bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into the organization of dorsal spinal cord pathways from an evolutionarily conserved raldh2 intronic enhancer
Authors: Castillo Hozana A. , Cravo Roberta M. , Azambuja Ana P. , Simões-Costa Marcos S. , Sura-Trueba Sylvia , Gonzalez Jose , Slonimsky Esfir , Almeida Karla , Abreu José G. , de Almeida Marcio A. Afonso , Sobreira Tiago P. , de Oliveira Saulo H. Pires , de Oliveira Paulo S. Lopes , Signore Iskra A. , Colombo Alicia , Concha Miguel L. , Spengler Tatjana S. , Bronner-Fraser Marianne , Nobrega Marcelo , Rosenthal Nadia , Xavier-Neto José
Published: January 2010

Comparative studies of the tetrapod raldh2 (aldh1a2) gene, which encodes a retinoic acid (RA) synthesis enzyme, have led to the identification of a dorsal spinal cord enhancer. Enhancer activity is directed dorsally to the roof plate and dorsal-most (dI1) interneurons through predicted Tcf- and Cdx-homeodomain binding sites and is repressed ventrally via predicted Tgif homeobox and ventral Lim-homeodomain binding sites. Raldh2 and Math1/Cath1 expression in mouse and chicken highlights a novel, transient, endogenous Raldh2 expression domain in dI1 interneurons, which give rise to ascending circuits and intraspinal commissural interneurons, suggesting roles for RA in the ontogeny of spinocerebellar and intraspinal proprioceptive circuits. Consistent with expression of raldh2 in the dorsal interneurons of tetrapods, we also found that raldh2 is expressed in dorsal interneurons throughout the agnathan spinal cord, suggesting ancestral roles for RA signaling in the ontogenesis of intraspinal proprioception.
Antagonistic Smad transcription factors control the dauer/non-dauer switch inC. elegans
Authors: Park Donha , Estevez Annette , Riddle Donald L.
Published: January 2010

The C. elegans daf-8 gene encodes an R-Smad that is expressed in a subset of head neurons, the intestine, gonadal distal tip cells and the excretory cell. We found that DAF-8, which inhibits the DAF-3 Co-Smad, is associated with DAF-3 and the DAF-14 Smad in vivo and in vitro. Overexpression of daf-8 conferred a dauer-defective phenotype and suppressed constitutive dauer formation in daf-8 and daf-14 mutants. In contrast to mammalian systems described thus far, active DAF-3 drives a feedback regulatory loop that represses transcription of daf-7 (a TGFβ ligand) and daf-8 by directly binding to their regulatory regions. Hence, DAF-8 and DAF-3 are mutually antagonistic. The feedback repression may reinforce the developmental switch by allowing DAF-3 to freely activate dauer transcription in target tissues, unless sufficiently inhibited by DAF-8 and DAF-14. In the adult, DAF-8 downregulates lag-2 expression in the distal tip cells, thus promoting germ line meiosis. This function does not involve DAF-3, thereby avoiding the feedback loop that functions in the dauer switch.
Pax6-dependent Shroom3 expression regulates apical constriction during lens placode invagination
Authors: Plageman Timothy F. , Chung Mei-I , Lou Ming , Smith April N. , Hildebrand Jeffrey D. , Wallingford John B. , Lang Richard A.
Published: January 2010

Embryonic development requires a complex series of relative cellular movements and shape changes that are generally referred to as morphogenesis. Although some of the mechanisms underlying morphogenesis have been identified, the process is still poorly understood. Here, we address mechanisms of epithelial morphogenesis using the vertebrate lens as a model system. We show that the apical constriction of lens epithelial cells that accompanies invagination of the lens placode is dependent on Shroom3, a molecule previously associated with apical constriction during morphogenesis of the neural plate. We show that Shroom3 is required for the apical localization of F-actin and myosin II, both crucial components of the contractile complexes required for apical constriction, and for the apical localization of Vasp, a Mena family protein with F-actin anti-capping function that is also required for morphogenesis. Finally, we show that the expression of Shroom3 is dependent on the crucial lens-induction transcription factor Pax6. This provides a previously missing link between lens-induction pathways and the morphogenesis machinery and partly explains the absence of lens morphogenesis in Pax6-deficient mutants.
An interview with Olivier Pourquié
Authors: Briscoe James
Published: January 2010

Olivier Pourquié is the new director of the Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Strasbourg, France, and as of this month takes on another crucially important role in the developmental community — that of Development's new Editor in Chief. Recently, we asked James Briscoe, in his capacity as a director of the Company of Biologists, to interview Olivier and to discover more about his research career and interests and how they will shape the future content and directions of Development.
Trajectory generation for road vehicle obstacle avoidance using convex optimization
Authors: Bevan G P , Gollee H , O'Reilly J
Published: January 2010

This paper presents a method for trajectory generation using convex optimization to find a feasible, obstacle-free path for a road vehicle. Consideration of vehicle rotation is shown to be necessary if the trajectory is to avoid obstacles specified in a fixed Earth axis system. The paper establishes that, despite the presence of significant non-linearities, it is possible to articulate the obstacle avoidance problem in a tractable convex form using multiple optimization passes. Finally, it is shown by simulation that an optimal trajectory that accounts for the vehicle's changing velocity throughout the manoeuvre is superior to a previous analytical method that assumes constant speed.
Study of control for the automated clutch of an automated manual transmission vehicle based on rapid control prototyping
Authors: Zhao Y-S , Liu Z-F , Cai L-G , Yang W-T , Yang J , Luo Z
Published: January 2010

Owing to external disturbances, parameter uncertainty, and measurement noise, it has been a challenging task to develop an appropriate controller for the automated clutch system. This paper proposes a new method for electromechanical clutch position control systems. First, a non-linear dynamic model for the screw-nut actuator associated with a clutch is derived, and then a dynamic sliding-mode controller with fuzzy adaptive tuning is developed. The fuzzy adaptive tuning arithmetic is used to improve the robustness and stability of the controller. At the same time, the chattering phenomenon is alleviated by adopting the proposed controller. Based on dSPACE and MATLAB—Simulink, the rapid control prototyping of the automated clutch is used as a method to demonstrate the efficiency and robustness of the proposed algorithm.
Optimization of a high-speed direct-injection diesel engine at low-load operation using computational fluid dynamics with detailed chemistry and a multi-objective genetic algorithm
Authors: Ge H-W , Shi Y , Reitz R D , Willems W
Published: January 2010

A passenger car high-speed direct-injection diesel engine operating at low-load conditions in the modulated kinetic combustion mode was optimized using a multi-dimensional computational fluid dynamics code and a multi-objective genetic algorithm. Spray targeting, piston bowl geometry, and swirl ratio were optimized. Since the combustion is mainly kinetics controlled, detailed chemistry was considered through a recently developed adaptive multi-grid chemistry (AMC) model. The numerical results from the AMC model, including the pressure and pollutant emissions, were first validated on the baseline engine for a parametric sweep by comparison with the results from the standard KIVA—CHEMKIN model. The AMC model was found to give consistent results with the KIVA—CHEMKIN model, with a computational cost that is less than half that of the KIVA—CHEMKIN model. Optimal designs from the optimization were also validated using the full KIVA—CHEMKIN model and were found to reduce the fuel consumption and/or pollutant emissions. Start-of-injection timing was found to be the primary parameter influencing the fuel consumption and soot emissions for the engine operating in the low-load condition. Later injection benefits the fuel consumption and soot reduction. However, further retardation of the injection timing leads to reduced combustion efficiency and even misfire, and results in higher unburned hydrocarbon emissions. Different piston bowl shapes have different responses to bulk flow motions and the resulting geometry-generated turbulence will affect soot formation and oxidation.
A dynamic convergence control scheme for the solution of the radial equilibrium equation in through-flow analyses
Authors: Pachidis V , Templalexis I , Pilidis P , Kotsiopoulos P
Published: January 2010

One of the most frequently encountered numerical problems in scientific analyses is the solution of non-linear equations. Often the analysis of complex phenomena falls beyond the range of applicability of the numerical methods available in the public domain, and demands the design of dedicated algorithms that will approximate, to a specified precision, the mathematical solution of specific problems. These algorithms can be developed from scratch or through the amalgamation of existing techniques. The accurate solution of the full radial equilibrium equation (REE) in streamline curvature (SLC) through-flow analyses presents such a case. This article discusses the development, validation, and application of an ‘intelligent’ dynamic convergence control (DCC) algorithm for the fast, accurate, and robust numerical solution of the non-linear equations of motion for two-dimensional flow fields. The algorithm was developed to eliminate the large extent of user intervention, usually required by standard numerical methods. The DCC algorithm was integrated into a turbomachinery design and performance simulation software tool and was tested rigorously, particularly at compressor operating regimes traditionally exhibiting convergence difficulties (i.e. far off-design conditions). Typical error histories and comparisons of simulated results against experimental are presented in this article for a particular case study. For all case studies examined, it was found that the algorithm could successfully ‘guide’ the solution down to the specified error tolerance, at the expense of a slightly slower iteration process (compared to a conventional Newton—Raphson scheme). This hybrid DCC algorithm can also find use in many other engineering and scientific applications that require the robust solution of mathematical problems by numerical instead of analytical means.
A simple suboptimal Kalman filter implementation for a gyro-corrected satellite attitude determination system
Authors: de Ruiter A
Published: January 2010

This article presents a simple Kalman filter implementation for correcting gyro-determined satellite attitude estimates with attitude measurements made using external sensors such as sun sensors, magnetometers, star trackers, and so on. This article first generalizes a recently developed non-linear observer for the gyro-corrected attitude determination problem. By implementing the steady-state Kalman filter in the framework of this non-linear observer, a computationally simple filter is obtained with suboptimal steady-state performance. This is important for applications where computational power is limited, such as in micro-/nano-satellite applications. Additionally, in the absence of process and measurement noise, this implementation of the Kalman filter is globally stable. The resulting filter uses constant steady-state Kalman filter gains. It is demonstrated that close-to-optimal steady-state performance is obtained.
Numerical simulation of transient flows in a vacuum ejector-diffuser system
Authors: Lijo V , Kim H D , Rajesh G , Setoguchi T
Published: January 2010

The objective of the present study is to analyse the transient flow through the vacuum ejector system with the help of a computational fluid dynamics method. An attempt is made to investigate the interesting and conflicting phenomenon of the continuous entrainment into the primary stream with limited mass supply from the secondary chamber. The results obtained show that the one and only condition in which a continuous mass entrainment can be possible in such types of ejectors is the generation of a recirculation zone near the primary nozzle exit. The flow in the secondary chamber attains a state of dynamic equilibrium of pressure at the onset of the recirculation zone. A steady flow assumption in such ejector systems is valid only after the dynamic equilibrium state.
Analysis of flows past airfoils at very low Reynolds numbers
Authors: Mateescu D , Abdo M
Published: January 2010

This article presents the special features of airfoil flows at very low Reynolds numbers, which are of interest for unmanned micro-air-vehicles. Airfoil flow solutions at low Reynolds numbers are obtained with an efficient numerical analysis based on a pseudo-time integration method using artificial compressibility for solving accurately the Navier—Stokes equations. The flow problem is solved in a rectangular computational domain obtained by a coordinate transformation from the physical flow domain around the airfoil at incidence. This method uses a second-order central differencing approach on a stretched staggered grid. A special decoupling procedure using the continuity equation reduces the problem to the solution of scalar tridiagonal systems of equations, which enhances substantially the computational efficiency of the method. The pressure distribution, lift, and drag coefficients are presented for several NACA airfoils at various incidences and low Reynolds numbers between 400 and 6000. Streamline contours for the flow with separations past several airfoils at low Reynolds numbers have also been generated and compared. For a better understanding of the complex flow separation phenomena in the viscous flows past airfoils at very low Reynolds numbers, the onset of separation and reattachment locations have been calculated, and a detailed study is presented on the influence of the Reynolds number, angle of attack, relative thickness and camber, and the maximum camber position along the chord.
An investigation of the flow field within patient-specific models of an abdominal aortic aneurysm under steady inflow conditions
Authors: O'Rourke M J , McCullough J P
Published: January 2010

The flow fields within three patient-specific models of an abdominal aortic aneurysm (AAA) were investigated under steady laminar inflow conditions over a range of Reynolds numbers. Each model extended from the renal arteries to downstream of the iliac bifurcation. The aneurysms (referred to as models A, B, and C) are mature, with D/ d ratios of 1.83, 1.57, and 1.95 respectively. The mass flowrates in each of the iliac arteries were equal. Using flow visualization it was observed that the flow proximally in the aneurysm was characterized by a primary jet that separated from either the posterior wall or the lateral wall or both, producing large recirculating zones. The primary jet impinged either normally or obliquely upon the anterior or right lateral wall in the distal half of the aneurysm, the flow distally in the aneurysm having been greatly disturbed. Measurements of the turbulence intensity along the median lumen centre-line showed that in each model the onset of transition and full turbulence occurred at Reynolds numbers much lower than those previously measured in idealized models. Computational fluid dynamics showed substantial differences in the velocity and stress fields when using the shear stress transport turbulence model as opposed to a laminar viscous model. It was also observed that turbulence was largely produced along the shear layers surrounding the primary jet and, in particular, at interfaces between the jet and the recirculating zones. In conclusion, turbulence may be expected to exist at Reynolds numbers typically encountered within an AAA, and it must be taken account of in an analysis of the flow field.
Experimental investigation of the performance of liquid gas jet pumps with inlet swirling
Authors: El-Sallak M , Hefny M M
Published: January 2010

In jet pumps, energy exchange between the jet and the secondary flow strongly determines its overall efficiency. In this article, the effects of introducing inlet swirling flow in the main jet of liquid jet gas pumps were investigated experimentally. Four different swirl components with degree of swirl covering the weak, moderate, and strong ranges were used. Experimental measurements were carried out on the transparent jet pump model with variable throat length and nozzle spacing under constant jet pump number n. Experimental results are provided concerning the effect of inlet swirl on jet break-up length and compared with the previous results. Good agreement is found between experimental results and theoretical predictions of one-dimensional model.
Exergy analysis of a gas turbine trigeneration system using the Brayton refrigeration cycle for inlet air cooling
Authors: Khaliq A , Choudhary K , Dincer I
Published: January 2010

Trigeneration with gas turbines as prime mover can improve energy utilization efficiency significantly because of their potential of high economic and energy saving characteristic. In this article, a novel method for compressor inlet air cooling in gas turbine trigeneration is achieved by the Brayton refrigeration cycle driven by the gas turbine and air is used as a working fluid. Introducing the air refrigeration cycle for inlet air cooling provides the advantage of quite low temperatures close to 0 °C and even lower, and enhances the performance significantly. The performance was evaluated by both energy and exergy efficiencies, with the latter providing good guidance for system improvement. The influences of key parameters, which include extraction pressure ratio, extraction mass rate, turbine inlet temperature (TIT), process heat pressure, and ambient relative humidity on the cycle performance parameters, have been investigated. It is found that the inlet air-cooled gas turbine trigeneration cycle has a good thermal performance, with first and second law efficiencies of 91 per cent and 55 per cent, respectively, for the base case studied (having a maximum cycle temperature of 1327 °C). For a minimum process heat pressure of 4 bar, the energy and exergy efficiencies were obtained as 89 per cent and 51 per cent, respectively. Gas turbine trigeneration plants with and without inlet air cooled by the Brayton refrigeration cycle are compared with each other, and the effect of inlet air cooling on energy and exergy efficiencies is clarified. Inlet air cooling increases the energy and exergy efficiencies and decreases the electrical to thermal energy ratio significantly. Exergy analysis indicates that maximum exergy is destroyed during combustion and steam generation, which represents around 65 per cent of the total exergy destruction in the overall system. The exergy destruction in major components of trigeneration varies significantly with TIT and process heat pressure. The present analysis provides further information on the role of inlet air cooling through extracted mass rate influence on the performance of a gas turbine-based trigeneration system.
Evaluation of lubrication conditions in gear contacts using contact resistance and bulk temperature measurements
Authors: Kleemola J , Lehtovaara A
Published: January 2010

Lubrication conditions have a major effect on lifetime and friction in gear contacts. Monitoring of relative changes in protecting film thickness provides an opportunity to understand the operating conditions before an initial fault appears. In this study, the lubrication conditions were detected on-line using contact resistance and bulk temperature measurements, which were applied to a modified FZG gear test device. Measurements were made with polished gear surfaces at operating conditions that are typical of industrial gears. The presented mean contact resistance includes the data points in different positions along the line of action and thus also considers transient effects. The bulk temperature and trend curves of the mean contact resistance at different pitch line velocities, loads, and oil inlet temperatures are reported and discussed as measures for analysing the lubrication condition.
On the tribo-cryogenic characteristics of titanium alloys
Authors: El-Tayeb N S M , Yap T C , Brevern P V
Published: January 2010

Friction and wear behaviours of Ti-6Al-4V (Ti64) and Ti-5Al-4V-0.6Mo-0.4Fe (Ti54) alloys sliding against a tungsten carbide wheel under dry and cryogenic sliding conditions were investigated at different sliding speeds, loads, and distances. Mathematical models utilizing response surface methodology were developed as a function of sliding conditions for predicting the friction and wear characteristics of both titanium alloys. The controlling variables were determined by utilizing design of experiments. The developed models are able to predict the measured friction coefficient and wear volume with reasonable degree of accuracy for both titanium alloys within the ranges of studied parameters.

Results showed no substantial difference between tribo-characteristics of both titanium alloys. Under cryogenic sliding condition, tribo-characteristics were lower than those obtained under dry sliding, except at higher load, cryogenic sliding surprisingly gave higher friction coefficient. Analyses of worn surfaces and wear debris by using scanning electron microscopy and energy-dispersive spectroscopy revealed that the role of cryogenic conditions at the sliding interface was partially attributed to changing material properties and possible hydrodynamic effect. Under dry sliding, the main wear modes were adhesion and delamination, while under cryogenic sliding, in addition to delamination, abrasion wear mode dominated.
Analysis of gate tunnelling currents in nanoscale metal—oxide—semiconductor field effect transistors (MOSFETs) with SiO2 and high-K gate dielectrics
Authors: Joshi G , Singh M , Chauhan M
Published: January 2010

In this paper, an analytical model for gate tunnelling current has been deployed by solving the Schrödinger equation using the Wentzel—Kramer—Brillouin approximation method for a trapezoidal potential barrier. The gate tunnelling current has been computed for direct tunnelling from channel to gate as well as for tunnelling from source drain extension region to gate. The effect of temperature variation on gate tunnelling current with an SiO2 thickness of 4nm down to 1nm has been studied at various gate voltages. Gate tunnelling in the case of high-K gate dielectrics and high-K stacks has also been analysed. In order to study the effect of temperature on gate tunnelling current in SiO2 and in high-K dielectrics, the related parameters have been modelled based on physics. The effect of variation of substrate doping concentration (Na) on gate tunnelling current in an n-type metal—oxide—semiconductor field effect transistor (n-MOSFET) with SiO2 has also been studied These studies have been used to bring out the design margins available in equivalent oxide thickness and Na.
The dynamic flow behaviour of an oar blade in motion using a hydrodynamics-based shell-velocity-coupled model of a rowing stroke
Authors: Sliasas A , Tullis S
Published: January 2010

The flow around a rowing oar blade during a stroke is highly complex owing to the proximity of the water surface and the rapidly changing blade flow incidence (here, greater than 180° in under 0.75s). This flow is simulated using a computational fluid dynamics (CFD) model with a rotating subdomain for blade rotation coupled to a model of the shell velocity. Based on the shell velocity and a specified oar angular velocity, the CFD model calculates the highly unsteady three-dimensional flow, providing instantaneous drag, lift, and propulsive forces on the blade. The propulsive force drives the shell velocity model, which also accounts for the shell drag and the motion of the rowers relative to the shell. The dynamic blade—water interaction is depicted in six distinct flow regimes, characterized by the relative motion of the blade and the temporal influence of drag and lift. It is seen that the propulsive force generated by the blade is largely lift induced during the first half of the stroke. Dynamic stall behaviour of the blade characterizes the flow during the second half of the stroke, where drag increasingly influences the propulsive force. At the end of the stroke, the propulsive force is once again largely lift induced.
Whole mount in situ hybridization detection of mRNAs using short LNA containing DNA oligonucleotide probes
Authors: Darnell Diana K. , Stanislaw Stacey , Kaur Simran , Antin Parker B.
Published: January 2010

In situ hybridization is widely used to visualize transcribed sequences in embryos, tissues, and cells. For whole mount detection of mRNAs in embryos, hybridization with an antisense RNA probe is followed by visual or fluorescence detection of target mRNAs. A limitation of this approach is that a cDNA template of the target RNA must be obtained in order to generate the antisense RNA probe. Here we investigate the use of short (12–24 nucleotides) locked nucleic acid (LNA) containing DNA probes for whole mount in situ hybridization detection of mRNAs. Following extensive protocol optimization, we show that LNA probes can be used to localize several mRNAs of varying abundances in chicken embryos. LNA probes also detected alternatively spliced exons that are processed in a tissue specific manner. The use of LNA probes for whole mount in situ detection of mRNAs will enable in silico design and chemical synthesis and will expand the general use of in situ hybridization for studies of transcriptional regulation and alternative splicing.
Understanding dichromic fluorescence manifested in certain indocyanine green (ICG) analogs
Authors: Zhang Zongren , Kao Jeff , D’Avignon André , Achilefu Samuel
Published: January 2010

Fluorescence has advanced our understanding in various aspects of biological processes. Fluorescence in the near infrared (NIR) region avoids background autofluorescence from biological samples, leading to improved image quality. In searching for indo-cyanine green (ICG) analogs that can be attached to biomolecules, we observed that dichromic fluorescence manifested in some mono reactive-group-functionalized ICG analogs. The two emission bands are distinctively separate from each other, making it a unique feature of fluorescent probes found in biological studies. We further demonstrated that the dichromism comes from the structure and is transferable from dye to its bioconjugates. In this paper, we used resonance theory and molecular orbital theory to explain the fluorophore photochemistry in an effort to understand the general fluorescence feature of ICG analogs and provide understanding of the secondary emission band.
Design, synthesis, and biological evaluation of novel substituted [1,2,3]triazolo[4,5-d]pyrimidines as HIV-1 Tat-TAR interaction inhibitors
Authors: Yu Fei , Pang Ruifang , Yuan Dekai , He Meizi , Zhang Chunlei , Chen Shuguang , Yang Ming
Published: January 2010

A novel series of compounds, derived from [1,2,3]triazolo[4,5-d]pyrimidines with a guanidyl group or amino group-terminated side chain was designed and synthesized as HIV-1 trans-activator of transcription–trans-activation responsive region (Tat–TAR) interaction inhibitors. Their ability to inhibit Tat–TAR RNA interaction was determined by a Tat-dependent HIV-1 long terminal repeat (LTR)-driven chloramphenicol acetyltransferase (CAT) assay and simian immunodeficiency virus (SIV)-induced syncytium evaluation. The binding of the compounds with TAR RNA was conducted by molecular modeling and capillary electrophoresis (CE) analysis. The results showed that all the compounds could block the Tat–TAR interaction and have antiviral activities.
Production of novel bioactive compounds by enzymes, and their application to food
Authors: Kometani Takashi
Published: January 2010

Recently, people have been paying greater attention to their health and, as a result, the need to use physiologically functional foods was found on the market. For these reasons, the market size of “foods for specified health use” (FOSHU) in Japan has grown and was approximately ¥700 billion in 2008. Many enzymes such as amylases and proteases have been used in food manufacturing because of their diversity, specificity, and mild condition in reaction. The aim of this investigation was the production of novel bioactive compounds by three kinds of transglycosylation reaction of the amylolytic enzymes, and the research and development of physiologically functional foods using these compounds. Phosphoryl oligosaccharides of calcium (POs-Ca) are a complex with Ca and phosphoryl oligosaccharides prepared from potato starch by a hydrolysis (transglycosylation to H2O) of amylolytic enzymes. The chewing gum included POs-Ca prevented dental caries in humans. Highly branched cyclic dextrin (HBCD) was produced from amylopectin by branching enzyme (intramolecular transglycosylation), which had a relatively narrow molecular-weight distribution compared with commercially available dextrins. The sports drink containing HBCD enhanced swimming endurance in mice and humans. α-Glycosylhesperidin (G-Hsp) was produced from starch and hesperidin, a flavonoid found abundantly in citrus fruits, by the intermolecular transglycosylation using cyclodextrin glucanotransferase. Oral administration of G-Hsp improved rheumatoid arthritis in mice and humans, and poor blood circulation in women. In this study, we looked to prove that this enzymatic modification technique was useful in creating unique and effective physiologically functional foods. These functional foods are expected to improve the health and quality of life of many people.
Auxin-producing Bacillus sp.: Auxin quantification and effect on the growth of Solanum tuberosum
Authors: Ahmed Ambreen , Hasnain Shahida
Published: January 2010

Plant-associated bacteria are known to improve plant growth and play a major role in the development of plants. The present study is concerned with the isolation of two auxin-producing plant growth-promoting bacteria (PGPB). On the basis of 16S rRNA sequencing, both of the strains are identified as Bacillus sp. Maximum auxin production was observed at 37 °C after 48 h of incubation. Increase in tryptophan concentration stimulated auxin production by the isolates. High-performance liquid chromatography analysis showed that the bacterial auxin exhibited similar retention time as the standard indole-3-acetic acid (IAA). Sprouts of Solanum tuberosum var. Desiree were inoculated with the isolates. Comparison of various growth parameters of inoculated plants with non-inoculated plants revealed the improvement of plant growth by bacterial inoculation. Almost 40 and 35 % increase in shoot length with P4 and S6 inoculation, respectively, was observed. Considerable improvement in root growth was observed with an increase in the number and length of roots. On the basis of the above findings, it is concluded that the plant growth-promoting Bacillus strains affect S. tuberosum beneficially, resulting in improved plant growth.
Arsenic species in seafood: Origin and human health implications
Authors: Francesconi Kevin A.
Published: January 2010

The presence of arsenic in marine samples was first reported over 100 years ago, and shortly thereafter it was shown that common seafood such as fish, crustaceans, and molluscs contained arsenic at exceedingly high concentrations. It was noted at the time that this seafood arsenic was probably present as an organically bound species because the concentrations were so high that if the arsenic had been present as an inorganic species it would certainly have been toxic to the humans consuming seafood. Investigations in the late 1970s identified the major form of seafood arsenic as arsenobetaine [(CH3)3As+CH2COO–], a harmless organoarsenic compound which, following ingestion by humans, is rapidly excreted in the urine. Since that work, however, over 50 additional arsenic species have been identified in marine organisms, including many important food products. For most of these arsenic compounds, the human toxicology remains unknown. The current status of arsenic in seafood will be discussed in terms of the possible origin of these compounds and the implications of their presence in our foods.
Hermansky-Pudlak Protein Complexes, AP-3 and BLOC-1, Differentially Regulate Presynaptic Composition in the Striatum and Hippocampus
Authors: Newell-Litwa Karen , Chintala Sreenivasulu , Jenkins Susan , Pare Jean-Francois , McGaha LeeAnne , Smith Yoland , Faundez Victor
Published: January 2010

Endosomal sorting mechanisms mediated by AP-3 and BLOC-1 are perturbed in Hermansky-Pudlak Syndrome, a human genetic condition characterized by albinism and prolonged bleeding (OMIM #203300). Additionally, mouse models defective in either one of these complexes possess defective synaptic vesicle biogenesis (Newell-Litwa et al., 2009). These synaptic vesicle phenotypes were presumed uniform throughout the brain. However, here we report that AP-3 and BLOC-1 differentially regulate the composition of presynaptic terminals in the striatum and dentate gyrus of the hippocampus. Quantitative immunoelectron microscopy demonstrated that the majority of AP-3 immunoreactivity in both wild-type striatum and hippocampus localizes to presynaptic axonal compartments, where it regulates synaptic vesicle size. In the striatum, loss of AP-3 (Ap3dmh/mh) resulted in decreased synaptic vesicle size. In contrast, loss of AP-3 in the dentate gyrus increased synaptic vesicle size, thus suggesting anatomically specific AP-3-regulatory mechanisms. Loss-of-function alleles of BLOC-1,Pldnpa/pa, andMutedmu/murevealed that this complex acts as a brain-region-specific regulator of AP-3. In fact, BLOC-1 deficiencies selectively reduced AP-3 and AP-3 cargo immunoreactivity in presynaptic compartments within the dentate gyrus both at the light and/or electron microscopy level. However, the striatum did not exhibit these BLOC-1-null phenotypes. Our results demonstrate that distinct brain regions differentially regulate AP-3-dependent synaptic vesicle biogenesis. We propose that anatomically restricted mechanisms within the brain diversify the biogenesis and composition of synaptic vesicles.
Attention-Like Deficit and Hyperactivity in aDrosophilaMemory Mutant
Authors: van Swinderen Bruno , Brembs Björn
Published: January 2010

The primary function of a brain is to produce adaptive behavioral choices by selecting the right action at the right time. In humans, attention determines action selection as well as memory formation, whereas memories also guide which external stimuli should be attended to (Chun and Turk-Browne, 2007). The complex codependence of attention, memory, and action selection makes approaching the neurobiological basis of these interactions difficult in higher animals. Therefore, a successful reductionist approach is to turn to simpler systems for unraveling such complex biological problems. In a constantly changing environment, even simple animals have evolved attention-like processes to effectively filter incoming sensory stimuli. These processes can be studied in the fruit fly,Drosophila melanogaster, by a variety of behavioral and electrophysiological techniques. Recent work has shown that mutations affecting olfactory memory formation inDrosophilaalso produce distinct defects in visual attention-like behavior (van Swinderen, 2007; van Swinderen et al., 2009). In this study, we extend those results to describe visual attention-like defects in theDrosophilamemory consolidation mutantradish1. In both behavioral and brain-recording assays,radishmutant flies consistently displayed responses characteristic of a reduced attention span, with more frequent perceptual alternations and more random behavior compared with wild-type flies. Some attention-like defects were successfully rescued by administering a drug commonly used to treat attention-deficit hyperactivity disorder in humans, methylphenidate. Our results suggest that a balance between persistence and flexibility is crucial for adaptive action selection in flies and that this balance requiresradishgene function.
Domain General Change Detection Accounts for “Dishabituation” Effects in Temporal–Parietal Regions in Functional Magnetic Resonance Imaging Studies of Speech Perception
Authors: Zevin Jason D. , Yang Jianfeng , Skipper Jeremy I. , McCandliss Bruce D.
Published: January 2010

Functional magnetic resonance imaging (fMRI) studies of speech sound categorization often compare conditions in which a stimulus is presented repeatedly to conditions in which multiple stimuli are presented. This approach has established that a set of superior temporal and inferior parietal regions respond more strongly to conditions containing stimulus change. Here, we examine whether this contrast is driven by habituation to a repeating condition or by selective responding to change. Experiment 1 directly tests this by comparing the observed response to long trains of stimuli against a constructed hemodynamic response modeling the hypothesis that no habituation occurs. The results are consistent with the view that enhanced response to conditions involving phonemic variability reflect change detection. In a second experiment, the specificity of these responses to linguistically relevant stimulus variability was studied by including a condition in which the talker, rather than phonemic category, was variable from stimulus to stimulus. In this context, strong change detection responses were observed to changes in talker, but not to changes in phoneme category. The results prompt a reconsideration of two assumptions common to fMRI studies of speech sound categorization: they suggest that temporoparietal responses in passive paradigms such as those used here are better characterized as reflecting change detection than habituation, and that their apparent selectivity to speech sound categories may reflect a more general preference for variability in highly salient or behaviorally relevant stimulus dimensions.
Combining Targeted Therapies: Practical Issues to Consider at the Bench and Bedside
Authors: Rodon Jordi , Perez Jose , Kurzrock Razelle
Published: January 2010

Numerous practical issues must be considered when combining targeted therapies in early clinical drug development. These include tumor resistance mechanisms, the existence of multiple, redundant signaling pathways, and the failure of single-agent therapies to achieve cures. The strategies adopted to examine combinatorial therapy include the goal of hitting more than one target by specifically inhibiting signal transduction cascades and suppressing specific mechanisms of action with the use of multitargeted kinase inhibitors made possible by high-throughput screening techniques, combinatorial chemistry, and chemoinformatics. Two complex considerations are: which agents to combine given the heterogeneity of tumors and their various underlying perturbations, including secondary mutations and feedback loops, and how to translate findings from the bench to the bedside or directly from the bedside. Another consideration is: When is there enough information to provide a rationale for instituting a phase I trial? Various strategies have been used in combining molecules, including targeting diverse pathways, inhibiting upstream and downstream signals, and adopting a synthetic lethality paradigm. Other issues are: determining appropriate target populations for treatment, how to combine therapeutics with diagnostics, and the frequency of targets in patients referred to clinical trials. Here, we review these issues and we propose various novel trial designs that are logical for determining the efficacy of a drug or drug combination for personalized treatment. A difficult issue that must be answered is how many and which drugs to combine. Recent technologies, such as multiplexed assay platforms and bioinformatics, will shape the future of clinical trials and help answer these questions surrounding combinatorial treatment.
Therapeutic Usefulness of Postoperative Adjuvant Chemotherapy with Tegafur–Uracil (UFT) in Patients with Breast Cancer: Focus on the Results of Clinical Studies in Japan
Authors: Nakayama Takahiro , Noguchi Shinzaburo
Published: January 2010

In Japan, the history of postoperative chemotherapy for breast cancer started with 5-fluorouracil (5-FU), launched in the 1980s. Currently, oral fluoropyrimidine–based regimens indicated for the treatment of breast cancer in Japan include tegafur plus uracil (UFT); tegafur, gimeracil, and oteracil (TS-1); doxifluridine; and capecitabine. In particular, UFT represents an important option for long-term treatment because of minimal adverse events and the potential for long-term maintenance of effective plasma concentrations of 5-FU to inhibit micrometastasis after surgery. Therefore, various clinical studies of postoperative adjuvant chemotherapy with UFT have been conducted in patients with completely resected tumors. Recent studies have shown that UFT prolongs survival after tumor resection in patients with gastric cancer, colorectal cancer, and lung cancer. In patients with breast cancer, large clinical trials of UFT-based postoperative chemotherapy conducted in Japan have shown that UFT is useful for the treatment of intermediate-risk patients with no lymph node metastasis. This paper reviews the results of clinical studies of UFT conducted in Japan to assess the therapeutic usefulness of this oral 5-FU. The types of patients most likely to benefit from UFT are discussed on the basis of currently available evidence and a global consensus of treatment recommendations. The optimal timing of endocrine therapy and strategies for postoperative adjuvant chemotherapy with UFT in patients with breast cancer are also discussed.
Histology Matters: Individualizing Treatment in Non-Small Cell Lung Cancer
Authors: Neal Joel W.
Published: January 2010

This editorial discusses the role of histology in non-small cell lung cancer treatment.
Adipogenesis is differentially impaired by thyroid hormone receptor mutant isoforms
Authors: Mishra Alok , Zhu Xu-guang , Ge Kai , Cheng Sheue-Yann
Published: January 2010

To understand the roles of thyroid hormone receptors (TRs) in adipogenesis, we adopted a loss-of-function approach. We generated 3T3-L1 cells stably expressing either TRα1 mutant (TRα1PV) or TRβ1 mutant (TRβ1PV). TRα1PV and TRβ1PV are dominant negative mutations with a frameshift in the C-terminal amino acids. In control cells, the thyroid hormone, tri-iodothyronine (T3), induced a 2.5-fold increase in adipogenesis in 3T3-L1 cells, as demonstrated by increased lipid droplets. This increase was mediated by T3-induced expression of the peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα), which are master regulators of adipogenesis at both the mRNA and protein levels. In 3T3-L1 cells stably expressing TRα1PV (L1-α1PV cells) or TRβ1PV (L1-β1PV cells), adipogenesis was reduced 94 or 54% respectively, indicative of differential inhibitory activity of mutant TR isoforms. Concordantly, the expression of PPARγ and C/EBPα at the mRNA and protein levels was more repressed in L1-α1PV cells than in L1-β1PV cells. In addition, the expression of PPARγ downstream target genes involved in fatty acid synthesis – the lipoprotein lipase (Lpl) and aP2 involved in adipogenesis – was more inhibited by TRα1PV than by TRβ1PV. Chromatin immunoprecipitation assays showed that TRα1PV was more avidly recruited than TRβ1PV to the promoter to preferentially block the expression of the C/ebpα gene. Taken together, these data indicate that impaired adipogenesis by mutant TR is isoform dependent. The finding that induction of adipogenesis is differentially regulated by TR isoforms suggests that TR isoform-specific ligands could be designed for therapeutic intervention for lipid abnormalities.
HP/HT Well Intervention by Coil Tubing—East Coast Case Histories
Authors: Mohammad Haidher Syed
Published: January 2010

Coil tubing is a single string of pipe, which can intervene into wells and perform specific jobs without mobilizing a rig. The basic applications are cleaning wellbore/perforations, stimulating selective zones, controlling wells, milling/drilling cement/tools/fish downhole, conveying tools in deviated/horizontal wells, gas lifting, setting cement plugs below production packer, and many other applications.

Operating coiled tubing units in HPHT and ultra HPHT wells requires conformance of specific parameters for safety and successful operations. Challenges of the operations and treatment design are exacerbated considering the environment downhole. The conditions become more severe in ultra HPHT environment if the well is deviated or approaches horizontal.

Intervention and treatment in ultra HPHT and in highly deviated or in horizontal wells requires special procedures, techniques and tools. The requirements include modified procedures as well as equipment and products to withstand the BHST temperatures for the entire operation.

As an example of complications in HPHT wells, on the east coast of India, bottomhole static temperatures could go as high as 507°F and mud weight could vary between 14 and 19 ppg in deviated wells. Experience has shown that conventionally calculated bottomhole circulating temperature alone is inadequate to determine the working temperature downhole. However, with the help of computer-aided temperature simulation and all the above techniques, many successful CTU operations have been executed under these difficult conditions.

Using case histories for illustration, this paper will share best practices developed from 4 years of successful interventions in HPHT and ultra-HPHT wells. These practices will include HPHT coil tubing intervention considerations, modified procedures, special techniques and product choices.
Feasibility of Air Injection in a Light Oil Field of Western India
Authors: Mitra Sujit , Bhushan B. V. , Raju P. V. , Kumar Subir , Sur Sidhartha , Mehta S. A. , Moore R. G.
Published: January 2010

Overall field settings like dip of 80, partial water drive, permeability of less than 50md and with 350 API oil make Field - A in Western India an ideal choice for gas injection. Non-availability of hydrocarbon / non-hydrocarbon gas makes air injection a preferred alternative. Viability of air injection process in laboratory was established through displacement tests in 1.83m long & 100mm diameter combustion tube using synthetic and natural core at IRS, ONGC.

In view of limitations of laboratory generated oil reactivity data for carrying out prediction in STARS, following workflow was adopted to estimate recovery from air injection.

Predicting recovery by immiscible gas injection – Pressure maintenance and Immiscible displacement Predicting Volumetric Sweep Efficiency – From miscible Gas Injection. It is felt that Miscible process mimics closely air injection as both these processes have displacement efficiency of more than 90% Predicting Recovery by Air Injection – Integrating immiscible flue gas with Nelson & McNeil derived profile after considering volumetric sweep from miscible gas displacement process. Air injection has the potential to enhance recovery from 19% to 62%.