bluuebunny/crossref_metadata_2025 huggingface dataset:
Variable second‐order inclusion probabilities during the sampling of industrial mixtures of particles
Authors: Geelhoed Bastiaan
Published: December 2006

During analysis and inspection of materials, the mass concentration of a compound in a sample is often used as an estimate for the mass concentration in the population. Depending upon the material and the analysis technique, sample masses vary from several grams to up to several kilograms. An equation for the relation between the sample mass and the variance of the sample concentration allows calculation of the minimum sample mass, defined as the sample mass for which the relative standard deviation of the sample estimator is equal to a maximum allowable value. Application of Gy's theory may result in inaccurate estimates for the minimum sample mass when the selections of the particles are dependent events. The minimum sample mass may be underestimated, resulting in a relatively high variance of the sample concentration, or overestimated, leading to higher sample processing costs. In this contribution, a variable second‐order inclusion probability is proposed. Two estimators for the variance are derived, including an estimator based on the Horvitz–Thompson estimator. The estimators are compared using samples of aggregates. Copyright © 2006 John Wiley & Sons, Ltd.
Interaction between stock indices via changepoint analysis
Authors: Lenardon Martin J. , Amirdjanova Anna
Published: December 2006

Stock market indices from several countries are modelled as discretely sampled diffusions whose parameters change at certain times. To estimate these times of parameter changes we employ both a sequential likelihood‐ratio test and a non‐parametric, spectral algorithm designed specifically for time series with multiple changepoints. Finally, we use point‐process techniques to model relationships between changepoints of different financial time series. Copyright © 2006 John Wiley & Sons, Ltd.
Experimental designs for 2‐colour cDNA microarray experiments
Authors: Nguyen Nam‐Ky , Williams E. R.
Published: December 2006

Kerr and Churchill (Biostatistics2001;2:183–201) showed how varieties (e.g. type of tissues, drug treatments, etc.) are paired onto arrays by a catalogue of A‐optimal incomplete block designs (IBDs) for 6–10 varieties (v), and number of blocks of size 2 betweenvand$ \left(v \atop 2 \right)$. These A‐optimal IBDs were obtained by (i) generating all non‐isomorphic connected graphs onvvertices using Brendan McKay's,MAKEGprogram (http://cs.anu.edu.au/people/bdm/nauty/) and (ii) comparing all designs of the same size on the basis of A‐optimality to obtain the best ones.

In this paper we will give a quick overview on IBDs and describe an algorithmic approach to extend the mentioned catalogue. We aim at IBDs with up to 100 varieties with equal as well as unequal replications. A catalogue of 2007 IBDs is given. We will also extend the concept ofevendesigns in Kerr and Churchill (Biostatistics2001;2:183–201) torow‐orthogonaldesigns. Copyright © 2006 John Wiley & Sons, Ltd.
Controlling‐dependent process steps using variable sample size control charts
Authors: Yang Su‐Fen , Su Hui‐Chun
Published: December 2006

The article considers the variable process control scheme for two dependent process steps. We construct variable sample size (VSS) ZX̄ and Zē control charts to effectively monitor the quality variable produced by the first process step and the quality variable produced by the second process step 2, respectively. The performance of the proposed VSS control charts is measured by the adjusted average time to signal (AATS) using a Markov chain approach. An example of producing cotton yarn system shows the application and performance of the proposed VSS ZX̄ and Zē control charts in detecting shifts in process mean. Furthermore, the performance of the VSS ZX̄ and Zē control charts and the fixed sample size (FSS) ZX̄ and Zē control charts are compared by numerical analysis results. These demonstrate that the former is much faster in detecting small shifts in mean. Copyright © 2006 John Wiley & Sons, Ltd.
Consistent Estimation of the Expected Brier Score in General Survival Models with Right‐Censored Event Times
Authors: Gerds Thomas A. , Schumacher Martin
Published: December 2006

In survival analysis with censored data the mean squared error of prediction can be estimated by weighted averages of time‐dependent residuals. Graf et al. (1999) suggested a robust weighting scheme based on the assumption that the censoring mechanism is independent of the covariates. We show consistency of the estimator. Furthermore, we show that a modified version of this estimator is consistent even when censoring and event times are only conditionally independent given the covariates. The modified estimators are derived on the basis of regression models for the censoring distribution. A simulation study and a real data example illustrate the results. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Demethyloleuropein and β‐glucosidase activity in olive fruits
Authors: Sivakumar Ganapathy , Briccoli Bati Caterina , Uccella Nicola
Published: December 2006

Demethyloleuropein plays a major role in the defense mechanism of olive fruits. To understand how this molecule is metabolized during different stages of maturation of olive fruits, a biomolecular approach to identify the demethyloleuropein chemistry was employed. The β‐glucosidase activity in crude extracts was assayed spectrophotometrically using the chromogenic substrate p‐nitrophenyl‐β‐D‐glucopyranoside. Demethyloleuropein was extracted and identified by HPLC‐MS from both infected and uninfected olive fruits at different physiological stages. The release of more functionally relevant dialdehydes in uninfected fruits was investigated using ESIMS/ MS. In fruits harvested in October, the activity of β‐glucosidase was significantly enhanced in uninfected fruits when compared to the infected fruits. Quantitative differences in the demethyloleuropein content from uninfected fruits showed the highest values (5.09 mg/g) in October, whereas lower levels (4.44 mg/g) were found in infected fruits. The results demonstrated that demethyloleuropein derivatives could be influenced by β‐glucosidase activity to improve the quality of the olive products with the best dialdehyde nutraceutical content.
One‐step purification of Taq DNA polymerase using nucleotide‐mimetic affinity chromatography
Authors: Melissis Sotirios , Labrou Nikolaos E. , Clonis Yannis D.
Published: December 2006

The thermostable Thermus aquaticus DNA polymerase (Taq Pol) has been the key factor in transforming the initial PCR method into one with huge impact in molecular biology and biotechnology. Therefore, the development of effective affinity adsorbents for the purification of Taq Pol, as well as other DNA polymerases, attracts the attention of the enzyme manufacturers and the research laboratories. In this report we describe a simple protocol for the purification of Taq Pol from E. coli lysates, leading to enzymes of high specific activity and purity. The protocol is based on a single affinity chromatography step, featuring an immobilized ligand selected from a structure‐biased combinatorial library of dNTP‐mimetic synthetic ligands. The ligand library was screened for its ability to bind and purify Taq Pol from E. coli lysates. One immobilized ligand (mABSGu) of the general formula X‐Trz‐Y, bearing 9‐aminoethylguanine (AEGu) and aniline‐2‐sulfonic acid (mABS) linked on the triazine scaffold (Trz), displayed the highest purifying ability. Adsorption equilibrium studies with this affinity ligand and Taq Pol determined a dissociation constant (KD) of 0.12 mM for the respective complex, whereas ATP prevented the formation of the mABSGu‐Taq Pol complex. The mABSGu affinity adsorbent was exploited in the development of a facile Taq Pol purification protocol, affording homogeneous enzyme (>99% purity, ∼61 500 U/mg) in a single chromatography step. Quality control tests showed that Taq Pol purified on the mABSGu affinity adsorbent is free of nucleic acids and contaminating nuclease activities.
Expression of an acetyl‐CoA synthase and a CoA‐transferase in Escherichia coli to produce modified taxanes in vivo
Authors: Loncaric Catherine , Ward Amanda F. , Walker Kevin D.
Published: December 2006

Previous in vitro studies revealed that the 10‐deacetylbaccatin III 10β‐O‐acetyltransferase (DBAT) from Taxus can catalyze the transfer of acetyl, propionyl or n‐butyryl from CoA to the C10‐hydroxyl of 10‐deacetylbaccatin III. Accordingly, Escherichia coli JM109 were transformed to recombinantly express dbat, and this enzyme function was coupled to that of acetyl‐CoA synthase (acs, EC 6.2.1.1) expressed from and regulated by genes encoded on the bacterial chromosome. Incubation of the bacteria with 10‐deacetylbaccatin III and increasing concentrations of acetic acid revealed an in vivo conversion (∼10%) of substrate to natural product baccatin III (C10‐acetylated), which was remarkably similar to the relative conversion without acid supplementation. Incubation of the modified E. coli with 5 mM propionic acid, revealed a fivefold increase in the conversion (∼13%) of 10‐deacetylbaccatin III to 10‐deacetyl‐10‐propionylbaccatin III, compared to ∼2% conversion in the absence of exogenous propionate. To produce the butyrylbaccatin III analog in vivo, bacteria were engineered to co‐express the dbat and atoAD (EC 2.8.3.8) genes; the latter encodes an acetoacetate: acetyl‐CoA CoA‐transferase that activates butyrate to butyryl CoA. The bacteria were incubated with 10‐deacetylbaccatin III and 25‐100 mM butyrate, and a maximum of ∼2.6% conversion to 10‐butyrylbaccatin III was observed compared to ∼0.6% conversion when no exogenous butyrate was supplied.
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles
Authors: Damborský Jiří , Petřek Martin , Banáš Pavel , Otyepka Michal
Published: December 2006

The knowledge of the access paths connecting interior of molecular systems with surrounding environment is important for the understanding of structurefunction relationships and engineering of molecules for biotechnological applications. CAVER is a computer program developed for calculations of tunnels, channels or pores in the biomolecules, inorganic materials and molecular ensembles. The algorithm performs a skeleton search based on a reciprocal distance function grid. The algorithm is implemented in the stand‐alone version, web version and as plug‐in for PyMol. CAVER is available from the website http://loschmidt.chemi.muni.cz/caver.
Effect of osteonectin‐derived peptide on the viscoelasticity of hydrogel/apatite nanocomposite scaffolds
Authors: Sarvestani Alireza S. , He Xuezhong , Jabbari Esmaiel
Published: December 2006

Hydrogel/apatite nanocomposites are the ideal biomaterial to mimic the physio‐chemical and biologic properties of the bone and to fabricate scaffolds for bone regeneration. The objective of this work was to investigate the effect of an osteonectin derived glutamic acid sequence on the viscoelastic properties of poly(lactide‐ethylene oxide‐fumarate) (PLEOF)/apatite composite, as a model degradable material in bone regeneration. Osteonectin is an extracellular acidic glycoprotein of the bone matrix, which is believed to be involved in linking the collagen network to hydroxyapatite (HA), the mineral phase of the bone. We synthesized a 6‐glutamic acid sequence in solid phase with affinity to HA crystals via ionic interactions. One end of the synthesized peptide was functionalized with an acrylate group to covalently attach the peptide (Ac‐Glu6) to the aqueous‐based biodegradable and in situ crosslinkable PLEOF hydrogel matrix. To determine the effect of energetic interactions between the fillers and hydrogel matrix, HA nanoparticles were also treated with an acrylate functionalized 6‐glycine amino acid peptide (Ac‐Gly6) that interacts with the fillers only by van der Waals and polar interactions (without ionic interactions). Crosslinked PLEOF/apatite scaffolds were prepared using PLEOF as the degradable macromer, HA nanofillers treated with Ac‐Glu6 peptide linker, and a neutral redox initiation system. The viscoelastic properties were studied by dynamic time sweep, strain sweep, and small amplitude oscillatory rheometry. Composites without surface treatment, treated with Ac‐Gly6, and treated with Ac‐Glu6 at different volume fractions and various particle sizes were examined. The results showed that the 6‐mer glutamic acid sequence significantly affects the shear modulus of the scaffold because of ionic interactions between the peptide and HA crystals. © 2006 Wiley Periodicals, Inc. Biopolymers 85:370–378, 2007.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Hyrtiosal, a PTP1B Inhibitor from the Marine Sponge Hyrtios erectus, Shows Extensive Cellular Effects on PI3K/AKT Activation, Glucose Transport, and TGFβ/Smad2 Signaling
Authors: Sun Tao , Wang Qi , Yu Zhiguo , Zhang Yu , Guo Yuewei , Chen Kaixian , Shen Xu , Jiang Hualiang
Published: December 2006

Protein tyrosine phosphatase 1B (PTP1B) negatively regulates insulin signaling, and PTP1B inhibitors have been seen as promising therapeutic agents against obesity and type 2 diabetes. Here we report that the marine natural product hyrtiosal, from the marine sponge Hyrtios erectus, has been discovered to act as a PTP1B inhibitor and to show extensive cellular effects on PI3K/AKT activation, glucose transport, and TGFβ/Smad2 signaling. This inhibitor wad able to inhibit PTP1B activity in dose‐dependent fashion, with an IC50 value of 42 μM in a noncompetitive inhibition mode. Further study with an IN Cell Analyzer 1000 cellular fluorescence imaging instrument showed that hyrtiosal displayed potent activity in abolishing the retardation of AKT membrane translocation caused by PTP1B overexpression in CHO cells. Moreover, it was found that this newly identified PTP1B inhibitor could dramatically enhance the membrane translocation of the key glucose transporter Glut4 in PTP1B‐overexpressed CHO cells. Additionally, in view of our recent finding that PTP1B was able to modulate insulin‐mediated inhibition of Smad2 activation, hyrtiosal was also tested for its capabilities in the regulation of Smad2 activity through the PI3K/AKT pathway. The results showed that hyrtiosal could effectively facilitate insulin inhibition of Smad2 activation. Our current study is expected to supply new clues for the discovery of PTP1B inhibitors from marine natural products, while the newly identified PTP1B inhibitor hyrtiosal might serve as a potential lead compound for further research.
Nitrosation of N‐Terminally Blocked Tryptophan and Tryptophan‐Containing Peptides by Peroxynitrite
Authors: Peyrot Fabienne , Ducrocq Claire
Published: December 2006

Tryptophan is known to be a major target of oxidative stress and to take part in electron transfer. In proteins, its fluorescence is extinguished after treatment with oxidative agents, like peroxynitrite (ONOO−/ONOOH)—the product of the reaction of NO. and superoxide anion (O2.−) radicals. The main reactions of N‐blocked tryptophan derivatives (melatonin or N‐acetyl‐L‐tryptophan) exposed to peroxynitrite at physiological pH are oxidation to formylkynuramine or formylkynurenine, respectively, and nitrosation, which leads to substituted 1‐nitrosoindoles. Here we show that peroxynitrite‐induced nitrosation is specific to N‐blocked L‐tryptophan derivatives and is not obtained with free L‐tryptophan. Such a nitrosation can be evaluated by using 4,5‐diaminofluorescein (DAF‐2), which is converted to the fluorescent triazolofluorescein by NO. donors and nitrosating agents. N‐acetyl‐L‐tryptophan was shown to be twice as efficient as melatonin in transferring NO from peroxynitrite to DAF‐2. DAF‐2 responses were then used to assess the ability of a series of L‐tryptophan‐containing peptides to give transient N‐nitrosoindoles upon treatment with peroxynitrite. Many peptides proved not to be susceptible to nitrosation under these conditions. However, the N‐terminally blocked peptide of endothelin‐1 (Ac–Asp–Ile–Ile–Trp) reacted in a very similar fashion to melatonin; this shows that tryptophan residue nitrosation could occur when it was exposed to peroxynitrite.
Mass Tansfer Characteristics of a Microchannel Device of Split‐Flow Type
Authors: Hotta T. , Nii S. , Yajima T. , Kawaizumi F.
Published: December 2006

A solute was transferred from an aqueous solution to deionized water in a microchannel device with a rectangular channel of 200 μm × 200 μm. The two liquid layers flowed in parallel within the rectangular channel. After making contact in the channel, the layers were split into two streams through a knife‐edge. The amount of solute transferred was determined by analyzing liquid samples taken from the outlet. Thus, conventional analytical instruments were readily available for obtaining the total concentration. Mass tansfer characteristics were examined through the measurement of diffusion coefficients for several solutes. Although the two liquids were carefully supplied at the same velocity, equal flow splitting was difficult to obtain. The unequal splitting led to scattering of the observed solute concentrations at a fixed supply flow rate. This could be a serious drawback as a mass tansfer device; however, a method was proposed to choose an appropriate value for equal splitting. The ratio of effluent flow rate of one liquid to another was changed intentionally. The solute concentration in the receiving liquid for the flow rate ratio of unity corresponds to the data for equal flow splitting. On the basis of the solute concentrations defined, the diffusion of benzoic acid was successfully analyzed using a conventional penetration model with a correction parameter. Furthermore, diffusion coefficients for sucrose and glycine were determined using the basic equation obtained with benzoic acid. The observed values compared fairly well with reported ones. The correction parameter expresses characteristics of the microchannel device; however, the physical picture is still unclear.
Prognostic significance of vascular endothelial growth factor protein levels in T1‐2 N0 laryngeal cancer treated with primary radiation therapy
Authors: Parikh Rahul R. , Yang Qifeng , Haffty Bruce G.
Published: December 2006

BACKGROUND.

The purpose of this study was to assess the prognostic value of vascular endothelial growth factor protein levels in a large cohort of patients with T1‐T2 N0 laryngeal cancer treated with primary radiation therapy (XRT).

METHODS.

Primary tumor specimens from a cohort of 123 patients with T1‐T2 N0 laryngeal cancer treated with XRT between 1975 and 2000 were constructed into a tissue microarray. Clinical prognostic factors included age, sex, T classification, and tumor subsite. Molecular prognostic factors included vascular endothelial growth factor, epidermal growth factor receptor, and p53 expression, determined by using immunohistochemistry on tissue microarrays. The association between vascular endothelial growth factor status, covariables, and outcome was assessed.

RESULTS.

With a median follow‐up of 9.9 years, 32 (26%) were diagnosed with local relapse (5‐year local relapse‐free rate, 70.4%). T2 tumor stage (31.7%) was a significant predictor of local relapse (relative risk [RR], 1.71; 95% confidence interval [CI], 1.21–2.43; P<.05). Positive expression of vascular endothelial growth factor, epidermal growth factor receptor, and p53 were: 8.5%, 58.7%, and 36.4%, respectively. In univariate analysis, vascular endothelial growth factor positivity was a significant predictor of overall survival (RR = 1.62; 95% CI, 0.99–2.42; P = .05). In multivariate analysis, positive vascular endothelial growth factor status maintained significant correlation with overall survival (RR, 2.79; 95% CI, 1.49–4.95; P = .002).

CONCLUSIONS.

Vascular endothelial growth factor positivity appeared to be a significant predictor of overall survival in a multivariate model. Further evaluation of vascular endothelial growth factor‐positive laryngeal cancers treated with primary XRT is warranted. Cancer 2007;109:566–573. © 2006 American Cancer Society.
Collateralization of the tectonigral projection with other major output pathways of superior colliculus in the rat
Authors: Coizet Véronique , Overton Paul G. , Redgrave Peter
Published: December 2006

Dopaminergic (DA) neurons exhibit a short‐latency, phasic response to unexpected, biologically salient stimuli. The superior colliculus (SC) is also sensitive to such stimuli and sends a projection directly to DA‐containing regions of the ventral midbrain. Recent evidence suggests that the SC is a critical relay for transmitting short‐latency visual information to DA neurons. An important question is whether the ventral midbrain is an exclusive target of tectonigral neurons, or whether the tectonigral projection is a collateral branch of other tectofugal pathways. Double‐label retrograde anatomical tracing techniques were used to address this issue. Injections of either Diamidino Yellow or Fluorogold into substantia nigra pars compacta (SNc) were combined with larger injections of True Blue into one of the following efferent projections of the SC: 1) target regions of the ipsilateral ascending projection to the thalamus; 2) the crossed descending tecto‐reticulo‐spinal pathway; 3) target structures of the ipsilateral descending projection; and 4) the contralateral superior colliculus. Moderate numbers of double‐labeled neurons were observed following combined injections into substantia nigra and individual nuclei in the thalamus (ventromedial nucleus, 21.3%; central lateral, 18.4%; parafasicular nucleus 6.0%). Much less double‐labeling was associated with injections into either of the descending projections (crossed, 1.0–3.2%; uncrossed, 0.2–2.7%) or the contralateral SC (0.7–1.9%). These results suggest: i) the SC may provide a coordinated input concerning the occurrence of unpredicted sensory events to both the substantia nigra and striatum (via the thalamus); and ii) few gaze‐related motor signals are simultaneously relayed to DA‐containing regions of the ventral midbrain. J. Comp. Neurol. 500:1034–1049, 2007. © 2006 Wiley‐Liss, Inc.
Distribution of vasopressin in the brain of the eusocial naked mole‐rat
Authors: Rosen Greta J. , De Vries Geert J. , Goldman Sharry L. , Goldman Bruce D. , Forger Nancy G.
Published: December 2006

Naked mole‐rats are eusocial rodents that live in large subterranean colonies in which one queen breeds with one to three males. All other animals are nonbreeding subordinates. The external features of male and female subordinates, including their genitalia, are remarkably monomorphic, as is their behavior. Because vasopressin (VP) is associated with social behaviors and sex differences in other species, its distribution in naked mole‐rats was of interest. We used immunohistochemistry to examine VP in the brains of subordinate and breeding naked mole‐rats of both sexes. As in other mammals, VP‐immunoreactive (‐ir) somata were found in the paraventricular (PVN) and supraoptic nuclei (SON) and VP‐ir projections from these nuclei ran through the internal and external zone of the median eminence. However, naked mole‐rats had very few VP‐ir cells in the bed nucleus of the stria terminalis (BST) and none in the suprachiasmatic nucleus (SCN); the extensive network of fine‐caliber VP‐ir fibers usually seen in projection sites of the BST and SCN were also absent. Equally unexpected was the abundance of large‐caliber VP‐ir fibers in the dorsomedial septum. VP immunoreactivity was generally similar in all groups, with the exception of VP‐ir cell number in the dorsomedial hypothalamus (DMH). Breeders had a population of labeled cells in the DMH that was absent, or nearly absent, in subordinates. Future studies on the function of VP in these areas are needed to determine how the atypical distribution of VP immunoreactivity relates to eusociality and the unusual physiology of naked mole‐rats. J. Comp. Neurol. 500:1093–1105, 2007. © 2006 Wiley‐Liss, Inc.
Identification of aldolase C compartments in the mouse cerebellar cortex by olivocerebellar labeling
Authors: Sugihara Izumi , Quy Pham Nguyen
Published: December 2006

Aldolase C (zebrin II) is expressed in Purkinje cells aligned in complicated longitudinal stripe‐shaped compartments. The tight link between these aldolase C compartments and the topographic olivocerebellar projection to them has made it possible to identify each compartment as a target of a specific subarea of the inferior olive and thus as a functionally distinct entity in the rat. However, it is unknown whether the overall organization of aldolase C compartments is preserved in other mammals. In this study, we tried to clarify this organization in the mouse, which is more useful in genetic studies than the rat, by identifying each aldolase C compartment in terms of the olivocerebellar projection pattern. First, aldolase C compartments were reconstructed from serial sections throughout the cerebellar cortex. Aldolase C and olivocerebellar climbing fibers were then doubly labeled by small injections of biotinylated dextran amine into various areas of the inferior olive. Climbing fibers were topographically distributed on a specific linked pair of aldolase C compartments in the rostral and caudal cerebellum. The overall relationship between aldolase C compartments and the topographic olivocerebellar projection to them in the mouse was similar to that in the rat, except for some minor differences, suggesting that the aldolase C compartments and olivocerebellar projection are organized according to a common fundamental organization in the mouse and rat. This allowed the unequivocal identification of all aldolase C compartments in the mouse by referring to the definition and nomenclature in the rat. J. Comp. Neurol. 500:1076–1092, 2007. © 2006 Wiley‐Liss, Inc.
Compensatory and transneuronal plasticity after early collicular ablation
Authors: Dunlop Sarah A. , Rodger Jenny , Beazley Lyn D.
Published: December 2006

Plasticity within the visual system was assessed in the quokka wallaby following unilateral superior collicular (SC) ablation at postnatal days (P) 8–10, prior to the arrival of retinal ganglion cell (RGC) axons. At maturity (P100), projections were traced from the eye opposite the ablation, and total RGC numbers were estimated for both eyes. Ablations were partial (28–89% of SC remaining) or complete (0–5% of SC remaining). Projections to the visual centers showed significant bilateral (P < 0.05) increases in absolute volume. Minor anomalous projections also formed within the deep, surviving non‐retino‐recipient layers of the ablated SC and via a small bundle of RGC axons recrossing the midline to innervate discrete patches in the SC contralateral to the lesion. Total absolute volume of projections did not differ between partial and complete ablations; moreover, values did not differ from normal (P > 0.05). Compared with normal, total RGC numbers were significantly (P < 0.05) reduced in the eye opposite the ablation but increased (P < 0.05) in the other eye. Consequently, the sum of the two RGC populations did not differ from normal (P > 0.05). As in rodents, the visual system in quokka compensates following injury by maintaining a set volume of arborization but does so by forming only minor anomalous projections. Furthermore, increased RGC numbers in the eye ipsilateral to the lesion indicate that compensation occurs transneuronally, thus maintaining total numbers of projecting neurons. The implication is that the visual system acts in concert following unilateral injury to maintain set values for RGC terminal arbors as well as their cell bodies. J. Comp. Neurol. 500:1117–1126, 2007. © 2006 Wiley‐Liss, Inc.
Functional and anatomical connection between the paraventricular nucleus of the thalamus and dopamine fibers of the nucleus accumbens
Authors: Parsons Matthew P. , Li Sa , Kirouac Gilbert J.
Published: December 2006

The shell of the nucleus accumbens (NacSh) receives a dense innervation from dopamine (DA) neurons in the ventral tegmental area (VTA) and from glutamate neurons in the paraventricular nucleus of the thalamus (PVT). The present study examined in urethane‐anesthetized rats the effects of electrical stimulation of the PVT on DA levels in the NacSh as measured with amperometry and chronoamperometry. Stimulation of the PVT (40 Hz, 1.0 ms, 400 μA, 5 seconds) resulted in a brief increase in electrochemical currents detected in the NacSh. Inhibition of DA neurons in the VTA using lidocaine (4%, 500 nL) or intravenous apomorphine (0.15 mg/kg) decreased the resting voltammetric signal but had no effect on PVT‐evoked responses. Blocking of ionotropic glutamate receptors in the NacSh with local administration of kynurenic acid attenuated the PVT‐evoked responses. Anterograde tracing with biotinylated dextran amine demonstrated that PVT targets regions of very dense tyrosine hydroxylase fiber staining in the NacSh. Consistent with the projection pattern of the PVT to the NacSh, stimulation of the PVT evoked the largest oxidation current changes in the NacSh, whereas small or no changes were elicited in other areas of the striatum. This study suggests that glutamate release from PVT terminals can act on ionotropic glutamate receptors in the NacSh to induce DA efflux. Modulation of DA levels in the NacSh by the PVT may be linked to arousal‐induced increases in DA tone and could be involved in the facilitation of specific behavioral patterns associated with arousal or stressful situations. J. Comp. Neurol. 500:1050–1063, 2007. © 2006 Wiley‐Liss, Inc.
Distribution of RET immunoreactivity in the rodent spinal cord and changes after nerve injury
Authors: Jongen Joost L.M. , Jaarsma Dick , Hossaini Mehdi , Natarajan Dipa , Haasdijk Elize D. , Holstege Jan C.
Published: December 2006

RET (for “rearranged during transfection”) is a transmembrane tyrosine kinase signaling receptor for members of the glial cell line‐derived neurotrophic factor (GDNF) family of ligands. We used RET immunohistochemistry (IHC), double‐labeling immunofluorescence (IF), and in situ hybridization (ISH) in adult naïve and nerve‐injured rats to study the distribution of RET in the spinal cord. In the dorsal horn, strong RET‐immunoreactive (‐ir) fibers were abundant in lamina II‐inner (IIi), although this labeling was preferentially observed after an antigen‐unmasking procedure. After dorsal rhizotomy, RET‐ir fibers in lamina IIi completely disappeared from the dorsal horn, indicating that they were all primary afferents. After peripheral axotomy, RET‐ir in primary afferents decreased in lamina IIi and appeared to increase slightly in laminae III and IV. RET‐ir was also observed in neurons and dendrites throughout the dorsal horn. Some RET‐ir neurons in lamina I had the morphological appearance of nociceptive projection neurons, which was confirmed by the finding that 53% of RET‐ir neurons in lamina I colocalized with neurokinin‐1. GDNF‐ir terminals were in close proximity to RET‐ir neurons in the superficial dorsal horn. In the ventral horn, RET‐ir was strongly expressed by motoneurons, with the strongest staining in small, presumably γ‐motoneurons. Increased RET expression following peripheral axotomy was most pronounced in α‐motoneurons. The expression and regulation pattern of RET in the spinal cord are in line with its involvement in regenerative processes following nerve injury. The presence of RET in dorsal horn neurons, including nociceptive projection neurons, suggests that RET also has a role in signal transduction at the spinal level. This role may include mediating the effects of GDNF released from nociceptive afferent fibers. J. Comp. Neurol. 500:1136–1153, 2007. © 2006 Wiley‐Liss, Inc.
Heterogeneity of horizontal cells in the chicken retina
Authors: Fischer Andy J. , Stanke Jennifer J. , Aloisio Gina , Hoy Heather , Stell William K.
Published: December 2006

Despite numerous reports that different markers are expressed by horizontal cells in the avian retina, it remains unknown whether different types of horizontal cells can be defined by differences in their immunocytochemical profiles. The purpose of this study was to rectify this deficiency. We identified horizontal cells by indirect immunofluorescence with antibodies to calretinin, trkA, GABA, Prox1, AP2α, Pax6, islet1, and Lim1 + 2. We found two major groups of horizontal cells, those that express trkA and those that express calretinin. The trkA‐immunoreactive (‐IR) horizontal cells had small, round somata and robust, bulbous dendritic endings, whereas calretinin‐IR horizontal cells had large, polygonal cell bodies and fine, diffuse dendritic endings, both contacting the calbindin‐IR pedicles of double cones. Weak γ‐aminobutyric acid (GABA) immunoreactivity was observed only in a few of the trkA‐IR horizontal cells, whereas the overlap of calretinin and GABA immunoreactivities was 100%. The majority of trkA‐IR horizontal cells expressed islet1, and the majority of calretinin‐IR horizontal cells expressed Lim1 + 2, AP2α, and Pax6. Islet1 immunoreactivity was observed in a small fraction of calretinin‐IR/non‐trkA‐IR cells. In agreement with previous reports, we detected Prox1 immunoreactivity in all types of horizontal cells. These immunolabeling profiles suggest that there are four immunochemically distinct subtypes of horizontal cells in the postnatal chick retina, which may match the four types that have been observed in Golgi‐impregnated pigeon and turtle retinas. J. Comp. Neurol. 500:1154–1171, 2007. © 2006 Wiley‐Liss, Inc.
Perisynaptic organization of plasma membrane calcium pumps in cerebellar cortex
Authors: Burette Alain , Weinberg Richard J.
Published: December 2006

Calcium, a ubiquitous intracellular messenger, regulates numerous intracellular signaling pathways. To permit specificity of signal transduction and prevent unwanted cross‐talk between pathways, sites of calcium entry in neurons are localized to specific membrane domains. To test whether Ca2+ extrusion pumps might exhibit analogous compartmentalization, we used immunohistochemistry to determine the subcellular localization of the two main plasma membrane Ca2+‐ATPase (PMCA) isoforms in the cortex of the rat cerebellum. We find that both PMCA2 and PMCA3 are targeted to distinct compartments within the plasma membrane. In the molecular layer, both isoforms were at highest levels within synaptic profiles, but PMCA2 was postsynaptic and PMCA3 was presynaptic. Moreover, inside these compartments, both pumps exhibited nonuniform distributions. These data imply that cerebellar neurons possess remarkably effective mechanisms to target and restrict PMCA2 and ‐3 to specific membrane domains, raising the possibility that calcium pumps contribute to local Ca2+ signaling. J. Comp. Neurol. 500:1127–1135, 2007. © 2006 Wiley‐Liss, Inc.
Estradiol enhances neurogenesis following ischemic stroke through estrogen receptors α and β
Authors: Suzuki Shotaro , Gerhold Lynnette M. , Böttner Martina , Rau Shane W. , Dela Cruz Christopher , Yang Enhua , Zhu Hong , Yu Jin , Cashion Adrienne B. , Kindy Mark S. , Merchenthaler Istvan , Gage Fred H. , Wise Phyllis M.
Published: December 2006

Neurogenesis persists throughout life under normal and degenerative conditions. The adult subventricular zone (SVZ) generates neural stem cells capable of differentiating to neuroblasts and migrating to the site of injury in response to brain insults. In the present study, we investigated whether estradiol increases neurogenesis in the SVZ in an animal model of stroke to potentially promote the ability of the brain to undergo repair. Ovariectomized C57BL/6J mice were implanted with capsules containing either vehicle or 17β‐estradiol, and 1 week later they underwent experimental ischemia. We utilized double‐label immunocytochemistry to identify the phenotype of newborn cells (5‐bromo‐2′‐deoxyuridine‐labeled) with various cellular markers; doublecortin and PSA‐NCAM as the early neuronal marker, NeuN to identify mature neurons, and glial fibrillary acidic protein to identify astrocytes. We report that low physiological levels of estradiol treatment, which exert no effect in the uninjured state, significantly increase the number of newborn neurons in the SVZ following stroke injury. This effect of estradiol is limited to the dorsal region of the SVZ and is absent from the ventral SVZ. The proliferative actions of estradiol are confined to neuronal precursors and do not influence gliosis. Furthermore, we show that both estrogen receptors α and β play pivotal functional roles, insofar as knocking out either of these receptors blocks the ability of estradiol to increase neurogenesis. These findings clearly demonstrate that estradiol stimulates neurogenesis in the adult SVZ, thus potentially facilitating the brain to remodel and repair after injury. J. Comp. Neurol. 500:1064–1075, 2007. © 2006 Wiley‐Liss, Inc.
Piecewise divergence‐free discontinuous Galerkin methods for Stokes flow
Authors: Hansbo Peter , Larson Mats G.
Published: December 2006

In this paper, we consider different possibilities of using divergence‐free discontinuous Galerkin methods for the Stokes problem in order to eliminate the pressure from the discrete problem. We focus on three different approaches: one based on a C0 approximation of the stream function in two dimensions (the vector potential in three dimensions), one based on the non‐conforming Morley element (which corresponds to a divergence‐free non‐conforming Crouzeix–Raviart approximation of the velocities), and one fully discontinuous Galerkin method with a stabilization of the pressure that allows the edgewise elimination of the pressure variable before solving the discrete system. We limit the analysis in the stream function case to two spatial dimensions, while the analysis of the fully discontinuous approach is valid also in three dimensions. Copyright © 2006 John Wiley & Sons, Ltd.
A Novel Methodological Approach for the Analysis of Host–Ligand Interactions
Authors: Strat Daniela , Missailidis Sotiris , Drake Alex F.
Published: December 2006

Traditional analysis of drug‐binding data relies upon the Scatchard formalism. These methods rely upon the fitting of a linear equation providing intercept and gradient data that relate to physical properties, such as the binding constant, cooperativity coefficients and number of binding sites. However, the existence of different binding modes with different binding constants makes the implementation of these models difficult. This article describes a novel approach to the binding model of host–ligand interactions by using a derived analytical function describing the observed signal. The benefit of this method is that physically significant parameters, that is, binding constants and number of binding sites, are automatically derived by the use of a minimisation routine. This methodology was utilised to analyse the interactions between a novel antitumour agent and DNA. An optical spectroscopy study confirms that the pentacyclic acridine derivative (DH208) binds to nucleic acids. Two binding modes can be identified: a stronger one that involves intercalation and a weaker one that involves oriented outer‐sphere binding. In both cases the plane of the bound acridine ring is parallel to the nucleic acid bases, orthogonal to the phosphate backbone. Ultraviolet (UV) and circular dichroism (CD) data were fitted using the proposed model. The binding constants and the number of binding sites derived from the model remained consistent across the different techniques used. The different wavelengths at which the measurements were made maintained the coherence of the results.
Toward Separation of Nuclear Spin Isomers with Coherent Light
Authors: Deeb Omar , Leibscher Monika , Manz Jörn , von Muellern Wulf , Seideman Tamar
Published: December 2006

We propose an approach for separating nuclear spin isomers with coherent light and illustrate it by numerical calculations using fulvene as a model system. The scheme employs the equivalence of torsion and interchange of equivalent H‐atoms in a class of molecules of which fulvene is a simple example. The exchange symmetry couples with the rotational symmetry to produce a spatial distinction between the two photo‐excited nuclear spin isomers, and wavepacket interferometry is applied to separate the species.
Myocardin‐related transcription factor B is required for normal mouse vascular development and smooth muscle gene expression
Authors: Wei Ke , Che Nam , Chen Fabian
Published: December 2006

Smooth muscle gene expression is required for the proper development and function of multiple organ systems. Expression of smooth muscle genes is critical for contractile function and tissue architectural integrity. One critical transcription factor for smooth muscle gene expression is the Serum Response Factor (SRF). SRF is expressed ubiquitously, but tissue‐specific transcriptional regulation is conferred by its binding to cofactors such as myocardin. Myocardin‐related transcription factor B (MRTF‐B) is a member of a family of genes (Myocardin(Myocd),Myocardin‐related transcription factor A(MRTF‐A),MRTF‐B) that provides tissue‐specificity and potentiate SRF‐dependent transcription. Unlike myocardin, which is expressed specifically in smooth and cardiac muscle, MRTF‐B is expressed in a wide variety of tissues. To examine the function of MRTF‐B, we generated mice containing an insertional mutation of MRTF‐B. MRTF‐B homozygous mutants die in late gestation with vascular defects and liver hemorrhage. At E9.5, MRTF‐B is expressed strongly in the septum transversum mesoderm critical for development of the vitelline system that produces the liver sinusoids and portal venous system. MRTF‐B deficiency results in defective smooth muscle gene expression in the liver sinusoids, vitelline veins, and yolk sac, which contributes significantly to the lethal phenotype. These data support our hypothesis that MRTF‐B has a unique role in regulating smooth muscle genes important for liver, yolk sac, and portal vascular development. Developmental Dynamics 236:416–425, 2007. © 2006 Wiley‐Liss, Inc.
Mass Flow Balances of Triclosan in Small Rural Wastewater Treatment Plants and the Impact of Biomass Parameters on the Removal
Authors: Winkler G. , Thompson A. , Fischer R. , Krebs P. , Griffin P. , Cartmell E.
Published: December 2006

Three United Kingdom (UK) wastewater treatment plants (WWTP) – rotating biological contactor (RBC), trickling filter (TF) and oxidation ditch (OD) – were analyzed for their triclosan contents at different treatment stages. Furthermore, selected wastewater and biomass parameters were determined to draw correlations between the biological treatment, biomass make‐up and the removal efficiency of triclosan. Within this study, triclosan bound to the extracellular polymeric substances (EPS) of sludge flocs in the oxidation ditch seemed to have an adverse effect on the effluent quality, reducing the triclosan overall removal due to re‐balancing effects within the final clarifier. Within this study of the three examined WWTPs, temperature and pH of the bulk phase and as well the lipid content of the biomass seemed to have the most significant effects on the triclosan removal. The triclosan overall removal for each site was shown to be significantly high, ranging on average between 81 % (RBC) and 96 % (OD). The most efficient plant regarding the triclosan overall removal was found to be the oxidation ditch, which can be explained due to high hydraulic retention times. Primary settling points were found to have a significant impact on the triclosan overall loss rate, which was associated with the high fat content of primary sludge and the hydrophobic properties of triclosan. Besides the fat content of sludge or biomass, the pH and temperature showed a significant impact on triclosan loss rates as well.
Spatial selectivity and theta phase precession in CA1 interneurons
Authors: Ego‐Stengel Valérie , Wilson Matthew A.
Published: December 2006

Traditionally, most of the information processing of neural networks is thought to be carried out by excitatory cells. Likewise, recent evidence for temporal coding comes from the study of the detailed firing patterns of excitatory neurons. In the CA1 region of the rat hippocampus, pyramidal cells discharge selectively when the animal is in specific locations in its environment, and exhibit a precise relationship with the ongoing rhythmic activity of the network (phase precession). We demonstrate that during a spatial exploratory behavior on a linear track, inhibitory interneurons also show spatial selectivity and phase precession dynamics. We found that the firing rate of interneurons is modulated reliably up and down around an ongoing baseline activity level for specific locations in the environment, producing robust place‐specific increases or decreases in discharge. On some sections of the track, the range of theta phases shifts progressively to earlier parts of the theta cycle as the rat advances, so that a negative correlation between phase and position could be demonstrated. Unlike pyramidal cells, phase and rate were not strongly correlated. We discuss the influence of the intrinsic firing properties of interneurons on a model of phase precession, as well as the influence of the detailed shape of the inhibitory oscillation. These results indicate that spatial selectivity and phase precession in CA1 are not properties restricted to pyramidal cells. Rather, they may be a more general expression of a common interaction between the different inputs impinging on both excitatory and inhibitory cells in CA1 and the intrinsic characteristics of those cells. Furthermore, they suggest that the role of interneurons may extend beyond a global damping of the network by participating in a finely‐tuned local processing with the pyramidal cells. © 2006 Wiley‐Liss, Inc.
Mechanical properties and biological behavior of carbon nanotube/polycarbosilane composites for implant materials
Authors: Wang Wei , Watari Fumio , Omori Mamoru , Liao Susan , Zhu Yuhe , Yokoyama Atsuro , Uo Motohiro , Kimura Hisamichi , Ohkubo Akira
Published: December 2006

Multiwalled carbon nanotube/polycarbosilane (MWCNT/PCS) composites were fabricated by the spark plasma sintering (SPS) method. The MWCNT/PCS composites consisted of MWCNTs and nanosized SiC particles pyrolyzed from PCS and possessing good mechanical properties for bone tissue repair or dental implantation. The MWCNT/PCS composites were implanted in the subcutaneous tissue and femur of rats at 1 and 4 weeks after implantation. Histological investigations showed that there was little inflammatory response in the subcutaneous tissue, and newly formed bone tissue was observed in the femur. These results indicated that the MWCNT/PCS composite had little prophlogistic effect and good osteoconductivity. The study suggested the possibility that the MWCNT/PCS composite could be a candidate bone‐substitute and dental‐implant material in the future. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 2006.