bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping of sex hormone receptors and their modulators along the nephron of male and female mice
Authors: Grimont Adrien , Bloch-Faure May , Abida Boutaïna El , Crambert Gilles
Published: May 2009

Renal functions are regulated by steroid sex hormones, but the exhaustive identification of their receptors along the nephron is still lacking. Here, we have localized all known nuclear or membrane‐bound sex hormone receptors and some of their activators along the nephron of male and female mice. Almost all receptors are present in male and female kidney, some of them having very restricted localization. Only one gene tested among 11 (ARA54) exhibits a gender difference in the level of its expression. This first “renal map” of sex steroid receptor expression may serve as a pre‐requisite for investigating the role of these hormones on kidney functions.
Does distant homology with Evf reveal a lipid binding site in Bacillus thuringiensis cytolytic toxins?
Authors: Rigden Daniel J.
Published: May 2009

The Cry and Cyt classes of insecticidal toxins derived from the sporulating bacterium Bacillus thuringiensis are valuable substitutes for synthetic pesticides in agricultural contexts. Crystal structures and many biochemical data have provided insights into their molecular mechanisms, generally thought to involve oligomerization and pore formation, but have not localised the site on Cyt toxins responsible for selective binding of phospholipids containing unsaturated fatty acids. Here, distant homology between the structure of Cyt toxins and Erwinia virulence factor (Evf) is demonstrated which, along with sequence conservation analysis, allows a putative lipid binding site to be localised in the toxins.
The p38 MAPK pathway inhibits tristetraprolin‐directed decay of interleukin‐10 and pro‐inflammatory mediator mRNAs in murine macrophages
Authors: Tudor Corina , Marchese Francesco P. , Hitti Edward , Aubareda Anna , Rawlinson Lesley , Gaestel Matthias , Blackshear Perry J. , Clark Andrew R. , Saklatvala Jeremy , Dean Jonathan L.E.
Published: May 2009

p38 mitogen‐activated protein kinase (MAPK) stabilises pro‐inflammatory mediator mRNAs by inhibiting AU‐rich element (ARE)‐mediated decay. We show that in bone‐marrow derived murine macrophages tristetraprolin (TTP) is necessary for the p38 MAPK‐sensitive decay of several pro‐inflammatory mRNAs, including cyclooxygenase‐2 and the novel targets interleukin (IL)‐6, and IL‐1α. TTP−/− macrophages also strongly overexpress IL‐10, an anti‐inflammatory cytokine that constrains the production of the IL‐6 despite its disregulation at the post‐transcriptional level. TTP directly controls IL‐10 mRNA stability, which is increased and insensitive to inhibition of p38 MAPK in TTP−/− macrophages. Furthermore, TTP enhances deadenylation of an IL‐10 3′‐untranslated region RNA in vitro.
Issues in Pregnancy Dating: Revisiting the Evidence
Authors: Hunter Linda A.
Published: May 2009

As the end point date in pregnancy, the estimated date of delivery provides guidance for the timing of specific prenatal tests, gauges fetal growth, and informs critical decision making for specific obstetric complications. It is prudent to use the most evidenced‐based methods available to accurately determine gestational age. This article explores the accuracy of both menstrual and ultrasound dating techniques and discusses some of the issues and limitations for each method. In addition, a simple formula called the rule of eights can be used to determine a final estimated date of delivery when a discrepancy between menstrual and ultrasound dating occurs.
“I Wasn't Alone”—A Study of Group Prenatal Care in the Military
Authors: Kennedy Holly Powell , Farrell Trisha , Paden Regina , Hill Shannon , Jolivet Rima , Willetts Jacqueline , Rising Sharon Schindler
Published: May 2009

The military has recognized that health and quality of life for service members are closely tied to the resources for their families, including how they are cared for during pregnancy and childbirth. However, there has been little examination of women's experience with different models of prenatal care (PNC) in military settings. The purpose of this article is to describe the results of a qualitative study of women's experiences with the CenteringPregnancy model of group PNC compared to individual PNC in two military health care settings. This clinical trial enrolled 322 women who were randomized into group or individual PNC at two military treatment facilities. Qualitative interviews were completed with 234 women during the postpartum period. Interpretative narrative and thematic analysis was used to identify three themes: 1) “I wasn't alone”—the experience with group PNC; 2) “I liked it but…”—recommendations to improve group PNC; and 3) “They really need to listen”—general concerns across the sample about PNC. Greatest concerns of women in individual PNC included lack of continuity and time with the provider. Our military families must be assured that their health care system meets their needs through personal and family‐centered care. Group PNC offers the potential for continuity of provider while also offering community with other women. In the process, women gain knowledge and power as a health care consumer.
Impact of Two Scheduling Systems on Early Enrollment in a Group Prenatal Care Program
Authors: Hackley Barbara , Applebaum Jo , Wilcox Wendy C. , Arevalo Sandra
Published: May 2009

Group care is an effective approach to prenatal care. Yet difficulties in recruiting, enrolling, and scheduling women into group care present obstacles to optimal program delivery. The purpose of this study was to determine whether the use of a scheduling system based on women's estimated date of delivery (EDD) decreased gestational age at entry to group care, increased attendance, and improved continuity of care. A total of 13 groups were held; seven groups used a scheduling system based on appointment availability and six groups used a scheduling system based on women's EDD. Compared with the availability‐based scheduling system, the EDD‐based system decreased mean gestational age (23.2 vs. 21.8 weeks; P = .058) and significantly decreased mean maximum gestational age (31.0 vs. 26.3 weeks; P = .002) at entry to group care. The EDD‐based system increased the mean number of sessions offered per group (6.7 vs. 8.2 sessions; P < .001); however, attendance rates were similar across systems. The EDD‐based system also increased the percentage of women who had the same initial visit and group provider (78.0% vs. 85.5%; P = .303). The use of this system by other health care facilities could ease the task of enrolling a sufficient number of participants into group care, minimize the need for women to change care providers if they desire group care, and allow more time for educational activities and the development of social networks for women by offering more sessions per group.
Risk Assessment and Risk Distortion: Finding the Balance
Authors: Jordan Robin G. , Murphy Patricia Aikins
Published: May 2009

Pregnancy and birth have been conceptualized as medically problematic, with all pregnant women considered at risk and in need of medical monitoring. Universal application of risk scoring and surveillance as preemptive strategies in an effort to reduce risk is now standard obstetric practice. Labeling women “high risk” can result in more unnecessary interventions and have negative psychologic sequelae. When perceived pregnancy risk is out of proportion to the real risk, and when risk management procedures are applied to all women with benefit for only a few, the use of technology in caring for pregnant women becomes normalized. A learned reliance on technology can diminish women's own authoritative knowledge of pregnancy and birth. This may also have the unintended consequence of contributing to birth fear, a phenomena becoming more widely recognized. Health care provider‐patient communication about pregnancy risk can be presented in a manner that encourages informed compliance rather than informed choice. Evidence‐based risk assessment is essential to providing optimal prenatal care. Using tools such as the Paling Palette can help health care providers present balanced and readily understood information about risk.
Women's Experience of Prenatal Care: An Integrative Review
Authors: Novick Gina
Published: May 2009

The objective of this study was to identify, synthesize, and critically analyze published research on women's experiences of prenatal care. A search of online databases and relevant citations for research published from 1996 to 2007 was conducted. Thirty‐six articles were reviewed. Qualitative analysis methods were used, assisted by research software. This review found that some women were treated respectfully and reported comprehensive, individualized care. However, some women experienced long waits and rushed visits, and perceived prenatal care as mechanistic or harsh. Women's preferences included reasonable waits, unhurried visits, continuity, flexibility, comprehensive care, meeting with other pregnant women in groups, developing meaningful relationships with professionals, and becoming more active participants in care. Some low‐income and minority women experienced discrimination or stereotyping and external barriers to care. Further research is recommended to understand women's experiences and to develop and implement evidence‐based, women‐centered approaches. Clinicians should inquire regarding women's needs and modify care accordingly and also advocate for institutional changes that reduce barriers to care. Implementing comprehensive, redesigned models of care may be one effective way to simultaneously address a variety of women's needs and preferences. If prenatal care becomes more attractive and more accessible, women's experience and pregnancy outcomes may both improve.
The Handbook of Nutrition and Pregnancy
Authors: Jordan Robin G.
Published: May 2009

By Carol Lammi‐Keefe, Sarah Couch, and Elliot Philipson, editors. Totowa, NJ: Humana Press, 2008. 375 pages. $129.00, hardcover.
Health Care Reform Now! A Prescription for Change
Authors: Van Hoover Cheri
Published: May 2009

By George Halvorson. San Francisco, CA: Jossey‐Bass, 2007. 384 pages. $27.95, hardcover.
Informed Consent for a Vaginal Birth After Previous Cesarean Delivery
Authors: Caughey Aaron B.
Published: May 2009

M.L. is a gravida 2, para 1 being seen for an initial prenatal visit. She is requesting midwifery care and wants to have a vaginal birth after cesarean (VBAC). Her previous pregnancy was uncomplicated. She had a cesarean delivery for failure to progress at 8 cm with a fetus in a persistent occiput posterior (OP) position 3 years ago. Her son was born with Apgar scores of 8 and 9. He weighed 7 lb. 9 oz at birth. M.L. did not have any signs of infection during the postpartum period and she went home with her son on postpartum day 4.
Fetal Loss: Addressing the Evaluation and Supporting the Emotional Needs of Parents
Authors: Rowland Amelia , Goodnight William H.
Published: May 2009

C.L., a 33‐year‐old healthy, gravida 1, para 1000, presents for her first gynecologic examination following an unexplained stillbirth at 38 weeks' gestation 2 years ago. During the encounter, C.L. questions whether or not it is “safe” to become pregnant again. She is very apprehensive about pregnancy because of her last pregnancy outcome. A thorough history is gathered during the visit. Her obstetric history was unremarkable before presentation in labor at 38 weeks' gestation. She was dilated to 4 to 5 cm when she arrived at the hospital with intact membranes. Once admitted, the stillbirth diagnosis was confirmed. Her membranes were artificially ruptured and meconium was noted. She delivered vaginally and an autopsy performed following delivery was normal. During the pregnancy, two ultrasounds were performed, both of which were normal. All routine laboratory values obtained during the pregnancy were normal, except for a diagnosis of iron‐deficiency anemia. She also had normal genetic screening results. The patient's gynecologic history included a diagnosis of polycystic ovarian syndrome managed with metformin that she continued during her pregnancy. She had a normal 1‐hour glucose tolerance screen during the second trimester of her pregnancy. Her medical, surgical, family, and social histories were unremarkable. She reported no drug or alcohol use during her pregnancy. However, she was a 1 pack per day smoker during that pregnancy. Since then, she has discontinued smoking. During pregnancy, her medication exposures included metformin, prenatal vitamins, and ferrous sulfate. C.L believes that she last felt fetal movement 2 to 3 days before presenting to the hospital in labor. C.L. confided that she desperately wanted to become pregnant but she “couldn't bear to go through the same thing again.” She states that she is finally feeling “okay” and not paralyzed by her grief. She asks if anything can be done to ensure that her next pregnancy is “healthy.”
SEVERAL SMALL STUDIES SHOW FERTILITY AND PREGNANCY OUTCOMES MAY IMPROVE AFTER BARIATRIC SURGERY
Authors: Bond Sharon
Published: May 2009

Maggard MA, Yermilov I, Zhaoping L, Maglione M, Newberry S, Suttorp M, et al. Pregnancy and fertility following bariatric surgery: A systematic review. JAMA 2008;300:2286–96.
THE ESSENTIAL NORM OF A WEIGHTED COMPOSITION OPERATOR FROM THE BLOCH SPACE TO H∞
Authors: HOSOKAWA TAKUYA
Published: May 2009

We express the operator norm of a weighted composition operator which acts from the Bloch space ℬ to H∞ as the supremum of a quantity involving the weight function, the inducing self-map, and the hyperbolic distance. We also express the essential norm of a weighted composition operator from ℬ to H∞ as the asymptotic upper bound of the same quantity. Moreover we study the estimate of the essential norm of a weighted composition operator from H∞ to itself.
New advances in automatic selection of eligible surface elements for grasping and fixturing
Authors: Zheng Y. , Qian W.-H.
Published: May 2009

Many object surfaces involve a number of pieces, expressed by different equations. Previous methods of optimal grasp planning can hardly cope with such cases. Ding et al. solve this problem by characterizing the object surface with convex facets and discrete points, then selecting the eligible ones for force-closure, and finally seeking the optimal contact positions on the selected elements. So far, however, no point contact with friction (PCwF) but only frictionless point contacts (FPC) can be used on the facets, while soft finger contacts (SFC) are excluded at all. In this paper, to the above two surface elements we add line segments. Moreover, the limitations on the contact types are completely removed. A general condition and a quantitative criterion of eligibility are presented, followed by a heuristic algorithm and an iterative algorithm for finding the better eligible elements. Three common examples show: the new advances make the formerly tough problems smoothly solvable.
Clause-final subjects in English and Scandinavian
Authors: Julien Marit
Published: May 2009

In English and in Scandinavian, presentational expletive constructions with clause-final subjects can be derived by moving the subject to a Spec position in the C-domain, and then raising the remainder of the clause across the subject to an even higher position. The discourse properties of the clause-final subjects then follow without further stipulations. Moreover, the view that the clause-final position of the subject is the result of a phonological operation is not tenable, which means that various problems that would arise from this view are avoided after all. The differences between English constructions with clause-final subjects and their Scandinavian counterparts are consequences of the properties of the respective expletives. While the English expletivetherecan be the partial spellout of a subject copy, Scandinavian expletives are always syntactic elements in their own right. Two constructions that to some degree resemble the construction under discussion are shown not to be derived in a parallel fashion. For locative inversion, no analysis is given, but it is shown that it is syntactically rather different from the presentational expletive construction. For the English construction with an expletive and a divalent verb, which Chomsky (2001) takes to involve obligatory movement of the subject to clause-final position, it is argued that it involves a verb with two internal arguments appearing in their base order. The same holds for the corresponding Norwegian construction.
Asymptotic Enumeration of Constellations and Related Families of Maps on Orientable Surfaces
Authors: CHAPUY GUILLAUME
Published: May 2009

We perform the asymptotic enumeration of two classes of rooted maps on orientable surfaces:m-hypermaps andm-constellations. Form= 2 they correspond respectively to maps with even face degrees and bipartite maps. We obtain explicit asymptotic formulas for the number of such maps with any finite set of allowed face degrees.

Our proofs combine a bijective approach, generating series techniques related to lattice walks, and elementary algebraic graph theory.

A special case of our results implies former conjectures of Z. Gao.
Advanced Learners’ Use of Dutch Second Person Pronouns During Residence Abroad
Authors: Vismans Roel
Published: May 2009

The complex sociolinguistic system for Dutch forms of address presents students of Dutch as a foreign language with particular difficulties in learning to use second person pronouns appropriately. This article discusses the role of a period of residence in the Low Countries in advancing these students’ proficiency in this respect. The research is based on interviews with final-year students of Dutch in the UK. The analysis is framed in terms of intercultural communicative competence and approaches to learning.
Europe and Rights: Taking Dialogue Seriously
Authors: Cartabia Marta
Published: May 2009

Judicial dialogue – protection of fundamental rights – common constitutional principles – judicial activism – Charter of Fundamental Rights – pluralistic nature of Europe – national particularism – preliminary reference procedure – duty of constitutional courts to participate in dialogue – protection of national constitutional values and traditions – judicial style of European Court of Justice
Spectrum efficiency gains resulting from the implementation of adaptive transmit power control in fixed terrestrial links at 38 GHz
Authors: Callaghan S. A. , Inglis I. , Hansell P.
Published: May 2009

Adaptive transmit power control (ATPC) can be used to improve the spectrum efficiency of terrestrial point‐to‐point fixed links by limiting the transmit power to that required to maintain a constant bit error rate regardless of the propagation conditions. This results in a reduced transmit power being used during clear‐sky conditions, lowering the interference resulting from the ATPC link. This improves the frequency reuse factor associated with a given band and geographic area, providing a spectrum efficiency gain. The project described in this paper found that implementing ATPC in the 38 GHz terrestrial fixed links band gives significant improvements in spectrum efficiency as measured by the increase in the number of links assigned to channel 1 (from ∼50% to ∼70%) and the decrease in the maximum bandwidth used (from ∼300 MHz to ∼180 MHz). However, a model plan exposed to an exceptionally intense frontal rain event showed a number of additional outages caused by ATPC, amounting to approximately 12% of the number of outages caused directly by rain. In comparison, when exposed to an annualized simulated rain database the number of extra outages in this case falls to 2.6%.
Characterization of time and spatial scales of a migrating rivermouth
Authors: Behrens Dane K. , Bombardelli Fabián A. , Largier John L. , Twohy Elinor
Published: May 2009

By analysis of a unique and extensive photographic and written record spanning several decades, we characterized the spatial and temporal scales of morphological adjustment of the inlet of the Russian River Estuary, on the California coast. We paired this record with in situ measurements of beach features to create a dataset consisting of daily values of inlet width, length, shape, and position for the period of 1991–2006. Available wave, tide, and river flow data were compared with these measurements. We show that the spatial and temporal scales associated with adjustments in inlet geometry and position are dictated by different mechanisms during periods of high and low river flow and also vary with periods of large‐scale climate oscillations. Our analysis of inlet shape reveals that several classes of inlet curvature correspond to unique flow, geometry, and risk of closure conditions.
Direct active measurements of movements of lunar dust: Rocket exhausts and natural effects contaminating and cleansing Apollo hardware on the Moon in 1969
Authors: O'Brien Brian
Published: May 2009

Dust is the Number 1 environmental hazard on the Moon, yet its movements and adhesive properties are little understood. Matchbox‐sized, 270‐gram Dust Detector Experiments (DDEs) measured contrasting effects triggered by rocket exhausts of Lunar Modules (LM) after deployment 17 m and 130 m from Apollo 11 and 12 LMs. Apollo 11 Lunar Seismometer was contaminated, overheated and terminated after 21 days operation. Apollo 12 hardware was splashed with collateral lunar dust during deployment. DDE horizontal solar cell was cleansed of nominally 0.3 mg cm−2 dust by 80% promptly at LM ascent and totally within 7 minutes. A vertical cell facing East was half‐cleaned promptly then totally over hundreds of hours. Each cell cooled slightly. For the first time lunar electrostatic adhesive forces on smooth silicon were directly measured by comparison with lunar gravity. Analyses imply this adhesive force weakens as solar angle of incidence decreases. If valid, future lunar astronauts may have greater problems with dust adhesion in the middle half of the day than faced by Apollo missions in early morning. A sunproof shed may provide dust‐free working environments on the Moon. Low‐cost laboratory tests with DDEs and simulated lunar dust can use DDE benchmark lunar data quickly, optimising theoretical modelling and planning of future lunar expeditions, human and robotic.
Meteorology of the Beaufort Sea
Authors: Overland James E.
Published: May 2009

The unique meteorology of the Beaufort Sea region is dominated by the presence of sea ice and a seasonal swing from a large heat loss in winter to a gain in summer. The primary determinant of this seasonal climate shift is the annual cycle of insolation from a maximum of 500 W/m2 near the summer solstice to darkness in winter, as the Beaufort Sea lies north of Alaska and northwestern Canada beyond 72°N. Even though the Sun angle is low in summer, the length of daylight provides as much energy to the surface as anywhere on the planet. As summer progresses, relative absorption of insolation at the surface increases as the albedo decreases due to snow and ice melt and increased open water area. This annual cycle results in a change from a winter continental‐like air mass similar to the adjacent land areas to a summertime marine air mass characterized by low cloud and fogs. In winter the region is also influenced by the polar atmospheric vortex with strong westerly winds centered in the stratosphere, whose presence is felt at the surface. Recent sea ice losses are changing the climatology of the region, with extended periods of increased temperatures through the autumn months.
Impact of atmospheric aerosol from biomass burning on Amazon dry‐season drought
Authors: Bevan Suzanne L. , North Peter R. J. , Grey William M. F. , Los Sietse O. , Plummer Stephen E.
Published: May 2009

It is becoming increasingly apparent that the future of the Amazon rainforest is under threat from both climate change and agricultural practices such as deforestation and biomass burning. Atmospheric aerosols are likely to play an important role in the interaction between deforestation, fire and drought, but until now, observations of aerosol optical depth (AOD) in this region have been limited to time series of less than 7 years for satellite retrievals, or to single‐site measurements. Here we use a 13‐year time series of Along Track Scanning Radiometer derived AOD measurements to examine the role of aerosols in biosphere‐climate interactions over the Amazon. The seasonal cycle of AOD shows peaks in March and September. The September peak is caused by local dry‐season biomass burning. The March peak has not been identified previously but is coincident with more remote fires located in northern South America. A decreasing trend in dry‐season AOD between 1995 and 2000 and a subsequent increase from 2000 to 2004 can be explained by deforestation practices driven by economic forces, whereas even higher AOD levels in 2005 were probably caused more by the exceptional drought of that year. Throughout the time series, dry‐season AODs are inversely correlated with dry‐season precipitation, suggesting a positive feedback between aerosols and drought that may contribute to enhanced drought under climate change.
Overshooting convection in tropical cyclones
Authors: Romps David M. , Kuang Zhiming
Published: May 2009

Using infrared satellite imagery, best‐track data, and reanalysis data, tropical cyclones are shown to contain a disproportionate amount of the deepest convection in the tropics. Although tropical cyclones account for only 7% of the deep convection in the tropics, they account for about 15% of the deep convection with cloud‐top temperatures below the monthly averaged tropopause temperature and 29% of the clouds that attain a cloud‐top temperature 15 K below the temperature of the tropopause. This suggests that tropical cyclones could play an important role in setting the humidity of the stratosphere.
Effect of elemental composition and size on electron confinement in self-assembled SiC quantum dots: A combinatorial approach
Authors: Das Arulsamy A. , Rider A. E. , Cheng Q. J. , Xu S. , Ostrikov K.
Published: May 2009

A high level of control over quantum dot (QD) properties such as size and composition during fabrication is required to precisely tune the eventual electronic properties of the QD. Nanoscale synthesis efforts and theoretical studies of electronic properties are traditionally treated quite separately. In this paper, a combinatorial approach has been taken to relate the process synthesis parameters and the electron confinement properties of the QDs. First, hybrid numerical calculations with different influx parameters for Si1−xCx QDs were carried out to simulate the changes in carbon content x and size. Second, the ionization energy theory was applied to understand the electronic properties of Si1−xCx QDs. Third, stoichiometric (x=0.5) silicon carbide QDs were grown by means of inductively coupled plasma-assisted rf magnetron sputtering. Finally, the effect of QD size and elemental composition were then incorporated in the ionization energy theory to explain the evolution of the Si1−xCx photoluminescence spectra. These results are important for the development of deterministic synthesis approaches of self-assembled nanoscale quantum confinement structures.
Mechanisms involved in HBr and Ar cure plasma treatments applied to 193 nm photoresists
Authors: Pargon E. , Menguelti K. , Martin M. , Bazin A. , Chaix-Pluchery O. , Sourd C. , Derrough S. , Lill T. , Joubert O.
Published: May 2009

In this article, we have performed detailed investigations of the 193 nm photoresist transformations after exposure to the so-called HBr and Ar plasma cure treatments using various characterization techniques (x-ray photoelectron spectroscopy, Fourier transformed infrared, Raman analyses, and ellipsometry). By using windows with different cutoff wavelengths patched on the photoresist film, the role of the plasma vacuum ultraviolet (VUV) light on the resist modifications is clearly outlined and distinguished from the role of radicals and ions from the plasma. The analyses reveal that both plasma cure treatments induce severe surface and bulk chemical modifications of the resist films. The synergistic effects of low energetic ion bombardment and VUV plasma light lead to surface graphitization or cross-linking (on the order of 10 nm), while the plasma VUV light (110–210 nm) is clearly identified as being responsible for ester and lactone group removal from the resist bulk. As the resist modification depth depends strongly on the wavelength penetration into the material, it is found that HBr plasma cure that emits near 160–170 nm can chemically modify the photoresist through its entire thickness (240 nm), while the impact of Ar plasmas emitting near 100 nm is more limited. In the case of HBr cure treatment, Raman and ellipsometry analyses reveal the formation of sp2 carbon atoms in the resist bulk, certainly thanks to hydrogen diffusion through the resist film assisted by the VUV plasma light.
Spatially resolved measurements of depletion properties of large gate two-dimensional electron gas semiconductor terahertz modulators
Authors: Kleine-Ostmann T. , Pierz K. , Hein G. , Dawson P. , Marso M. , Koch M.
Published: May 2009

In this paper we discuss the room-temperature modulation properties of terahertz modulators, which depend on the depletion of a two-dimensional electron gas. By changing the electron density of the two-dimensional electron gas in a AlGaAs/GaAs heterostructure by applying an external gate voltage, the transmission and reflection properties of the device change. We studied the modulation properties of different modulator designs using terahertz time-domain spectroscopy and reported a detailed analysis of the electronic properties. We found that the nonideal depletion properties of terahertz modulators can be attributed to an incomplete depletion at low voltages underneath the center of large gates.
Transitional probabilities for the four-state random walk on a lattice in the presence of partially reflecting boundaries
Authors: Janaswamy R.
Published: May 2009

The four-state random walk (4RW) model, wherein the particle is endowed with two states of spin and two states of directional motion in each space coordinate, permits a stochastic solution of the Schrödinger equation (or the equivalent parabolic equation) without resorting to the usual analytical continuation in complex space of the particle trajectories. Analytical expressions are derived here for the various transitional probabilities in a 4RW by employing generating functions and eigenfunction expansions when the particle moves on a 1+1 space-time lattice with two-point boundary conditions. The most general case of dissimilar boundaries with partially reflecting boundary conditions is treated in this paper. The transitional probabilities are all expressed in terms of a finite summation involving trigonometric functions and/or Chebyshev polynomials of the second kind that are characteristics of diffusion and Schrödinger equations, respectively, in the 4RW model. Results for the special case of perfectly absorbing boundaries are compared to numerical values obtained by directly counting paths in the random walk simulations.
A cubic boron nitride film-based fluorescent sensor for detecting Hg2+
Authors: Liu W. M. , Zhao W. W. , Zhang H. Y. , Wang P. F. , Chong Y. M. , Ye Q. , Zou Y. S. , Zhang W. J. , Zapien J. A. , Bello I. , Lee S. T.
Published: May 2009

Cubic boron nitride (cBN) film-based sensors for detecting Hg2+ ions were developed by surface functionalization with dansyl chloride. To immobilize dansyl chloride, 3-aminopropyltriethoxy silane was modified on hydroxylated cBN surfaces to form an amino-group-terminated self-assembled monolayer. The covalent attachment of the amino groups was confirmed by x-ray photoelectron spectroscopy. The selectivity and sensitivity of the sensors to detect diverse metal cations in ethanol solutions were studied by using fluorescence spectroscopy, revealing a great selectivity to Hg2+ ions. Significantly, the dansyl-chloride-functionalized cBN film sensors were recyclable after the sensing test.
Generalized plane gravitational waves of weakened field equations in general relativity
Authors: Katore S. D. , Rane R. S.
Published: May 2009

In this paper, we propose to obtain a generalized plane gravitational waves in a set of five vacuum weakened field equations in the space-time introduced by Takeno (1961). These vacuum field equations have been suggested as alternatives to the Einstein vacuum field equations of general relativity. Physical significance of modified gravitational waves for the space-time is obtained. The dispersion relation for gravitational waves in vacuo is derived. We have obtained some useful results in the form of theorems under the curvature properties with conclusions.
Sub-ppm NO2 detection by Al2O3 contact passivated carbon nanotube field effect transistors
Authors: Mattmann Moritz , Helbling Thomas , Durrer Lukas , Roman Cosmin , Hierold Christofer , Pohle Roland , Fleischer Maximilian
Published: May 2009

We investigate carbon nanotube field effect transistors (CNFETs) with aluminum oxide (Al2O3) passivated contacts for NO2 detection. For the CNFETs, consisting of one individual pristine single walled carbon nanotube (SWNT), the measurements indicate a strong influence of adsorbed NO2 gas molecules on the exposed CNFET channel and NO2 concentrations as low as 100 ppb were detected. Applied to the contact-SWNT interfaces, Al2O3 is a suitable material to protect the metal contacts from NO2 molecules and other undesired environmental influences. We discuss the effect of the different processing steps on the CNFET characteristics and show device recovery after short heat treatment.
Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs
Authors: Alian Akram , Griner Sarah L. , Chiang Vicki , Tsiang Manuel , Jones Gregg , Birkus Gabriel , Geleziunas Romas , Leavitt Andrew D. , Stroud Robert M.
Published: May 2009

HIV-1 integration into the host cell genome is a multistep process catalyzed by the virally-encoded integrase (IN) protein. In view of the difficulty of obtaining a stable DNA-bound IN at high concentration as required for structure determination, we selected IN–DNA complexes that form disulfide linkages between 5′-thiolated DNA and several single mutations to cysteine around the catalytic site of IN. Mild reducing conditions allowed for selection of the most thermodynamically-stable disulfide-linked species. The most stable complexes induce tetramer formation of IN, as happens during the physiological integration reaction, and are able to catalyze the strand transfer step of retroviral integration. One of these complexes also binds strand-transfer inhibitors of HIV antiviral drugs, making it uniquely valuable among the mutants of this set for understanding portions of the integration reaction. This novel complex may help define substrate interactions and delineate the mechanism of action of known integration inhibitors.
Both treated and untreated tumors are eliminated by short hairpin RNA-based induction of target-specific immune responses
Authors: Gu Wenyi , Cochrane Melanie , Leggatt Graham R. , Payne Elizabeth , Choyce Allison , Zhou Fang , Tindle Robert , McMillan Nigel A. J.
Published: May 2009

RNA interference (RNAi) for cancer treatment relies on the ability to directly kill cancer cells via down-regulation of target genes, but issues of delivery and efficacy have limited clinical adoption. Furthermore, current studies using immune-deficient animal models disregard potential interactions with the adaptive immune system. It has previously been observed that certain viral antigens appear to be more rapidly presented to the immune system than normal proteins due to the production of defective ribosomal products by the virus. Given that RNAi could potentially result in the generation of truncated mRNAs, we wondered whether a similar mechanism of immune presentation of a target gene was possible. Here we show that RNAi-cleaved mRNAs can be translated into incomplete protein, and if cleavage was downstream of cytotoxic T cell epitopes, resulted in increased presentation of target protein and the generation of a tumor-protective immune response. We show that mice inoculated with tumor cells treated with such short hairpin RNAs (shRNAs) were protected from subsequent challenge with untreated tumors. However, protection was only found if shRNAs were targeted downstream of the dominant cytotoxic T cell (CTL) epitope. Our work suggests that RNAi can alter immunity to targets and shows that not all tumor cells require direct RNAi exposure for treatment to be effective in vivo, pointing the way to a new class of RNAi-based therapy.
Resting GABA concentration predicts peak gamma frequency and fMRI amplitude in response to visual stimulation in humans
Authors: Muthukumaraswamy Suresh D. , Edden Richard A.E. , Jones Derek K. , Swettenham Jennifer B. , Singh Krish D.
Published: May 2009

Functional imaging of the human brain is an increasingly important technique for clinical and cognitive neuroscience research, with functional MRI (fMRI) of the blood oxygen level-dependent (BOLD) response and electroencephalography or magnetoencephalography (MEG) recordings of neural oscillations being 2 of the most popular approaches. However, the neural and physiological mechanisms that generate these responses are only partially understood and sources of interparticipant variability in these measures are rarely investigated. Here, we test the hypothesis that the properties of these neuroimaging metrics are related to individual levels of cortical inhibition by combining magnetic resonance spectroscopy to quantify resting GABA concentration in the visual cortex, MEG to measure stimulus-induced visual gamma oscillations and fMRI to measure the BOLD response to a simple visual grating stimulus. Our results demonstrate that across individuals gamma oscillation frequency is positively correlated with resting GABA concentration in visual cortex (R = 0.68;
P
< 0.02), BOLD magnitude is inversely correlated with resting GABA (R = −0.64;
P
< 0.05) and that gamma oscillation frequency is strongly inversely correlated with the magnitude of the BOLD response (R = −0.88;
P
< 0.001). Our results are therefore supportive of recent theories suggesting that these functional neuroimaging metrics are dependent on the excitation/inhibition balance in an individual's cortex and have important implications for the interpretation of functional imaging results, particularly when making between-group comparisons in clinical research.
Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner
Authors: Lu David V. , Brown Randall H. , Arumugam Manimozhiyan , Brent Michael R.
Published: May 2009

Motivation: The most accurate way to determine the intron–exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics.

Results: We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created ‘perfect’ simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat.

We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner.

Availability: Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

Contact:  davidlu@wustl.edu; brent@cse.wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction
Authors: Cheng Chunrong , Shen Kui , Song Chi , Luo Jianhua , Tseng George C.
Published: May 2009

Motivation: Reproducibility analyses of biologically relevant microarray studies have mostly focused on overlap of detected biomarkers or correlation of differential expression evidences across studies. For clinical utility, direct inter-study prediction (i.e. to establish a prediction model in one study and apply to another) for disease diagnosis or prognosis prediction is more important. Normalization plays a key role for such a task. Traditionally, sample-wise normalization has been a standard for inter-array and inter-study normalization. For gene-wise normalization, it has been implemented for intra-study or inter-study predictions in a few papers while its rationale, strategy and effect remain unexplored.

Results: In this article, we investigate the effect of gene-wise normalization in microarray inter-study prediction. Gene-specific intensity discrepancies across studies are commonly found even after proper sample-wise normalization. We explore the rationale and necessity of gene-wise normalization. We also show that the ratio of sample sizes in normal versus diseased groups can greatly affect the performance of gene-wise normalization and an analytical method is developed to adjust for the imbalanced ratio effect. Both simulation results and applications to three lung cancer and two prostate cancer data sets, considering both binary classification and survival risk predictions, showed significant and robust improvement of the new adjustment. A calibration scheme is developed to apply the ratio-adjusted gene-wise normalization for prospective clinical trials. The number of calibration samples needed is estimated from existing studies and suggested for future applications. The result has important implication to the translational research of microarray as a practical disease diagnosis and prognosis prediction tool.

Contact:  ctseng@pitt.edu

Availability:  http://www.biostat.pitt.edu/bioinfo/

Supplementary information:  Supplementary data are available at Bioinformatics online.
Variation in spatial distribution and migration of Icelandic summer-spawning herring
Authors: Óskarsson Gudmundur J. , Gudmundsdottir A. , Sigurdsson T.
Published: May 2009

Óskarsson, G. J., Gudmundsdottir, A., and Sigurdsson, T. 2009. Variation in spatial distribution and migration of Icelandic summer-spawning herring. – ICES Journal of Marine Science, 66: 1762–1767. The distribution of the fishable stock of Icelandic summer-spawning herring (Clupea harengus L.) and the overwintering grounds have changed with fishing seasons from 1978/1979 through 2006/2007. The possible causes investigated include variation in sea temperatures, stock size, and annual recruitment. The stock collapsed as a result of overfishing and environmental changes during the late 1960s, since when the spawning stock has gradually increased, from 11 kt in 1972 to 800 kt in 2006. These changes coincided with geographic variation in its distribution. We identify five phases, based on a graphic analysis and the centre of gravity of the fishery. Investigations on a large geographic scale gave no clear indication that sea temperature has affected the distribution. Changes were also not clearly related to stock size or year-class strength. The distribution change in the late 1990s may be partly explained by year classes adopting a new migration pattern when entering the fishable stock.
Acoustic species identification of schooling fish
Authors: Korneliussen Rolf J. , Heggelund Yngve , Eliassen Inge K. , Johansen Geir O.
Published: May 2009

Korneliussen, R. J., Heggelund, Y., Eliassen, I. K., and Johansen, G. O. 2009. Acoustic species identification of schooling fish. – ICES Journal of Marine Science, 66: 1111–1118. The development of methods for the acoustic identification of fish is a long-term objective aimed at reducing uncertainty in acoustic-survey estimates. The relative frequency response r(f) measured simultaneously at several frequencies is one of the main acoustic features that characterize the targets, but the relationship between nearest neighbours, school morphology, and environmental and geographical data are also important characteristics in this context. The number of acoustic categories that can be separated with a high spatial resolution is limited by the stochastic nature of the measurements. Because the acoustic categorization of larger ensembles is more reliable than for single targets, spatial smoothing of the backscattering within the school boundaries before that process allows the separation of more categories than is possible with the raw, highly resolved data. Using the mean r(f) of an entire school gives even more reliable categorization, but determining whether or not the school is monospecific sets a new challenge. This problem is evaluated here. The methods are tested and verified. Identification of acoustic categories with similar acoustic properties is done for schooling fish, although the results have limited spatial resolution. The reliability of the categorization is further improved when knowledge of school morphology and geographical distribution of the species are taken into account.
Aprepitant in a Multimodal Approach for Prevention of Postoperative Nausea and Vomiting in High-Risk Patients: Is There Such a Thing as “Too Many Modalities”?
Authors: Hache John J. , Vallejo Manuel C. , Waters Jonathan H. , Williams Brian A.
Published: May 2009

Postoperative and postdischarge nausea and vomiting (PONV and PDNV, respectively) add morbidity to perioperative outcomes. Combining some antiemetic agents of different mechanisms is more effective than using single agents, although this concept has not yet been tested extensively with aprepitant. Consecutive high-risk patients for PONV (n = 100) were given preoperative aprepitant 40 mg before surgery and were followed perioperatively. Female patients receiving general anesthesia (n = 81) were selected for data analysis. The primary endpoints were PONV/PDNV in the 48 h after surgery. For patients included in the data analysis, using Apfel PONV risk factors, the median risk count was four out of four. PONV and PDNV incidences were 21% (95% CI: 14-31%) and 37% (95% CI: 27-48%), respectively. Two patients experienced PACU (postanesthesia care unit) vomiting and two patients experienced emesis postdischarge. When using regression modeling and comparing patients who received one or two vs. three or four mechanistically unique antiemetics (added to preoperative aprepitant), while adjusting for surgical case duration, the three or four additional antiemetic group showed more PONV/PDNV (Odds Ratio 3.73, 95% CI 1.3-10.9,p= 0.016) than did the one or two additional drug group. There were no other predictors of PONV/PDNV (transabdominal surgery, four vs. three Apfel risk factors) in these patients. The low incidence of vomiting (2-5%) suggests the potential importance of aprepitant in a multimodal antiemetic regimen. However, there may be the potential that too many unique antiemetic mechanisms combined with preoperative aprepitant may actually increase the incidence of perioperative nausea.