bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of Prostasin Serine Protease and Protease Nexin-1 (PN-1) in Rhesus Monkey Ovary During Menstrual Cycle and Early Pregnancy
Authors: Zhang Heng , Lin Hai-Yan , Yang Qing , Wang Hong-Xing , Chai Karl X. , Chen Li-Mei , Zhu Cheng
Published: September 2007

Serine proteases and their cognate serpin-class inhibitors are involved in the controlled proteolytic events during follicular development, ovulation, formation, and maintenance of the corpus luteum (CL). In this study, we investigated the expression patterns of prostasin serine protease and protease nexin-1 (PN-1), a serine protease inhibitor also called serpin-E2, in rhesus monkey ovaries during the menstrual cycle and early pregnancy, by using in situ hybridization and immunohistochemistry. Expression of prostasin was localized in oocyte, granulosa cells, and/or theca cells of early antral follicles and antral follicles, with high levels observed in preovulatory follicles. Prostasin was also localized at high levels of abundance in the CL during the menstrual cycle and early pregnancy. During the menstrual cycle, PN-1 was coordinately localized with prostasin in oocytes, granulosa cells, and theca cells of antral follicles and preovulatory follicles and in the CL. In addition, the PN-1 expression level in macaque CL during early pregnancy increased as pregnancy proceeded. We propose that prostasin may be involved in follicular development, ovulation, and CL formation, whereas PN-1 may be present to regulate the proteolysis in these processes.
Hyaluronan in Breast Cancer: Correlations With Nitric Oxide Synthases and Tyrosine Nitrosylation
Authors: Karihtala Peeter , Soini Ylermi , Auvinen Päivi , Tammi Raija , Tammi Markku , Kosma Veli-Matti
Published: September 2007

Reactive oxygen species (ROS), including nitric oxide (NO•), are associated with all steps of carcinogenesis. Hyaluronan (HA), a high-molecular-mass glycosaminoglycan over-expressed in a variety of human malignancies also has ROS-scavenging properties. We histochemically studied the level of HA in breast carcinoma cells and their stroma and compared it with the expression of NO• synthases (NOSs), major antioxidant enzymes, and nitrotyrosine. We also assessed whether the level of HA correlates with traditional prognostic factors of breast cancer and survival. Stromal HA level was moderate or high in all the samples studied ( n=185), and 84% of the lesions showed HA-positive carcinoma cells. Intense stromal HA signal was associated with high neuronal NOS expression ( p=0.009), whereas tumor-cell associated HA was inversely correlated with nitrotyrosine expression ( p=0.027). Of the traditional prognostic factors, tumor cell-associated HA was correlated with poor differentiation ( p=0.011), and high stromal HA levels were associated with aggressive features of the carcinomas such as large primary tumor ( p=0.002), poor differentiation ( p=0.019), and estrogen ( p=0.012) and progesterone receptor negativity ( p=0.009). High stromal HA level also significantly predicted poorer survival. The strong positive correlation between neuronal NOS and stromal HA could reflect NO•-stimulated synthesis of HA, an extracellular matrix alteration that favors breast cancer progression. Furthermore, it is suggested that, while acting as a scavenger of NO•-derived radicals, cell-associated HA undergoes partial fragmentation, release from receptors, and further degradation in lysosomes, and thus becomes undetectable in histological sections.
LacZ Transgenic Mice and Immunoelectron Microscopy: An Ultrastructural Method for Dual Localization of β-Galactosidase and Horseradish Peroxidase
Authors: John Patricia L. St. , Abrahamson Dale R.
Published: September 2007

Transgenic animals bearing the reporter gene, LacZ, encoding the histochemical enzyme, β-galactosidase, are increasingly becoming available. Similarly, antibody conjugates consisting of specific IgGs coupled to horseradish peroxidase (HRP) are widely used for Western blotting, ELISA, and immunohistochemistry. Here we provide a detailed fixation and histochemical protocol for the simultaneous electron microscopic visualization and discrimination of β-galactosidase and peroxidase reaction products within mouse kidney. After incubation of transgenic LacZ tissues with IgG-HRP conjugates, samples were lightly fixed with 2% paraformaldehyde and 0.4% glutaraldehyde and processed for peroxidase histochemistry. Tissues underwent β-galactosidase histochemistry, were refixed with glutaraldehyde, osmicated, and embedded. In Flk1/ LacZ mice, we immunolocalized anti-laminin β1 chain IgG-HRP specifically to developing glomerular basement membranes, whereas Flk1/ LacZ was expressed only by glomerular endothelial cells. In Epas1/ LacZ mice, we immunolocalized anti-platelet endothelial cell adhesion molecule-1 specifically to glomerular endothelial plasma membranes, whereas Epas1/ LacZ was expressed by both glomerular endothelial and mesangial cells. This dual ultrastructural localization technique should be broadly applicable for immunoelectron microscopic studies in LacZ transgenic animals, particularly those where LacZ expression and antibody-HRP binding are both relatively abundant.
Mechanisms of Low-Glucose Sensitivity in Carotid Body Glomus Cells
Authors: García-Fernández María , Ortega-Sáenz Patricia , Castellano Antonio , López-Barneo José
Published: September 2007

OBJECTIVE—Glucose sensing is essential for the adaptive counterregulatory responses to hypoglycemia. We investigated the mechanisms underlying carotid body (CB) glomus cells activation by low glucose.

RESEARCH DESIGN/METHODS AND RESULTS—Removal of extracellular glucose elicited a cell secretory response, abolished by blockade of plasma membrane Ca2+ channels, and a reversible increase in cytosolic Ca2+ concentration. These data indicated that glucopenia induces transmembrane Ca2+ influx and transmitter secretion. In patch-clamped glomus cells, exposure to low glucose resulted in inhibition of macroscopic outward K+ currents and in the generation of a depolarizing receptor potential (DRP). The DRP was abolished upon removal of extracellular Na+. The membrane-permeable 1-oleoyl-2-acetyl-sn-glycerol induced inward currents of similar characteristics as the current triggered by glucose deficiency. The functional and pharmacological analyses suggest that low glucose activates background cationic Na+-permeant channels, possibly of the transient receptor potential C subtype. Rotenone, a drug that occludes glomus cell sensitivity to hypoxia, did not abolish responsiveness to low glucose. The association of Glut2 and glucokinase, characteristic of some high glucose–sensing cells, did not seem to be needed for low glucose detection.

CONCLUSIONS—Altogether, these data support the view that the CB is a multimodal chemoreceptor with a physiological role in glucose homeostasis.
Loss of TR4 Orphan Nuclear Receptor Reduces Phosphoenolpyruvate Carboxykinase–Mediated Gluconeogenesis
Authors: Liu Ning-Chun , Lin Wen-Jye , Kim Eungseok , Collins Loretta L. , Lin Hung-Yun , Yu I-Chen , Sparks Janet D. , Chen Lu-Min , Lee Yi-Fen , Chang Chawnshang
Published: September 2007

OBJECTIVE—Regulation of phosphoenolpyruvate carboxykinase (PEPCK), the key gene in gluconeogenesis, is critical for glucose homeostasis in response to quick nutritional depletion and/or hormonal alteration.

RESEARCH DESIGN/METHODS AND RESULTS— Here, we identified the testicular orphan nuclear receptor 4 (TR4) as a key PEPCK regulator modulating PEPCK gene via a transcriptional mechanism. TR4 transactivates the 490-bp PEPCK promoter-containing luciferase reporter gene activity by direct binding to the TR4 responsive element (TR4RE) located at −451 to −439 in the promoter region. Binding to TR4RE was confirmed by electrophoretic mobility shift and chromatin immunoprecipitation assays. Eliminating TR4 via knockout and RNA interference (RNAi) in hepatocytes significantly reduced the PEPCK gene expression and glucose production in response to glucose depletion. In contrast, ectopic expression of TR4 increased PEPCK gene expression and hepatic glucose production in human and mouse hepatoma cells. Mice lacking TR4 also display reduction of PEPCK expression with impaired gluconeogenesis.

CONCLUSIONS—Together, both in vitro and in vivo data demonstrate the identification of a new pathway, TR4 → PEPCK → gluconeogenesis → blood glucose, which may allow us to modulate metabolic programs via the control of a new key player, TR4, a member of the nuclear receptor superfamily.
Immunohistological evaluation of immune cell infiltrate in cutaneous Kaposi's sarcoma
Authors: Hussein Mahmoud R.
Published: September 2007

Typically, Kaposi's sarcoma (KS) also presents with immune cell infiltrates. This study does immunophenotype characterization for demographics of some of these cells to test the hypothesis that ‘development of end‐stage (nodular/tumor) KS is associated with numeric alteration in immune cell infiltrates.’ Fifteen cases of classic‐KS (nodular/tumor) and 20 normal biopsies were examined using antigen‐antibody reactions and immunoperoxidase staining for histiocytes (CD68), B cells (CD20) and T cells (CD3). Variations between normal and lesions were observed with significant increases in immune cell infiltrates (2.3 ± 0.6 vs. 6.4 ± 0.4); CD68+ (4.0 ± 1.0 vs. 7.0 ± 0.5); CD3+ (3.0 ± 1.1 vs. 10.1 ± 0.8); and CD20+ (0.0 ± 0.0 vs. 0.3 ± 0.0). Increased density of immune cells in the nodular lesions of KS may reflect increased antigenicity of these lesions; the increase in T cells suggests enhanced T cell activity in KS. However, these issues should be tested by further studies.
Phenotypically and functionally distinct subsets of natural killer cells in human PBMCs
Authors: Fan Yan‐ying , Yang Bin‐yan , Wu Chang‐you
Published: September 2007

Human natural killer (NK) cells are one major component of lymphocytes that mediate early protection against viruses and tumor cells, and play an important role in immune regulatory functions. In this study, we demonstrated that human NK cells could be divided into four subsets, CD56hiCD16−, CD56loCD16−, CD56+CD16+ and CD56−CD16+, based on the expression of cell surface CD56 and CD16 molecules. Phenotypic analysis of NK cell subsets indicated that the expression of activation markers, adhesion molecules, memory cell markers, inhibitory and activating receptors, and intracellular proteins (granzyme B and perforin) were heterogeneous. Following interleukin (IL)‐2 stimulation, interferon‐γ was preferentially produced by CD56+CD16− NK cells and this subset showed more proliferative capacity. The cytolytic activity of both CD56+CD16− and CD56+/−CD16+ subsets could be augmented in response to IL‐2. The data provided a new definition for NK cell subsets demonstrating their phenotypic and functional diversity and possible stage of NK cell differentiation in peripheral blood.
Antisense oligonucleotide Elk‐1 suppresses the tumorigenicity of human hepatocellular carcinoma cells
Authors: Ying Tsung‐Ho , Hsieh Yi‐Hsien , Hsieh Yih‐Shou , Liu Jer‐Yuh
Published: September 2007

In previous studies, we showed that reducing Ets‐like protein‐1 (Elk‐1) expression inhibited protein kinase C alpha (PKCα) expression and decreased cell migration and invasion in human hepatocellular carcinoma (HCC). In this study, we have investigated the role of Elk‐1 in tumorigenesis. SK‐Hep‐1 HCC cells were transfected with the ElK‐1 antisense oligonucleotide (ODN). In the pretreated cells we detected a reduction of mRNA level using RT—PCR. The inhibitory rate of cell growth was measured by MTT assay. Pretreated‐SK‐Hep‐1 HCC cells were implanted subcutaneously into nude mice to observe the tumor growth and calculate tumor inhibitory rate. The results showed that 5 μM of the antisense ODN Elk‐1 suppressed both Elk‐1 and PKCα production by SK‐Hep‐1 HCC cells after cationic liposome‐mediated transfection, to 8% and 1% of control values, respectively, and the growth of SK‐Hep‐1 HCC cells was inhibited at 2–5 μM doses of the antisense ODN Elk‐1. The control reagent, sense ODN Elk‐1, showed no effects. In BALB/nude mice, SK‐Hep‐1 HCC cells transfected with the 5 μM antisense ODN Elk‐1 formed tumors much smaller than those of sense ODN Elk‐1 pretreated cells. The maximum inhibitory rate of tumor growth was 80.8 ± 12.6% and the tumor formation time was prolonged from 13 to 25 days. These findings suggested the usefulness of antisense ODN Elk‐1 as a new reagent for liver cancer therapy.
Three‐dimensional matrix induces sustained activation of ERK1/2 via Src/Ras/Raf signaling pathway
Authors: Damianova Ralica , Stefanova Nadezhda , Cukierman Edna , Momchilova Albena , Pankov Roumen
Published: September 2007

Research in cell signaling often depends on tissue culture, but the artificial substrates used to grow cellsin vitroare likely to distort the conclusions, particularly when adhesion‐mediated signaling events are investigated. Studies of signal transduction pathways operating in cells grown in three‐dimensional (3D) matrices provide a better system, giving a closer insight of the cell signalingin vivo. We compared the steady‐state levels of ERK1/2 activity in primary human fibroblasts, induced by cell‐derived 3D fibronectin matrix or fibronectin, coated on flat surfaces. 3D environment caused ERK1/2 stimulation concomitant with a 2.5‐fold increase in Ras GTP loading and Src activation. Under these conditions FAK autophosphorylation was suppressed. Treatment with Src inhibitor PP2 abolished these effects indicating that 3D fibronectin matrix activated ERK1/2 through Src/Ras/Raf pathway, bypassing FAK. These observations suggest that withinin vivo‐like conditions Src may have a leading role in the induction of sustained ERK1/2 activation.
Involvement of Na+/H+ exchangers in induction of cyclooxygenase‐2 by vacuolar‐type (H+)‐ATPase inhibitors in RAW 264 cells
Authors: Kamachi Fumitaka , Yanai Maiko , Ban Hyun Seung , Ishihara Kenji , Hong JangJa , Ohuchi Kazuo , Hirasawa Noriyasu
Published: September 2007

In the mouse macrophage‐like cell line RAW 264, vacuolar‐type (H+)‐ATPase (V‐ATPase) inhibitors, bafilomycin A1 and concanamycin A, increased the level of cyclooxygenase (COX)‐2 protein and its mRNA. The V‐ATPase inhibitor‐induced expression of COX‐2 was suppressed by inhibitors of c‐jun N‐terminal kinase (JNK) and nuclear factor‐κB, and by inhibitors of Na+/H+ exchangers (NHEs). The bafilomycin A1‐induced activation of JNK but not degradation of IκB‐α was suppressed by NHE inhibitors and by an inhibitor of Na+/Ca2+ exchanger SN‐6. These results suggested that V‐ATPase inhibitors induce the expression of COX‐2 via NHE‐dependent and ‐independent pathways.
Midwives' Practices and Beliefs About Discharging Clients from Their Practice
Authors: Schorn Mavis N.
Published: September 2007

Discharging a client from a practice is a choice clinicians may need to make when conflicts arise that cannot be resolved. The legal and ethical considerations before discharging a client are presented. This preliminary survey of 111 certified nurse‐midwives was conducted to determine their practices and beliefs about discharging clients. Most (83.7%) participants had discharged five or fewer clients from their practice throughout their careers, including 36.9% who had never discharged a client from their practice. In contrast, 77.5% of participants said that midwives should definitely discharge clients from their practice under some circumstances. Antepartum care was the most frequent period during which clients were discharged, and 59% of those discharged were for noncompliance with the therapeutic regimen, obnoxious or abusive behavior as subjectively identified by the midwife and her colleagues, or failure to keep appointments. When asked why they might not discharge a client from their practice, 60% identified empathy or sympathy for the client as the reason. When asked why they did not discharge clients in the past, 23 (21%) respondents selected “colleagues disagreed” as the reason.
Sexually Compulsive/Addictive Behaviors in Women: A Women's Healthcare Issue
Authors: Roller Cyndi Gale
Published: September 2007

Sexually compulsive/addictive behavior is a pattern of sexual behaviors that cause distress and/or impairment of social functioning. It is marked by obsessive thoughts, compulsive behaviors, and the individual's inability to stop the behaviors despite negative consequences. Women experiencing sexually compulsive/addictive behavior are preoccupied with sex not as a response to desire but rather as a behavior that serves the purpose of anxiety reduction. Sexually compulsive/addictive behavior is associated with a number of health consequences, including sexually transmitted infections, unwanted pregnancies, abortions, and violence. It is important for providers to have an understanding of the addiction process, assessment, diagnosis, and interventions for these women.
Midwives' Knowledge, Perceptions, Beliefs, and Practice Supports Regarding Tobacco Dependence Treatment
Authors: Abatemarco Diane J. , Steinberg Michael B. , Delnevo Cristine D.
Published: September 2007

Clinical practice guidelines and evidence‐based reviews confirm the efficacy of tobacco dependence treatment for pregnant women. The purpose of this study was to examine tobacco dependence treatment practices among certified nurse‐midwives who treat pregnant women who smoke. Midwives were surveyed to determine knowledge, perceptions, and beliefs about tobacco cessation treatment and to identify practice environmental factors that support treatment practices. Half of all midwives had not heard of the US Public Health Service Guidelines (5 A's) to assist smokers in cessation treatment. We found varying levels of adherence to the clinical practice guidelines. Nearly all midwives routinely ask, advise, and assess; while fewer encourage patients to set a quit date or discuss medication options (assist) and perform follow‐up activities (arrange). Barriers significantly associated with clinical tobacco treatment practice are lack of training and competing priorities in the visit. One‐office support, a system in place to provide smoking cessation information and resources, was associated with increased practice. In summary, midwives believe they should be providing tobacco dependence treatment, yet they identify a need for training. The findings of this study also indicate that sustained practice change, which includes the entire practice environment, should be targeted to enhance tobacco dependence treatment.
Midwifery and the Development of Nursing Capacity in the Dominican Republic: Caring, Clinical Competence, and Case Management
Authors: Foster Jennifer , Heath Annemarie
Published: September 2007

The contribution of midwifery care to positive health outcomes has been acknowledged both nationally and internationally, yet currently there are insufficient numbers of midwives and nurses to meet the maternal‐infant health needs around the globe. Project ADAMES, (ADelante, Asegurando Madres E Infantes Sanos; in English: Onward! Assuring Healthy Mothers and Babies), is a non‐profit nongovernmental organization created as a collaborative, community‐based partnership between the maternity nurses in a hospital in the Dominican Republic and a group of certified nurse‐midwives from the United States. After attending a series of educational conferences in midwifery over the course of 3 years, a subset of motivated Dominican nurses and auxiliaries (the Comité) have trained hospital volunteers to be doulas, to provide the caring and supportive role to laboring women they do not have the time to provide themselves. The Comité also proposed to initiate a postpartum assessment flow sheet and precept nursing student volunteers from Project ADAMES to demonstrate the performance of routine assessments among postpartum women. The Comité desires to train nurses in other neighboring hospitals. As the nurses and midwives implement improvements in quality of care, they strive to develop a sustainable, transferable program that could be available to other sites where nurses similarly manage vaginal deliveries.
Retrieving the susceptibility from time-resolved terahertz experiments
Authors: Schins J. M. , Hendry E. , Bonn M. , Muller H. G.
Published: September 2007

We present an analytical expression for the observed signal in time- and phase-resolved pump-probe studies, with particular emphasis on terahertz time-domain spectroscopy. Maxwell’s equations are solved for the response of damped, harmonic oscillators to a driving probe field in the perturbative regime. Our analytical expressions agree with the one previously reported in the literature [Nemec et al., J. Chem. Phys. 122, 104503 (2005)] in the Drude limit; however, they differ in the case of a vibrational resonance.
Role of diffusion in excitation energy transfer and migration
Authors: Misra V. , Mishra H.
Published: September 2007

Effect of diffusion on excitation energy transfer and migration in a dye pair sodium fluorescein (donor) and Rhodamine-6G (acceptor) has been studied for different viscosities by both steady state and time domain fluorescence spectroscopic measurements. The donor-donor interaction appears to be weaker as compared to donor-acceptor interaction and thus favors direct Förster-type energy transfer. Interestingly, at low viscosity (water in this case) transfer appears to be controlled by material diffusion/energy migration. Further, acceptor dynamics reveals the fact that direct Förster transfer dominates in viscous media.
Evidence for the surface origin of point defects in ice: Control of interior proton activity by adsorbates
Authors: Devlin J. Paul , Buch Victoria
Published: September 2007

Spectroscopic studies are presented of H–D isotopic exchange in the interior of ice nanocrystals. The exchange process is dominated by ionic and orientational defects long viewed as governing the electrical properties of ice. A new finding that interior exchange rates can be controlled by acidic and basic adsorbates is evidence that the defects originate at the ice surface. In particular, it is argued that interior isotopic exchange is a reflection of proton concentrations equilibrated at the ice surface.
Modeling of plane Couette flow. I. Large scale flow around turbulent spots
Authors: Lagha Maher , Manneville Paul
Published: September 2007

Numerical simulations of a model of plane Couette flow focusing on its in-plane spatio-temporal properties are used to study the dynamics of turbulent spots. While the core of a spot is filled with small-scale velocity fluctuations, a large-scale flow extending far away and occupying the full gap between the driving plates is revealed upon filtering out small scales. It is characterized by streamwise inflow towards the spot and spanwise outflow from the spot, giving it a quadrupolar shape. A correction to the base flow is present within the spot in the form of a spanwise vortex with vorticity opposite in sign to that of the base flow. The Reynolds stresses are shown to be at the origin of this recirculation, whereas the quadrupolar shape of the in-plane flow results from the transport of this recirculation by the base flow that pumps it towards the spot in the streamwise direction and flushes it in the spanwise direction to insure mass conservation. These results shed light on earlier observations in plane Couette flow or other wall flows experiencing a direct transition to turbulence by spot nucleation.
Theory of a double-layer in an expanding electronegative plasma
Authors: Chabert P. , Lichtenberg A. J. , Lieberman M. A.
Published: September 2007

A theory is developed for formation of a weak electronegative double layer (DL) just outside of an upstream source chamber connected to a larger diameter, downstream expansion chamber. The double layer is described using four groups of charged particles: thermal positive ions, monoenergetic accelerated positive ions flowing downstream, accelerated negative ions flowing upstream, and non-Maxwellian electrons. The upstream source is modeled as a stratified plasma with an electropositive edge, and the downstream equations are solved in a spherically expanding approximation. The DL equations are solved using a non-Maxwellian electron distribution, with the solution required to be approximately self-consistent with the upstream and downstream equilibria. Particle balance upstream is used to determine the double layer potential. The theory is found to be in good agreement with experiments.
Electro-optic effect caused by polar nanoregion switching in lanthanum-modified lead zirconate titanate epitaxial films
Authors: Sato Keisuke , Kondo Masao , Kurihara Kazuaki
Published: September 2007

Lanthanum-modified lead zirconate titanate epitaxial films with (100), (101), and (111) orientations are grown, respectively, on (100), (101), and (111) niobium, lending conductivity to strontium titanate through chemical solution deposition. This study investigates changes in the ordinary and extraordinary refractive index (no and ne) induced by the electric field in these films by using the prism-coupling method. Electro-optic effects arise from three effects: Kerr effect, isotropy effect, and switching among polar nanoregions. With the Kerr effect, in which birefringence is proportional, the quadratic electric field is smaller than the other effects. The isotropy effect (Δne=Δno) is independent of the applied electric field direction and crystal axis. The electro-optic effect Δne−Δno is mainly caused by rotation of the refractive indicatrix accompanying the switching of the polar nanoregions.
Electrical passivation of Si∕SiGe∕Si structures by 1-octadecene monolayers
Authors: Antonova Irina V. , Soots Regina A. , Guliaev Mitrofan B. , Prinz Victor Ya. , Kagan Miron S. , Kolodzey James
Published: September 2007

The passivating effects of organic monolayers of 1-octadecene deposited onto the silicon surfaces of both n and p conductivities were studied for Si∕SiGe∕Si structures grown by molecular beam epitaxy and chemical vapor deposition. Measurements of the capacitance versus voltage and current versus voltage were made on structures covered with the organic monolayer and compared with unpassivated structures covered with native silicon dioxide. The results demonstrate that the organic passivation provides a decrease of surface charge and an increase of carrier concentration in the near-surface layers and/or the SiGe quantum wells.
Modeling light propagation in photonic crystal devices: Simplification of the Bloch mode scattering matrix method
Authors: Vahn Gah-Yi , White T. P. , Steel M. J. , de Sterke C. M. , Dossou K. , Botten L. C.
Published: September 2007

We derive semianalytic models of two types of photonic crystal resonators by simplifying the Bloch mode scattering matrix method. Essential to the models are two parameters, which are interpreted to be the phase change upon reflection and the measure of orthogonality between modes of adjacent waveguides. The models can predict the resonance position to better than 0.02% and the full width at half maximum to within 10%.
Organic-based distributed feedback lasers by direct electron-beam lithography on conjugated polymers
Authors: Stabile Ripalta , Camposeo Andrea , Persano Luana , Tavazzi Silvia , Cingolani Roberto , Pisignano Dario
Published: September 2007

The authors demonstrate direct electron-beam writing on conjugated polymers as patterning route to realize plastic optoelectronic devices. Lithography was carried out by a 20kV electron beam dose in the range of 0–360μC∕cm2, with no need for masking or development/etching processes. The features could be employed for the fabrication of polymer distributed feedback lasers, exhibiting optically pumped lasing in the range of 607–620nm, with a spectral linewidth around 1nm and a threshold excitation fluence of 34μJ∕cm2.
Initial/final state selection of the spin polarization in electron tunneling across an epitaxial Fe∕GaAs(001) interface
Authors: Kurebayashi H. , Steinmuller S. J. , Laloë J. B. , Trypiniotis T. , Easton S. , Ionescu A. , Yates J. R. , Bland J. A. C.
Published: September 2007

Spin dependent electron transport across epitaxial Fe∕GaAs(001) interfaces has been investigated using photoexcitation techniques. Spin filtering is observed in the forward bias regime and its sign is switched by using different photon energies. First principles calculations suggest that the spin polarization of the Fe layer is positive within the energy region into which spin polarized electrons tunnel. The authors attribute this sign switching to the initial and final states of the electrons tunneling across the interface, whose spin polarizations are determined by the selection rules in GaAs during photoexcitation and spin polarization of the Fe(001) layer, respectively.
Selective imaging in second-harmonic-generation microscopy by polarization manipulation
Authors: Chu Shi-Wei , Tai Shih-Peng , Sun Chi-Kuang , Lin Chi-Hung
Published: September 2007

Second-harmonic-generation (SHG) has proved itself as an important contrast mechanism in microscopic applications. Its noninvasiveness, optical sectioning capability, and high-penetrability provide attractive features in observation of thick biological tissues. Fibrous proteins, such as myosin and collagen, are dominant SHG harmonophores in vertebrates. Due to their biophotonic crystal nature, SHGs from these proteins are known to exhibit specific polarization dependencies, reflecting local molecule arrangements. Here the authors demonstrate a scheme to distinguish SHG from myosin-based muscle fibers and intertwined collagenous perimysium through polarization selection, without complicated staining or sample/image processing required.
Temperature and angle tuning of second harmonic generation in media with a short-range order
Authors: Sheng Yan , Dou Junhong , Li Jingjuan , Ma Dongli , Cheng Bingying , Zhang Daozhong
Published: September 2007

The authors theoretically study the nonlinear optical characterization of the short-range ordered structure and deduce the analytical expression of the effective nonlinear optical coefficient. The dependences of the second harmonic conversion efficiency on crystal temperature, incident angle, and reversed domain cycle are measured. They find that for a substantial range of parameters, the short-range ordered structure has a broader tuning response than the periodic or the quasiperiodic structures. The experimental results accord well with the theory.
RNAi-mediated gene silencing reveals involvement of
Arabidopsis
chromatin-related genes in
Agrobacterium
-mediated root transformation
Authors: Crane Yan Ma , Gelvin Stanton B.
Published: September 2007

We investigated the effect of RNAi-mediated gene silencing of 109
Arabidopsis thaliana
chromatin-related genes (termed “chromatin genes” hereafter) on
Agrobacterium
-mediated root transformation. Each of the RNAi lines contains a single- or low-copy-number insertion of a hairpin construction that silences the endogenous copy of the target gene. We used three standard transient and stable transformation assays to screen 340 independent RNAi lines, representing 109 target genes, for the rat (resistant to
Agrobacterium
transformation) phenotype. Transformation frequency was not affected by silencing 85 of these genes. Silencing of 24 genes resulted in either a weak or strong rat phenotype. The rat mutants fell into three general groups: (
i
) severely dwarfed plants exhibiting a strong rat phenotype (
CHC1
); (
ii
) developmentally normal plants showing a reduced response to three transformation assays (
HAG3
,
HDT1
,
HDA15
,
CHR1
,
HAC1
,
HON5
,
HDT2
,
GTE2
,
GTE4
,
GTE7
,
HDA19
,
HAF1
,
NFA2
,
NFA3
,
SGA1
, and
SGB2
); or (
iii
) varying response among the three transformation assays (
DMT1
,
DMT2
,
DMT4
,
SDG1
,
SDG15
,
SDG22
, and
SDG29
). A direct molecular assay indicated that
SGA1
,
HDT1
, and
HDT2
are important for T-DNA integration into the host genome in
Arabidopsis
roots.
Chicken cathelicidin-B1, an antimicrobial guardian at the mucosal M cell gateway
Authors: Goitsuka Ryo , Chen Chen-lo H. , Benyon Lesley , Asano Yusuke , Kitamura Daisuke , Cooper Max D.
Published: September 2007

Mucosal epithelial M cells provide an efficient portal of entry for microorganisms. Initially defined by their irregular microvilli and abundant transcytotic channels in the avian bursa of Fabricius, M cells also are found in the lymphoid follicle-associated epithelium of the mammalian appendix, Peyer's patches, and other mucosal surface-lymphoid interfaces. We describe here a previously unrecognized cathelicidin gene in chickens,chCATH-B1, that is expressed exclusively in the epithelium of the bursa of Fabricius. Like the mature peptides of previously identified cathelicidins, the carboxyl-terminal peptide of chCATH-B1 has broad antimicrobial activity against Gram-positive and Gram-negative bacteria.chCATH-B1expression is restricted to the secretory epithelial cell neighbors of the M cells, whereas its mature peptide is transported to become concentrated on the fibrillar network surrounding basolateral surfaces of the M cells that overlie the bursal lymphoid follicles. We conclude that chCATH-B1 is well placed to serve a protective antimicrobial role at the M cell gateway.
TAGster: efficient selection of LD tag SNPs in single or multiple populations
Authors: Xu Zongli , Kaplan Norman L. , Taylor Jack A.
Published: September 2007

Summary: Genetic association studies increasingly rely on the use of linkage disequilibrium (LD) tag SNPs to reduce genotyping costs. We developed a software package TAGster to select, evaluate and visualize LD tag SNPs both for single and multiple populations. We implement several strategies to improve the efficiency of current LD tag SNP selection algorithms: (1) we modify the tag SNP selection procedure of Carlson et al. to improve selection efficiency and further generalize it to multiple populations. (2) We propose a redundant SNP elimination step to speed up the exhaustive tag SNP search algorithm proposed by Qin et al. (3) We present an additional multiple population tag SNP selection algorithm based on the framework of Howie et al., but using our modified exhaustive search procedure. We evaluate these methods using resequenced candidate gene data from the Environmental Genome Project and show improvements in both computational and tagging efficiency.

Availability: The software Package TAGster is freely available at http://www.niehs.nih.gov/research/resources/software/tagster/

Contact:  taylor@niehs.nih.gov

Supplementary information: Additional information, including a tutorial, detailed algorithm and detailed evaluation results, is also available from TAGster web site (see above).
Exploiting sample variability to enhance multivariate analysis of microarray data
Authors: Möller-Levet Carla S. , West Catharine M. , Miller Crispin J.
Published: September 2007

Motivation: Biological and technical variability is intrinsic in any microarray experiment. While most approaches aim to account for this variability, they do not actively exploit it. Here, we consider a novel approach that uses the variability between arrays to provide an extra source of information that can enhance gene expression analyses.

Results: We develop a method that uses sample similarity to incorporate sample variability into the analysis of gene expression profiles. This allows each pairwise correlation calculation to borrow information from all the data in the experiment. Results on synthetic and human cancer microarray datasets show that the inclusion of this information leads to a significant increase in the ability to identify previously characterized relationships and a reduction in false discovery rate, when compared to a standard analysis using Pearson correlation. The information carried by the variability between arrays can be exploited to significantly improve the analysis of gene expression data.

Availability: Matlab script files are available from the author.

Contact:  cmoller@picr.man.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Modeling protein loops with knowledge-based prediction of sequence-structure alignment
Authors: Peng Hung-Pin , Yang An-Suei
Published: September 2007

Motivation: As protein structure database expands, protein loop modeling remains an important and yet challenging problem. Knowledge-based protein loop prediction methods have met with two challenges in methodology development: (1) loop boundaries in protein structures are frequently problematic in constructing length-dependent loop databases for protein loop predictions; (2) knowledge-based modeling of loops of unknown structure requires both aligning a query loop sequence to loop templates and ranking the loop sequence-template matches.

Results: We developed a knowledge-based loop prediction method that circumvents the need of constructing hierarchically clustered length-dependent loop libraries. The method first predicts local structural fragments of a query loop sequence and then structurally aligns the predicted structural fragments to a set of non-redundant loop structural templates regardless of the loop length. The sequence-template alignments are then quantitatively evaluated with an artificial neural network model trained on a set of predictions with known outcomes. Prediction accuracy benchmarks indicated that the novel procedure provided an alternative approach overcoming the challenges of knowledge-based loop prediction.

Availability:  http://cmb.genomics.sinica.edu.tw

Contact:  yangas@gate.sinica.edu.tw

Supplementary information: Supplementary data are available at Bioinformatics online.
The Role of Phosphoenolpyruvate Carboxylase during C4 Photosynthetic Isotope Exchange and Stomatal Conductance
Authors: Cousins Asaph B. , Baroli Irene , Badger Murray R. , Ivakov Alexander , Lea Peter J. , Leegood Richard C. , von Caemmerer Susanne
Published: September 2007

Phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) plays a key role during C4 photosynthesis and is involved in anaplerotic metabolism, pH regulation, and stomatal opening. Heterozygous (Pp) and homozygous (pp) forms of a PEPC-deficient mutant of the C4 dicot Amaranthus edulis were used to study the effect of reduced PEPC activity on CO2 assimilation rates, stomatal conductance, and 13CO2 (Δ13C) and C18OO (Δ18O) isotope discrimination during leaf gas exchange. PEPC activity was reduced to 42% and 3% and the rates of CO2 assimilation in air dropped to 78% and 10% of the wild-type values in the Pp and pp mutants, respectively. Stomatal conductance in air (531 μbar CO2) was similar in the wild-type and Pp mutant but the pp mutant had only 41% of the wild-type steady-state conductance under white light and the stomata opened more slowly in response to increased light or reduced CO2 partial pressure, suggesting that the C4 PEPC isoform plays an essential role in stomatal opening. There was little difference in Δ13C between the Pp mutant (3.0‰ ± 0.4‰) and wild type (3.3‰ ± 0.4‰), indicating that leakiness (ϕ), the ratio of CO2 leak rate out of the bundle sheath to the rate of CO2 supply by the C4 cycle, a measure of the coordination of C4 photosynthesis, was not affected by a 60% reduction in PEPC activity. In the pp mutant Δ13C was 16‰ ± 3.2‰, indicative of direct CO2 fixation by Rubisco in the bundle sheath at ambient CO2 partial pressure. Δ18O measurements indicated that the extent of isotopic equilibrium between leaf water and the CO2 at the site of oxygen exchange (θ) was low (0.6) in the wild-type and Pp mutant but increased to 0.9 in the pp mutant. We conclude that in vitro carbonic anhydrase activity overestimated θ as compared to values determined from Δ18O in wild-type plants.
A Central Role of Abscisic Acid in Drought Stress Protection of Agrobacterium-Induced Tumors on Arabidopsis
Authors: Efetova Marina , Zeier Jürgen , Riederer Markus , Lee Chil-Woo , Stingl Nadja , Mueller Martin , Hartung Wolfram , Hedrich Rainer , Deeken Rosalia
Published: September 2007

Crown gall tumors induced by Agrobacterium tumefaciens represent a sink that has to be provided with nutrients and water by the host plant. The lack of an intact epidermis or cuticle results in uncontrolled loss of water. However, neither the tumor nor the host plant displays wilting. This phenomenon points to drought adaptation in both tumors and the crown gall host plant. To understand the underlying molecular mechanisms of protection against desiccation the gene expression pattern of Arabidopsis (Arabidopsis thaliana) tumors was integrated with the profile of stress metabolites: Arabidopsis tumors accumulated high amounts of abscisic acid (ABA), the ethylene precursor aminocyclopropyl carboxylic acid, osmoprotectants, and form a suberized periderm-like protective layer. Suberization of the outer tumor cell layers most likely is mediated by ABA since external application of ABA induced suberization of Arabidopsis roots. However, the expression level of the classical marker genes, known to respond to drought stress and/or ABA, was lower in tumors. Instead another set of drought and/or ABA-inducible genes was more highly transcribed. Elevated transcription of several ABA-dependent aquaporin genes might indicate that ABA controls the water balance of the tumor. The retarded tumor growth on abi and aba mutant plants underlined the importance of a tumor-specific ABA signaling pathway. Taken together, we propose that ABA is an important signal for protection of tumors against desiccation and thus supports tumor development.
AP2-ERF Transcription Factors Mediate Nod Factor–Dependent MtENOD11Activation in Root Hairs via a Novelcis-Regulatory Motif
Authors: Andriankaja Andry , Boisson-Dernier Aurélien , Frances Lisa , Sauviac Laurent , Jauneau Alain , Barker David G. , de Carvalho-Niebel Fernanda
Published: September 2007

Rhizobium Nod factors (NFs) are specific lipochitooligosaccharides that activate host legume signaling pathways essential for initiating the nitrogen-fixing symbiotic association. This study describes the characterization of cis-regulatory elements and trans-interacting factors that regulate NF-dependent and epidermis-specific gene transcription in Medicago truncatula. Detailed analysis of the Mt ENOD11 promoter using deletion, mutation, and gain-of-function constructs has led to the identification of an NF-responsive regulatory unit (the NF box) sufficient to direct NF-elicited expression in root hairs. NF box–mediated expression requires a major GCC-like motif, which is also essential for the binding of root hair–specific nuclear factors. Yeast one-hybrid screening has identified three closely related AP2/ERF transcription factors (ERN1 to ERN3) that are able to bind specifically to the NF box. ERN1 is identical to an ERF-like factor identified recently. Expression analysis has revealed that ERN1 and ERN2 genes are upregulated in root hairs following NF treatment and that this activation requires a functional NFP gene. Transient expression assays in Nicotiana benthamiana have further shown that nucleus-targeted ERN1 and ERN2 factors activate NF box–containing reporters, whereas ERN3 represses ERN1/ERN2-dependent transcription activation. A model is proposed for the fine-tuning of NF-elicited gene transcription in root hairs involving the interplay between repressor and activator ERN factors.
Information Science at City University London
Authors: Bawden David
Published: September 2007

Purpose

The paper seeks to introduce a special issue of Aslib Proceedings, which contains a series of papers written by staff and research students at the Department of Information Science, City University London.

Design/methodology/approach

This introductory paper introduces the other papers in the special issue and sets them in context.

Findings

This editorial argues that the information science discipline, which has always been the focus of City's research and scholarship, is a valid academic discipline with a positive future.

Originality/value

The paper points out the particular strengths and historical continuity of the City Information Science Department.
Flickr and Democratic Indexing: dialogic approaches to indexing
Authors: Rafferty Pauline , Hidderley Rob
Published: September 2007

Purpose

The purpose of this paper is two‐fold: to examine three models of subject indexing (i.e. expert‐led indexing, author‐generated indexing, and user‐orientated indexing); and to compare and contrast two user‐orientated indexing approaches (i.e. the theoretically‐based Democratic Indexing project, and Flickr, a working system for describing photographs).

Design/methodology/approach

The approach to examining Flickr and Democratic Indexing is evaluative. The limitations of Flickr are described and examples are provided. The Democratic Indexing approach, which the authors believe offers a method of marshalling a “free” user‐indexed archive to provide useful retrieval functions, is described.

Findings

The examination of both Flickr and the Democratic Indexing approach suggests that, despite Shirky's claim of philosophical paradigm shifting for social tagging, there is a residing doubt amongst information professionals that self‐organising systems can work without there being some element of control and some form of “representative authority”.

Originality/value

This paper contributes to the literature of user‐based indexing and social tagging.
Corrosion of chromate conversion films on aluminium in electrically bonded interfaces
Authors: Shoja Razavi Reza
Published: September 2007

Purpose

The present study aims to investigate the corrosion and electrical properties of the chromate conversion coatings on aluminium alloy Type 6061 in electrically bonded interfaces.

Design/methodology/approach

Tests were carried out to obtain the optimum conditions for chromate bath composition and immersion time for standard requirement provisions such as corrosion resistance in the salt‐spray test, electrical resistance and coating quality. The applied coatings were tested electrochemically in seawater and distilled water. The protection mechanism was evaluated from Tafel and cyclic polarisation curves in the said environments.

Findings

The evaluations showed that the passive film layer contained chromate with alumina formed on the substrate. The good performance of the conversion coating in terms of its corrosion and electrical conductivity was probably due to the characteristics of this protective film.

Originality/value

The paper presents findings on the corrosion of chromate conversion films on aluminium in electrically bonded interfaces.
Corrosion inhibition of copper in sulphuric acid by some nitrogen heterocyclic compounds
Authors: Shahrabi T. , Tavakholi Hossein , Hosseini M.G.
Published: September 2007

Purpose

In this paper, the main aim is to study the influence of some nitrogen heterocyclic compounds, namely 2‐mercaptobenzimidazole (2‐MBI), 2‐mercaptobenzoxazole (2‐MBO) and 2‐mercaptobenzothiazole (2‐MBT) on the corrosion inhibition of copper in 0.5 M sulphuric acid.

Design/methodology/approach

Measurements were carried out in a three‐electrode cell that was connected to the corrosion measurement system using software for Tafel polarization. Impedance measurements were carried out at open circuit potential using an electrochemical interface and frequency response analyzer at frequencies from 100 kHz to 10 MHz.

Findings

For all the compounds, a consistent trend of increase in inhibition efficiency was observed as a function of concentration. The adsorption of all the compounds on to the copper surface in the acidic solution was found to obey the Langmuir Adsorption Isotherm. The values of activation energy and free energy of adsorption for all the compounds also were calculated. The Tafel polarization studies indicated that all the compounds were mixed inhibitors.

Research limitations/implications

In order to further the performance of heterocyclic compounds and also to identify their synergistic effects with some additives (such as surfactants) it is suggested that further research into the behaviour of these heterocyclic compounds with other metals be carried out.

Originality/value

The results of this paper can be used for acid descaling of copper in which suitable inhibitor systems with the highest efficiencies are required.