversity, and low levels of poverty. The mean achievement of students and school spending levels do not have much correlation with the schools’ tracking decisions. Logit regressions indicate that the number of students in a school and its racial diversity are most important, and that other factors (most notably the diversity of achievement) are not. These results lend credence to those who suggest that grouping is not necessarily done for academic reasons, but rather is a subtle way to segregate by race or class.
Integration of nucleic acid amplification test results into hepatitis C virus supplemental serologic testing algorithms: implications for donor counseling and revision of existing algorithms
Authors: Kleinman Steven H. , Stramer Susan L. , Brodsky Jaye P. , Caglioti Sally , Busch Michael P.
Published: May 2006

BACKGROUND:  The routine use of hepatitis C virus (HCV) nucleic acid amplification testing (NAT) donor screening assays has provided an opportunity for revision of the current HCV supplemental testing algorithm, which requires that recombinant immunoblot assay (RIBA) be performed on every HCV enzyme immunoassay (EIA)‐repeat‐reactive donation. The FDA has approved variance requests to use a new algorithm that eliminates the need to perform RIBA when HCV NAT results are reactive. Data are provided in support of this new algorithm.

STUDY DESIGN AND METHODS:  HCV EIA (including signal‐to‐cutoff optical density ratio), RIBA, and NAT data were compiled from 33.2 million donations screened over an approximately 4‐year period by the American Red Cross and Blood Systems Laboratories. Further, donations having specific combinations of HCV EIA, RIBA, and minipool (MP) NAT results were evaluated, with more sensitive individual‐donation (ID) NAT, to construct improved counseling messages for donors.

RESULTS:  Of 47,041 EIA‐repeat‐reactive donations, 49.3 percent were RIBA‐positive, 17.1 percent RIBA‐indeterminate, and 33.5 percent RIBA‐negative. NAT‐reactive rates were 79.2, 2.5, and 0.18 percent for RIBA‐positive, ‐indeterminate, and ‐negative donations, respectively. The new algorithm classified an additional 1 percent of donations as HCV‐infected while at the same time detecting all infections classified as HCV‐infected under the current algorithm. An additional 2.4 percent of RIBA‐positive, MP NAT–nonreactive donations were reactive when a frozen‐thawed aliquot was retested by ID NAT.

CONCLUSION:  Integrating HCV NAT results with RIBA results for purposes of donor notification allows more appropriate counseling messages to be given to EIA‐repeat‐reactive donors. The new HCV supplemental algorithm is an acceptable alternative to the current algorithm because it provides equivalent or superior accuracy in formulating donor counseling messages and may also result in reduced costs and more timely notification of infected donors.
Urokinase plasminogen activator receptor (uPAR) expression is reduced by tyrosine kinase inhibitors
Authors: SKOGSETH HAAKON , LARSSON ERIK , HALGUNSET JOSTEIN
Published: May 2006

Previously we reported that tyrosine kinase inhibitors (TKI) produced a reduction in uPA expression in prostatic cancer cells, and that TKI‐treated cells were less invasive compared to untreated cells. Nevertheless, no change in cell migration was observed when TKI‐treated cells were supplied with external uPA, thus indicating more complex mechanisms leading to decreased cell invasion. uPAR expression was measured with an enzyme‐ linked immunosorbent assay (ELISA) in PC‐3 and DU‐145 prostate carcinoma cells treated with the two TKI genistein and AG‐1478. uPAR mRNA levels were measured with real‐time reverse transcriptase‐polymerase chain reaction (RT‐PCR). uPAR immunocytochemistry was used to examine the receptor distribution in cells grown on a reconstituted basal lamina. Immunocytochemistry showed an intense uPAR immunostaining in invading cells, particularly in the leading edge membrane. Treatment with genistein and AG‐1478 led to a decreased expression of uPAR in DU‐145, but not in PC‐3. Furthermore, a reduction of uPAR mRNA was found in TKI‐treated DU‐145 cells, while PC‐3 was not affected. Our results indicate a possible role of TKI as cancer suppressors by acting as a regulator of uPAR expression.
Female urethral adenocarcinoma with a heterogeneous phenotype
Authors: KURODA N. , SHIOTSU T. , OHARA M. , HIROUCHI T. , MIZUNO K. , MIYAZAKI E.
Published: May 2006

We here report a very rare case of female urethral adenocarcinoma. A 77‐year‐old woman presented with urinary retention. Cystoscopy showed a urethral tumor and the biopsy material showed adenocarcinoma. Macroscopically, the tumor measuring 3.0×3.0×2.4 cm was predominantly observed around the periurethral area on the proximal side. Histologically, patterns of columnar/mucinous adenocarcinoma, clear cell adenocarcinoma and papillary/micropapillary carcinoma were observed, but there was no evidence of a cribriform pattern. Immunohistochemically, neoplastic cells of at least one of three components were positive for CK7 and CK20 or CA125. We suggest that female urethral adenocarcinoma with a histologically and immunohistochemically heterogeneous phenotype may originate from cells within urethral or paraurethral tissue, such as urethritis glandularis or intestinal metaplastic epithelium and Mullerian tissue.
Uterine evaluation and gestation diagnosis in owl monkey (Aotus azarai infulatus) using the B mode ultrasound
Authors: Monteiro Frederico O B , De Koivisto Marion B , Vicente Wilter R R , De Amorim Carvalho Reinaldo , Whiteman Christina W , Castro Paulo H G , Maia Celsemy E
Published: May 2006

Background  Gynecological and obstetrical ultrasonography has become an indispensable tool in the routine management, health evaluation and research on captive non‐human primates.

Methods  Ultrasound was used to evaluate the uterus and estimate the gestation of owl monkeys. Twelve couples were selected, where five were primiparous and seven multiparous females from the National Primate Center reproductive colony, Ananindeua‐PA, Brazil. The procedures were carried out using the GE® Logiq 100 MP, equipped with a 7.5 MHz linear probe.

Results  The females showed a simple uterus, of elongated shape, regular outline and homogeneous echogenic texture. In the uterine measurements craniocaudal diameter, dorsoventral diameter and uterine volume (UV), significant differences were identified (P < 0.05) between ultrasound examinations of primiparous and multiparous females. The UV showed a positive correlation with the number of births. The gestational sac and the embryonic echo were visible between 28 and 38 days after mating. Between 48 and 68 days after mating, embryonic death was identified in all the gestations.

Conclusions  The chemical (use of tranquilizers) and husbandry factors (capture stress) may be related to the prenatal death. The establishing methods of conditioning the female to the ultrasonographic exam may offer a solution to this problem.
Co‐operative mineralization and protein self‐assembly in amelogenesis: silica mineralization and assembly of recombinant amelogenins in vitro
Authors: Fowler Christabel E. , Beniash Elia , Yamakoshi Yasuo , Simmer James P. , Margolis Henry C.
Published: May 2006

An amorphous silica mineralization technique was used to produce inorganic/protein composites to elucidate the structure and mechanism of formation of amelogenin assemblies, which may play an important role in regulating enamel structure during the initial stages of amelogenesis. Full‐length recombinant amelogenins from mouse (rM179) and pig (rP172) were investigated along with key degradation products (rM166 and native P148) lacking the hydrophilic C terminus found in parent molecules. The resulting products were examined using transmission electron microscopy and/or small‐angle X‐ray scattering. Using protein concentrations of 0.1–3 mg ml−1, large monodisperse spheres of remarkably similar mean diameters were observed using rM179 (124 ± 4 nm) and rP172 (126 ± 7 nm). These spheres also exhibited ‘internal structure’, comprising nearly spherical monodisperse particles of ≈ 20 nm in diameter. In the presence of rM166, P148, and bovine serum albumin (control), large unstructured and randomly shaped particles (250–1000 nm) were observed. Without added protein, large dense spherical particles of silica (mean ≈ 500 nm) lacking internal structure were produced. These findings demonstrate that full‐length amelogenins have the ability to form higher‐order structures, whereas amelogenins that lack the hydrophilic C terminus do not. The results also suggest that full‐length amelogenin can guide the formation of organized mineralized structures through co‐operative interactions between assembling protein and forming mineral.
Assembly and processing of an engineered amelogenin proteolytic product (rP148)
Authors: Sun Zhi , Ahsan Mohammad M. , Wang Hongjun , Du Chang , Abbott Christopher , Moradian‐Oldak Janet
Published: May 2006

The purpose of this study was to express, characterize, and investigate the self‐assembly of a recombinant porcine amelogenin lacking the hydrophilic 24 C‐terminal amino acids (rP148). To gain further insight into the function of amelogenin processing during enamel mineralization, this protein was also used as a substrate to examine the action of matrix metalloproteinase‐20 (MMP‐20). The assembly properties of rP148 were monitored by dynamic light scattering (DLS). In general, rP148 molecules assemble into monomers, dimers, oligomers, and some nanosphere‐like particles. Depending on the solution conditions, large aggregates were also observed. Matrix metalloproteinase‐20 cleaved the rP148 molecule at a few sites, creating a number of different products, including the tyrosine‐rich amelogenin polypeptide (TRAP). Our data suggest that although rP148 self‐assembles into small particles, its assembly properties are different from those of the full‐length rP172, indicating that the C‐terminal 24 amino acids play a critical role in nanosphere assembly. We further demonstrate that MMP‐20 digests rP148 in a manner that generates a similar proteolytic pattern, as would be expected to occur in vivo.
Differentiation of human ameloblast‐lineage cells in vitro
Authors: Yan Qiaomei , Zhang Yan , Li Wu , DenBesten Pamela K.
Published: May 2006

Previous studies have shown that ameloblast‐like cells can be selectively cultured from the enamel organ in a serum‐free medium with low calcium concentrations. The purpose of this study was to further characterize this culture system to identify differentiated ameloblast‐lineage cells. Tooth organs from 19–24‐wk‐old fetal cadavers were either frozen and cryosectioned for immunostaining, or digested in collagenase/dispase for cell culture. The cells were grown in keratinocyte media supplemented with 0.05 mM calcium, and characterized by morphology and immunofluorescence. Epithelial clones with two distinct morphologies, including smaller cobblestone‐shaped cells and larger (5–15 times in size) rounded cells, began to form between day 8 and day 12 after culture. The cobblestone‐shaped cells continued to proliferate in culture, while the larger cells proliferated slowly or not at all. These larger cells formed filopodia, usually had two or more nuclei and a radiating cytoplasm at the cell margin, and were more abundant with increasing time in culture. Both cell types stained for cytokeratin 14, and the larger cells appeared more differentiated, showing stronger staining for amelogenin and ameloblastin. Immunofluorescence of the tooth bud sections showed staining for these matrix proteins as ameloblasts differentiated from the inner enamel epithelium. These results show the successful culture of differentiating ameloblast‐lineage cells, and lay a foundation for use of these cells to further understand ameloblast biology with application to tooth enamel tissue engineering.
Vitamin D and tissue non‐specific alkaline phosphatase in dental cells
Authors: Lézot Frédéric , Descroix Vianney , Hotton Dominique , Mauro Nicole , Kato Shigeaki , Berdal Ariane
Published: May 2006

Dental epithelium comprises different cell populations, including ameloblasts and stratum intermedium cells. Ameloblasts are vitamin D targets, and at least five proteins undergo specific modulation of their expression following the addition of 1α,25(OH)2 vitamin D3[1α,25(OH)2D3]. Stratum intermedium cells have not been studied in any great detail regarding vitamin D impact. Interestingly, in these cells, the tissue non‐specific alkaline phosphatase (TNAP) is overexpressed. On the other hand, TNAP is a reliable bone marker of vitamin D action, similar to calbindins in kidney and intestine, previously used for studies of vitamin D activity in ameloblasts. Here, TNAP expression and activity were investigated in vivo in the microdissected epithelium and mesenchyme of mandible incisors. Physiological doses of 1α,25(OH)2D3 injected in control rats failed to modify TNAP activity in both dental epithelium and mesenchyme. No significant differences were observed in the steady‐state levels of TNAP mRNAs of dental tissues from wild‐type and vitamin D nuclear receptor (VDRnuc)‐deficient mice of the same litters. These data suggest that, in contrast to ameloblasts, stratum intermedium cells are not sensitive to 1α,25(OH)2D3. An explanation for such a responsiveness of stratum intermedium cells to 1α,25(OH)2D3 is proposed based on the respective expressions of both vitamin D receptors (VDRnuc and 1,25D3‐[MARRS]) and the Dlx2 homeobox gene.
1139939111 TLR6 protects first trimester trophoblast cells from TLR2/TLR1 mediated apoptosis
Authors: Abrahams VM , Aldo PB , Romero R , Mor G
Published: May 2006

Introduction:  Increased trophoblast apoptosis has been observed in pregnancy complications such as preeclampsia. The factors promoting this cell death are unknown. Trophoblasts express Toll‐like receptors (TLR), enabling them to recognize microorganisms. In response to the TLR2 ligand peptidoglycan (PDG), trophoblasts undergo apoptosis suggesting that gram‐positive bacteria may promote trophoblast apoptosis. The objective of this study was to characterize the cellular mechanism by which TLR2 induces apoptosis. We report the role of TLR6 in the regulation of TLR2 mediated apoptosis following ligation by PDG.

Methods:  First trimester trophoblast cell lines express TLR1 and TLR2 but lack TLR6 and are sensitive to PDG‐mediated apoptosis. Three stable transfectants were made to express either a TLR1 dominant negative (TLR1‐DN), a TLR2 dominant negative (TLR2‐DN) or full length TLR6. Cells were treated with PDG (40 μg/mL) after which cell viability, caspase‐3 activity and cytokine production were evaluated.

Results:  Trophoblasts expressing the TLR2‐DN showed a 57.4 ± 1.2% inhibition in PDG‐induced caspase‐3 activity compared with wildtype cells, while the TLR1‐DN inhibited PDG‐induced caspase‐3 activity by 61.6 ± 1.1%. Expression of TLR6 by trophoblasts, reversed PDG‐mediated apoptosis as shown by reduced caspase‐3 activity (77.6 ± 1.2%) and increased cytokine production.

Conclusion:  These results suggest that a gram‐positive bacterial infection during pregnancy may promote trophoblast apoptosis via TLR2/TLR1 heterodimers. Expression of TLR6, however, may protect the trophoblast from PDG‐induced apoptosis and instead promote an inflammatory response. These findings shed new light on the mechanisms by which infection may affect placental function and pregnancy outcome.
1141249685 MyD88‐positive ovarian cancer cells regulate monocyte migration and differentiation
Authors: Alvero A , Mor G
Published: May 2006

Background:  The presence of immune infiltrate in tumor sites has been thought to represent an immune response against the tumor. However, new evidences indicate that these immune cells may be supporting tumor growth rather than inhibiting it. Previously, we described a sub‐group of epithelial ovarian cancer (EOC) cells that express TLR‐4 and MyD88 and produce several cytokines and chemokines. We hypothesize that EOC cells could recruit immune cells and induce their differentiation toward tumor‐supporting immune cells. The objective of this study is to determine the consequence of an activated TLR‐4‐MyD88 signaling pathway on migration and differentiation of the monocyte‐like THP‐1 cells.

Materials and Methods:  R182 (MyD88‐positive) and CP70 (MyD88‐negative) EOC cells were incubated in the presence or absence of 10 μg/mL LPS for 48 hr and cell‐free conditioned media (CM) was prepared. THP‐1 cells were incubated in 50% CM for 24 hr. Cytokine profile (IL‐6, IL‐8, IL‐10, IL‐12, MIF, MCP‐1, GROα, RANTES, IFNγ, and TNFα) of cell‐free supernatants and THP‐1 lysates was characterized using Beadlyte Human Multicytokine kit and xMAP technology. Migration assay was performed using QCM 24‐well Colorimetric Cell Migration Assay kit.

Results:  THP‐1 cells migrate towards R182‐ and CP70‐CM equally. However, enhanced migration was observed towards CM from LPS‐treated‐R182 (45%) than towards CM from LPS‐treated CP70 (9%). When incubated with CM from LPS‐treated‐R182, THP‐1 cells express a cytokine profile characteristic of M2 macrophages (high levels of MCP‐1, MIF and IL‐6). This was not observed when THP‐1 was incubated with LPS alone or with CM from LPS‐treated–CP70.

Conclusion:  In the present study we demonstrate that EOC cells have the capacity to attract THP‐1 cells. Furthermore, we demonstrate that MyD88+ EOC cells are able to differentiate THP‐1 cells into growth‐promoting macrophages and establish a pro‐tumor environment that can induce cancer cell proliferation. Our data suggest that cancer cells have the ability to attract and ‘educate’ immune cells to support its growth.
1141478634 Amniochorion secretes chemotactic signals for leukocytes during human labor
Authors: Gomez N , Estrada‐Gutierrez G , Giono Cerezo S , Vega‐Sanchez R , Vadillo‐Ortega F
Published: May 2006

Objective:  Leukocytes arriving to choriodecidua during labor are capable to secrete cytokines and collagenases that may play a role in extracellular matrix degradation leading to the rupture of amniochorion. The aim of this work was to study the role of amniochorion in the active recruitment of leukocytes through production of specific chemokynes during labor.

Methods:  Amniochorion explants were obtained from women at term with spontaneous labor (n = 4) and subjected to cesarean section without labor (n = 4). Explant cultures were carried out during 24 hr and an homogenate including the culture media was made after this period. Cell free extracts were tested in Boyden chambers for chemotaxis using leukocytes from maternal blood obtained from women with (n = 2) and without labor (n = 2). Attracted cells were analyzed by flow cytometry for count and immunophenotype. Chemokynes were identified in the extracts using a commercial chemiarray.

Results:  All tested amniochorion extracts induced chemotaxis for leukocytes; however, those from labor tissues induced a higher chemotactic activity than the correspondent non‐in‐labor tissues (P = 0.003). Chemotactic effect was higher over leukocytes from labor women (P = 0.001). More than 80% of the attracted cells were polymorphonuclears in all cases. IL‐8 was the main chemokyne found in all extracts; however its concentration was increased in extracts from labor.

Conclusions:  Fetal membranes induced chemotaxis for leukocytes and this condition is enhanced by the presence of labor. Amniochorion under active labor secretes IL‐8 which induces a preferential chemotaxis for polymorphonuclears. Infiltration of these cells in choriodecidua during labor may play a role in the amniochorion degradation associated to rupture.
1141526807 Expression of inducible microsomal prostaglandin E synthase in local endometriosis lesions
Authors: Chishima F , Hayakawa S , Sugitani M , Karasaki‐Suzuki M , Ohta H , Sugita K , Yamamoto M
Published: May 2006

Recently, an inducible microsomal human prostaglandin E synthase (mPGES) was identified. This enzyme converts the cyclooxygenase (COX) product prostaglandin (PG) H2 to PGE2, an eicosanoid that has been linked to carcinogenesis. Increased amounts of PGE2 have been observed in many tumor types including colorectal adenomas and cancers. We have already reported increased expression of COX‐2 mRNA in local lesions of endometriosis. To further elucidate the mechanism responsible for increased levels of PGE2 in endometriosis, we investigated the expression of mPGES. Formalin fixed and paraffin embedded 15 samples were examined with immunohistochemistry. Immunostaining was carried out with a rabbit mPGES‐1 anti‐human polyclonal antiboby. In selected cases, expression of mPGES mRNA was examined by RT‐PCR using total RNA extracted from frozen samples. Immunohistochemistry revealed increased mPGES immunoreactivity in endometriosis samples compared with eutopic endometria. Immunoreactivity of mPGES was observed in both epithelia and stromal or inflammatory cells. Increased expression of mPGES‐1 mRNA was detected in most of endometriosis samples. Taken together, our results suggested that overexpression of mPGES in addition to COX‐2 contributes to possible increased PGE2 production in endometriosis patients.
1141644472 Surface Enhanced Laser Desorption and Ionization (SELDI) mass spectrometry for investigation of human embryo conditioned IVF culture medium
Authors: Neubeck S , Koehn S , Poehlmann TG , Bleul A , Von Eggeling F , Starker W , Hoppe I , Markert UR
Published: May 2006

Introduction:  The human pre‐implantation embryo metabolism is still widely unknown. Mass spectrometry is a very sensitive proteomic method to detect the entire spectrum of molecules in samples below 1 μL. Surface Enhanced Laser Desorption Ionisation – Time Of Flight (SELDI – TOF) mass spectrometry is a further advanced method to reduce overlapping signals from different substances.

Material and Methods:  A total of 22 different pre‐implantation embryo supernatants (10 μL each) from 16 different single‐cultured embryos were analyzed. From 6 embryos, supernatants were obtained both at day 3 and 5. Embryo stage was defined by microscopy. Different stages including arrested embryos, 4‐ or 8‐cell stage, early and expanded blastocysts were investigated. SELDI combines a chip‐based separation technology with mass spectrometry. All samples were fractioned by applying six different pH milieus and then exposed to chips with six differently coated surfaces. All fractions were analyzed on a mass spectrometer type ProteinChip System, Series 4000 (Ciphergen Biosystems, Inc.).

Results:  By comparing the protein profiles of the analyzed embryos the implemented bioinformatic software was able to classify blinded samples correctly into groups of embryos as defined by microscopy. The use of IMAC‐chips (copper‐coated) and CM10‐chips (cation‐exchange) led to highest resolution of peaks. Although the masses of numerous molecules in culture media are assessed by this method, the exact definition of substances needs application of further techniques.

Conclusions:  These first SELDI mass spectrometric analyses of embryo culture media demonstrate the capability of discriminating different stages of human pre‐implantation embryos by their protein expression profiles.
1142292807 Expression of CD4+CD25+FOXP3+ regulatory T cells in women with idiopathic recurrent spontaneous abortion and implantation failure: 3‐color flow cytometric analysis
Authors: Lee S , Kwak‐Kim J , Gilman‐Sachs A
Published: May 2006

Introduction:  A population of CD4+CD25+ regulatory T (Treg) cells is thought to regulate alloreactive T cells in many autoimmune diseases. Lack of Treg cells resulted in abortions in mice and transfer of them prevented miscarriage. FOXP3 is now considered the most specific marker for Treg cells. In this study, we investigated whether levels of peripheral blood Treg cells in women with recurrent spontaneous abortion (RSA) of unknown etiology or with repeated implantation failures (IF) are different from those of normal fertile women.

Materials and Methods:  Non‐pregnant women with a history of idiopathic RSA or repeated IF were enrolled in the study group (n = 15) and non‐pregnant fertile females served as controls (n = 7). A flow cytometry assay was used. Peripheral blood mononuclear cells (PBMCs) were isolated and stained with appropriate monoclonal antibodies that identify Treg cells: for surface markers, such as anti‐CD4 and anti‐CD25, and for intracellular marker, anti‐FOXP3.

Results:  The proportions of CD4+CD25+FOXP3+ Treg cells were significantly different between the patients and controls, 1.5% versus 2.4%, respectively (P < 0.05). In addition, an alteration in the expression of surface CD25 was noted after permeabilization of PBMC which allows antibodies to enter the cells and bind to FOXP3. The mean percentage of CD25+ cells before permeabilization, 9.9 + 4.8%, was decreased to 5.3+3.5% after permeabilization (P < 0.01). The ratios of CD4+CD25+/CD4+ between the surface and the intracellular staining also decreased by 46% (P < 0.001).

Conclusion:  CD4+CD25+FOXP3+ cells were significantly lower in the patients with idiopathic RSA or multiple IF than in the controls. Permeabilization for intracellular staining induces a decrease in expression of surface markers.
Failure Surfaces for Finitely Strained Two-Phase Periodic Solids Under General In-Plane Loading
Authors: Triantafyllidis N. , Nestorović M. D. , Schraad M. W.
Published: May 2006

For ductile solids with periodic microstructures (e.g., honeycombs, fiber-reinforced composites, cellular solids) which are loaded primarily in compression, their ultimate failure is related to the onset of a buckling mode. Consequently, for periodic solids of infinite extent, one can define as the onset of failure the first occurrence of a bifurcation in the fundamental solution, for which all cells deform identically. By following all possible loading paths in strain or stress space, one can construct onset-of-failure surfaces for finitely strained, rate-independent solids with arbitrary microstructures. The calculations required are based on a Bloch wave analysis on the deformed unit cell. The presentation of the general theory is followed by the description of a numerical algorithm which reduces the size of stability matrices by an order of magnitude, thus improving the computational efficiency for the case of continuum unit cells. The theory is subsequently applied to porous and particle-reinforced hyperelastic solids with circular inclusions of variable stiffness. The corresponding failure surfaces in strain-space, the wavelength of the instabilities, and their dependence on micro-geometry and macroscopic loading conditions are presented and discussed.
Characteristics of Small Vortices in a Turbulent Axisymmetric Jet
Authors: Chhabra Sudhaker , Huq Pablo , Prasad Ajay K.
Published: May 2006

Characteristics of small vortices were studied in axisymmetric jets wherein the Kolmogorov scale was approached by progressively decreasing the Reynolds number while still maintaining turbulent flow. A periodic forcing introduced far upstream of the jet nozzle ensured that the jet was turbulent. A vortex eduction tool was developed and applied to the high-pass filtered 2D velocity field in the axial plane of a turbulent jet while varying Re between 140 and 2600. Vortex population, energy, vorticity, and rms (root-mean-square velocity fluctuations) of the high-pass filtered field were measured to elucidate vortex characteristics. The observed population of vortices decreases dramatically at the Kolmogorov scale. The observed increase in vortex population with decreasing vortex size appears to be in accord with the space-filling argument, in that the vortex population in a two-dimensional domain should grow as R−2. The energy density curve obtained from vortex statistics reproduces the −5∕3 slope for the inertial subrange, and the high-pass filtered field accounts for approximately two-thirds of the total rms.
Analysis of Chemically Reacting Transport Phenomena in an Anode Duct of Intermediate Temperature SOFCs
Authors: Yuan Jinliang , Sundén Bengt
Published: May 2006

The internal reforming and electrochemical reactions appear in the porous anode layer, and may lead to inhomogeneous temperature and gas species distributions according to the reaction kinetics. In this study, a fully three-dimensional calculation method has been further developed to simulate and analyze chemically reacting transport processes in a thick anode duct. The composite duct investigated consists of a porous anode, the fuel flow duct and solid current connector. Momentum and heat transport together with gas species equations have been solved by coupled source terms and variable thermophysical/transport properties of the fuel gas mixture. Furthermore, the heat transfer due to the fuel gas diffusion is implemented into the energy balance based on multicomponent diffusion models. The fuel cell conditions such as the combined thermal boundary conditions on solid walls, mass balances (generation and consumption) associated with the various reactions, and gas permeation between the porous anode and flow duct are applied in the analysis. Simulation results show that the internal reforming and the electrochemical reactions, and cell operating conditions are significant for species distribution, fuel gas transport and heat transfer in the subdomains of the anode.
Dissipation in Implicit Turbulence Models: A Computational Study
Authors: Margolin L. G. , Smolarkiewicz P. K. , Wyszogradzki A. A.
Published: May 2006

We describe a series of computational experiments that employ nonoscillatory finite volume methods to simulate the decay of high Reynolds number turbulence. These experiments cover a broad range of physical viscosities and numerical resolutions. We have extracted a data set from these experiments detailing the energy dissipation by physical viscosity and by the numerical algorithm. We offer a preliminary analysis of this data, including new insights into the (computational) transition between direct numerical simulation and large eddy simulation.
Hydrogen Production Performance of a 10-Cell Planar Solid-Oxide Electrolysis Stack
Authors: O’Brien J. E. , Stoots C. M. , Herring J. S. , Hartvigsen J.
Published: May 2006

An experimental study is under way to assess the performance of solid-oxide cells operating in the steam electrolysis mode for hydrogen production over a temperature range of 800-900°C. Results presented in this paper were obtained from a ten-cell planar electrolysis stack, with an active area of 64cm2 per cell. The electrolysis cells are electrolyte supported, with scandia-stabilized zirconia electrolytes (∼140μm thick), nickel-cermet steam/hydrogen electrodes, and manganite air-side electrodes. The metallic interconnect plates are fabricated from ferritic stainless steel. The experiments were performed over a range of steam inlet mole fractions (0.1–0.6), gas flow rates (1000-4000sccm), and current densities (0-0.38A∕cm2). Steam consumption rates associated with electrolysis were measured directly using inlet and outlet dewpoint instrumentation. Cell operating potentials and cell current were varied using a programmable power supply. Hydrogen production rates up to 100Nl∕h were demonstrated. Values of area-specific resistance and stack internal temperatures are presented as a function of current density. Stack performance is shown to be dependent on inlet steam flow rate.
Hybrid dosimetry: Feasibility of mixing angulated and parallel needles in planning prostate brachytherapy
Authors: Fu Lei , Liu Haisong , Ng Wan Sing , Rubens Deborah , Strang John , Messing Edward , Yu Yan
Published: May 2006

Pubic arch interference (PAI) often caused inadequate prostate coverage during transperineal brachytherapy using all parallel needles. In this paper, a hybrid implantation approach is presented in which additional angulated needles can be used to avoid PAI. This approach can be applied in prostate brachytherapy using a robotic assisted device. To examine the feasibility of this approach, volume data from three prostate seed implant patients were selected, which represent small, medium, and large prostates. As the blocking area was artificially increased simulating pubic arch overlap, the dosimetry outcomes and ratio of number of angulated needles to the total number of needles were analyzed. The hybrid dosimetry broke down when blocking is over 42%. As the percent of blocking increased, the ratio of the number of angulated needles to the total number of needles increased, while the dosimetry outcomes only had a slight trend of worsening. When close to the breakdown point, the dosimetry outcomes worsen drastically. Therefore, for moderate PAI the hybrid dosimetry is feasible.
Automated 2D‐3D registration of a radiograph and a cone beam CT using line‐segment enhancementa)
Authors: Munbodh Reshma , Jaffray David A. , Moseley Douglas J. , Chen Zhe , Knisely Jonathan P. S. , Cathier Pascal , Duncan James S.
Published: May 2006

The objective of this study was to develop a fully automated two‐dimensional (2D)–three‐dimensional (3D) registration framework to quantify setup deviations in prostate radiation therapy from cone beam CT (CBCT) data and a single AP radiograph. A kilovoltage CBCT image and kilovoltage AP radiograph of an anthropomorphic phantom of the pelvis were acquired at 14 accurately known positions. The shifts in the phantom position were subsequently estimated by registering digitally reconstructed radiographs (DRRs) from the 3D CBCT scan to the AP radiographs through the correlation of enhanced linear image features mainly representing bony ridges. Linear features were enhanced by filtering the images with “sticks,” short line segments which are varied in orientation to achieve the maximum projection value at every pixel in the image. The mean (and standard deviations) of the absolute errors in estimating translations along the three orthogonal axes in millimeters were 0.134 (0.096) AP(out‐of‐plane), 0.021 (0.023) ML and 0.020 (0.020) SI. The corresponding errors for rotations in degrees were 0.011 (0.009) AP, 0.029 (0.016) ML (out‐of‐plane), and 0.030 (0.028) SI (out‐of‐plane). Preliminary results with megavoltage patient data have also been reported. The results suggest that it may be possible to enhance anatomic features that are common to DRRs from a CBCT image and a single AP radiography of the pelvis for use in a completely automated and accurate 2D–3D registration framework for setup verification in prostate radiotherapy. This technique is theoretically applicable to other rigid bony structures such as the cranial vault or skull base and piecewise rigid structures such as the spine.
Lipids, Genes, and Health
Authors: Ntambi James M.
Published: May 2006

How Fat Works
.
By Philip A. Wood
. Harvard University Press, Cambridge, MA, 2006. 263 pp. $35, £21.95, €32.30. ISBN 0-674-01947-4.

The author offers an accessible account of fatty acid metabolism and the consequences of disrupting that metabolic balance.
Wolbachia
Infections in the Cimicidae: Museum Specimens as an Untapped Resource for Endosymbiont Surveys
Authors: Sakamoto Joyce M. , Feinstein Julie , Rasgon Jason L.
Published: May 2006

Wolbachia
spp. are obligate maternally inherited endosymbiotic bacteria that infect diverse arthropods and filarial nematodes. Previous microscopic and molecular studies have identified
Wolbachia
in several bed bug species (Cimicidae), but little is known about how widespread
Wolbachia
infections are among the Cimicidae. Because cimicids of non-medical importance are not commonly collected, we hypothesized that preserved museum specimens could be assayed for
Wolbachia
infections. For the screening of museum specimens, we designed a set of primers that specifically amplify small diagnostic fragments (130 to 240 bp) of the
Wolbachia
16S rRNA gene. Using these and other previously published primers, we screened 39 cimicid species (spanning 16 genera and all 6 recognized subfamilies) and 2 species of the sister family Polyctenidae for
Wolbachia
infections using museum and wild-caught material. Amplified fragments were sequenced to confirm that our primers were amplifying
Wolbachia
DNA. We identified 10 infections, 8 of which were previously undescribed. Infections in the F supergroup were common in the subfamily Cimicinae, while infections in the A supergroup were identified in the subfamilies Afrocimicinae and Haematosiphoninae. Even though specimens were degraded, we detected infections in over 23% of cimicid species. Our results indicate that
Wolbachia
infections may be common among cimicids and that archived museum material is a useful untapped resource for invertebrate endosymbiont surveys. The new screening primers listed in this report will be useful for other researchers conducting
Wolbachia
surveys with specimens with less-than-optimum DNA quality.
Inhibition of Plant-Pathogenic Bacteria by Short Synthetic Cecropin A-Melittin Hybrid Peptides
Authors: Ferre Rafael , Badosa Esther , Feliu Lidia , Planas Marta , Montesinos Emili , Bardají Eduard
Published: May 2006

Short peptides of 11 residues were synthesized and tested against the economically important plant pathogenic bacteriaErwinia amylovora,Pseudomonas syringae, andXanthomonas vesicatoriaand compared to the previously described peptide Pep3 (WKLFKKILKVL-NH2). The antimicrobial activity of Pep3 and 22 analogues was evaluated in terms of the MIC and the 50% effective dose (ED50) for growth. Peptide cytotoxicity against human red blood cells and peptide stability toward protease degradation were also determined. Pep3 and several analogues inhibited growth of the three pathogens and had a bactericidal effect at low micromolar concentrations (ED50of 1.3 to 7.3 μM). One of the analogues consisting of a replacement of both Trp and Val with Lys and Phe, respectively, resulted in a peptide with improved bactericidal activity and minimized cytotoxicity and susceptibility to protease degradation compared to Pep3. The best analogues can be considered as potential lead compounds for the development of new antimicrobial agents for use in plant protection either as components of pesticides or expressed in transgenic plants.
Modeling Shifts in Microbial Populations Associated with Health or Disease
Authors: Dalwai F. , Spratt D. A. , Pratten J.
Published: May 2006

Stable microbial communities associated with health can be disrupted by altered environmental conditions. Periodontal diseases are associated with changes in the resident oral microflora. For example, as gingivitis develops, a key change in the microbial composition of dental plaque is the ascendancy of
Actinomyces
spp. and gram-negative rods at the expense of
Streptococcus
spp. We describe the use of an in vitro model to replicate this population shift, first with a dual-species model (
Actinomyces naeslundii
and
Streptococcus sobrinus
) and then using a microcosm model of dental plaque. The population shift was induced by environmental changes associated with gingivitis, first by the addition of artificial gingival crevicular fluid and then by a switch to a microaerophilic atmosphere. In addition to the observed population shifts, confocal laser scanning microscopy also revealed structural changes and differences in the distribution of viable and nonviable bacteria associated with the change in environmental conditions. This model provides an appropriate system for the further understanding of microbial population shifts associated with gingivitis and for the testing of, for example, antimicrobial agents.
Multilaboratory Comparison of Hepatitis C Virus Viral Load Assays
Authors: Caliendo A. M. , Valsamakis A. , Zhou Y. , Yen-Lieberman B. , Andersen J. , Young S. , Ferreira-Gonzalez A. , Tsongalis G. J. , Pyles R. , Bremer J. W. , Lurain N. S.
Published: May 2006

We report a multilaboratory evaluation of hepatitis C virus (HCV) viral load assays to determine their linear range, reproducibility, subtype detection, and agreement. A panel of HCV RNA samples ranging in nominal concentration from 1.0 to 7.0 log
10
IU/ml was constructed by diluting a clinical specimen (genotype 1b). Replicates of the panel were tested in multiple laboratories using the Abbott TaqMan analyte-specific reagent (Abbott reverse transcription-PCR [RT-PCR]), Roche TaqMan RUO (Roche RT-PCR), Roche Amplicor Monitor HCV 2.0 (Roche Monitor), and Bayer VERSANT HCV RNA 3.0 (Bayer bDNA) assays. Bayer bDNA-negative specimens were tested reflexively using the Bayer VERSANT HCV RNA qualitative assay (Bayer TMA). Abbott RT-PCR and Roche RT-PCR detected all 28 replicates with a concentration of 1.0 log
10
IU/ml and were linear to 7.0 log
10
IU/ml. Roche Monitor and Bayer bDNA detected 27 out of 28 and 13 out of 28 replicates, respectively, of 3.0 log
10
IU/ml. Bayer TMA detected all seven replicates with 1.0 log
10
IU/ml. Bayer bDNA was the most reproducible of the four assays. The mean viral load values for panel members in the linear ranges of the assays were within 0.5 log
10
for the different tests. Eighty-nine clinical specimens of various genotypes (1 through 4) were tested in the Bayer bDNA, Abbott RT-PCR, and Roche RT-PCR assays. For Abbott RT-PCR, mean viral load values were 0.61 to 0.96 log
10
greater than the values for Bayer bDNA assay for samples with genotype 1, 2, or 3 samples and 0.08 log
10
greater for genotype 4 specimens. The Roche RT-PCR assay gave mean viral load values that were 0.28 to 0.82 log
10
greater than those obtained with the Bayer bDNA assay for genotype 1, 2, and 3 samples. However, for genotype 4 samples the mean viral load value obtained with the Roche RT-PCR assay was, on average, 0.15 log
10
lower than that of the Bayer bDNA. Based on these data, we conclude that the sensitivity and linear range of the Abbott and Roche RT-PCR assays enable them to be used for HCV diagnostics and therapeutic monitoring. However, the differences in the viral load values obtained with the different assays underscore the importance of using one assay when monitoring response to therapy.
Clinical Significance of Azole Antifungal Drug Cross-Resistance in
Candida glabrata
Authors: Panackal Anil A. , Gribskov Jennifer L. , Staab Janet F. , Kirby Katherine A. , Rinaldi Michael , Marr Kieren A.
Published: May 2006

Candida glabrata
, which can become resistant to fluconazole, is a common cause of bloodstream infection. This study was performed to determine the significance of cross-resistance to new azole drugs among
C. glabrata
isolates recovered as a cause of infection in azole-treated hematopoietic stem cell transplant (HSCT) recipients. Seven cases of invasive candidiasis caused by
C. glabrata
occurred in HSCT recipients who were receiving azole therapy between January 2000 and December 2004 in our institution. Case characteristics were ascertained. Sequential colonizing and invasive isolates were examined to determine susceptibilities to fluconazole, itraconazole, and voriconazole, and molecular relatedness by restriction fragment length polymorphism (RFLP) analysis. Twenty-three
C. glabrata
isolates were recovered from 4 patients who developed candidemia while receiving fluconazole and three patients who developed candidemia while receiving voriconazole. The mode MICs of fluconazole, itraconazole, and voriconazole for these isolates were ≥64 μg/ml (range, 4 to ≥64 μg/ml), 2 μg/ml (range, 0.25 to ≥16 μg/ml), and 1 μg/ml (range, 0.03 to ≥16 μg/ml), respectively. Kendall
tau
b correlation coefficients demonstrated significant associations between the MICs of voriconazole with fluconazole (
P
= 0.005) and itraconazole (
P
= 0.008). Colonizing and invasive isolates exhibiting variable susceptibilities had similar RFLP patterns. These observations suggest that
C. glabrata
exhibits considerable clinically significant cross-resistance between older azole drugs (fluconazole and itraconazole) and voriconazole. Caution is advised when considering voriconazole therapy for
C. glabrata
candidemia that occurs in patients with extensive prior azole drug exposure.
PCR Amplification of the IS
6110
Insertion Element of
Mycobacterium tuberculosis
in Fecal Samples from Patients with Intestinal Tuberculosis
Authors: Balamurugan Ramadass , Venkataraman Subramanian , John K. R. , Ramakrishna Balakrishnan S.
Published: May 2006

PCR amplification of insertion element IS
6110
of
Mycobacterium tuberculosis
in fecal samples was evaluated in the diagnosis of intestinal tuberculosis (ITB). The numbers of samples that tested positive by PCR with SalI digestion were 16/18 untreated-ITB samples, 0/8 treated-ITB samples, 12/14 smear-positive pulmonary tuberculosis samples, and 0/30 control samples. The sensitivity, specificity, positive predictive value, and negative predictive value of fecal PCR were 88.8%, 100%, 100%, and 93.7%, respectively.
Spondylodiscitis Caused by
Candida krusei
: Case Report and Susceptibility Patterns
Authors: Pemán Javier , Jarque Isidro , Bosch María , Cantón Emilia , Salavert Miguel , de Llanos Rosario , Molina Araceli
Published: May 2006

A 62-year-old man with amphotericin B-resistant
Candida krusei
spondylodiscitis, following an episode of candidemia caused by the same strain, was successfully treated with caspofungin plus voriconazole. Amphotericin B fungicidal concentrations were better predictors of the clinical outcome than were MICs. This is the first case of
C. krusei
spondylodiscitis reported in the literature.
Studies of specifically fluorinated carbohydrates. Part II. Nuclear magnetic resonance studies of pentopyranosyl fluoride derivatives
Authors: Hall L. D. , Manville J. F.
Published: May 2006

Detailed studies, by 1H and 19F nuclear magnetic resonance spectroscopy, of a series of fully esterified pentopyranosyl fluorides, show that all such derivatives favor that conformer in which the fluorine substituent is axially oriented. This conclusion is supported by separate considerations of the vicinal and geminal19F–1H and 1H–1H coupling constants, of the long-range (4J) 1H–1H and 19F–1H coupling constants and of the 19F chemical shifts. The limitations of the above conformational model are discussed.
Synthesis of 3-acetamido-2,3,6-trideoxy-D-lyxo-hexose (N-acetyl-D-daunosamine) and its D-arabino isomer
Authors: Baer Hans H. , Čapek Karel , Cook Martin C.
Published: May 2006

Two syntheses of 3-acetamido-2,3,6-trideoxy-D-lyxo-hexose (N-acetyl-D-daunosamine, 14) are described. The first one starts from methyl 3-acetamido-2,3-dideoxy-β-D-arabino-hexopyranoside (1) which is converted via its 6-O-tosylate (2) and 4-O-acetyl 6-O-tosylate (3) into methyl 3-acetamido-4-O-acetyl-2,3,6-trideoxy-6-iodo-β-D-arabino-hexopyranoside (5). Under certain conditions the last step involves a partial anomerization giving the α-anomer (6) as an additional product. Both 5 and 6 may be reductively dehalogenated to the corresponding 4-O-acetates having a 6-deoxy function (7 and 8). Preferably, 5 is reduced and simultaneously de-O-acetylated to methyl 3-acetamido-2,3,6-trideoxy-β-D-arabino-hexopyranoside (9). This glycoside is converted into its β-D-lyxo isomer (13) by solvolysis of the 4-O-mesylate (12). Hydrolyses of 9 give 3-acetamido-2,3,6-trideoxy-D-arabino-hexose (10) and the corresponding amino sugar hydrochloride (11), while hydrolyses of 13 give N-acetyl-D-daunosamine (14) and a syrupy amino sugar hydrochloride. The second synthesis of 14 departs from the D-lyxo isomer (15) of 1 and proceeds in a similar sequence via the 4-O-acetylated derivatives with 6-O-tosyl (16), 6-deoxy-6-iodo (17), and 6-deoxy (18) functions, the two last-mentioned compounds being α-glycosides due to anomerization in the step 16 → 17.