bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved air stability of n-channel organic thin-film transistors with surface modification on gate dielectrics
Authors: Chen Fang-Chung , Liao Cheng-Hsiang
Published: September 2008

The air stability of n-channel organic thin film transistors based on N,N′-dioctyl-3,4,9,10-perylene tetracarboxylic diimide is improved when modifying the dielectric surfaces with polymer insulators. The hydrophobic nature of the polymer surface inhibits protonation of the siloxyl groups on the SiO2 surface, leading to fewer SiO− groups that can behave as electron traps. Among the polymer insulators tested, the devices modified with hydroxyl-free polymers exhibited the best air stabilities.
Site-controlled growth and luminescence of InAs quantum dots using in situ Ga-assisted deoxidation of patterned substrates
Authors: Atkinson P. , Kiravittaya S. , Benyoucef M. , Rastelli A. , Schmidt O. G.
Published: September 2008

Site-controlled growth of single and pairs of InAs quantum dots is demonstrated on ex situ electron-beam patterned (001) GaAs substrates using in situ Ga-assisted deoxidation prior to overgrowth. 6–8 ML of gallium deposited at a substrate temperature of 460°C in the absence of arsenic followed by a brief anneal under arsenic is used to remove the surface oxide without damaging a pattern consisting of ∼100nm wide, ∼20nm deep holes. Single dot luminescence is shown from a dilute array (10μm spacing) of such site-controlled dots, located only 8nm from the regrowth interface.
Plasmon resonances and electron phase shifts near Au nanospheres
Authors: Petersen T. C. , Bosman M. , Keast V. J. , Anstis G. R.
Published: September 2008

Quantitative phase maps from Au and polystyrene nanospheres were obtained using the transport of intensity equation approach for phase retrieval in the electron microscope. These were compared to surface plasmon maps, as generated by electron energy loss spectroscopy. Large phase excursions were observed in the vacuum regions surrounding the Au nanospheres, yet not near adjacent polystyrene nanospheres. It is proposed that these phase excursions are associated with surface plasmon excitation. These results suggest that phase retrieval offers an alternative means for sensing and interpreting the optical response of nanostructured metals.
Single-photon-emitting diode at liquid nitrogen temperature
Authors: Dou X. M. , Chang X. Y. , Sun B. Q. , Xiong Y. H. , Niu Z. C. , Huang S. S. , Ni H. Q. , Du Y. , Xia J. B.
Published: September 2008

We report on the study of a single-photon-emitting diode at 77K. The device is composed of InAs∕GaAs quantum dots embedded in the i-region of a p-i-n diode structure. The high signal to noise ratio of the electroluminescence, as well as the small second order correlation function at zero-delay g(2)(0), implies that the device has a low multiphoton emission probability. By comparing the device performances under different excitation conditions, we have, in detail, discussed the basic parameters, such as signal to noise ratio and g(2)(0), and provided some useful information for the future application.
Improvement in scintillation performance of Ce, Er codoped yttrium aluminum garnet crystals by means of a postgrowth treatment
Authors: Solodovnikov D. , Weber M. H. , Lynn K. G.
Published: September 2008

Samples of Ce, Er codoped yttrium aluminum garnet were annealed in ambient air or under oxygen flow and then sputter coated with Al and annealed in Ar. After this treatment Al diffused in the bulk and filled cation vacancy but this process is possible only after oxygen vacancy coupled to the cation vacancy is filled by an oxygen atom. The scintillator performance was improved from 13.2% full width at half maximum at 662keV to 3.4% for a 10×10×6mm size crystal. These findings provide an effective original approach to defect treatment in garnet crystals.
Hydrothermal epitaxy of ZnO:Co diluted magnetic semiconducting single crystalline films
Authors: Zhang Y. B. , Li S. , Goh G. K. L. , Tripathy S.
Published: September 2008

ZnO:Co films with room-temperature ferromagnetism have been hydrothermally grown in water at 90 °C using a ZnO seed layer on MgAl2O4 (111) substrates. High-resolution x-ray diffraction shows an epitaxial ZnO:Co single crystalline film with an out-of-plane orientation of ZnO:Co⟨001⟩∥MgAl2O4⟨111⟩ and an in-plane orientation of ZnO:Co[110]∥MgAl2O4[−1−12] and ZnO:Co[−110]∥MgAl2O4[−110]. A saturation magnetization of 0.83 emu/cm3 and a coercivity of 40 Oe were obtained for the epitaxial Zn0.98Co0.02O film at room temperature. Hydrogen unintentionally incorporated in the hydrothermal synthesis is suggested to contribute to the ferromagnetic properties in the diluted magnetic semiconductor by enhancing carrier concentration as a shallow donor.
Thermal characterization of light-emitting diodes in the frequency domain
Authors: Vitta P. , Žukauskas A.
Published: September 2008

We report on a method for the measurement of thermal relaxation time constants within light-emitting diodes (LEDs) in the frequency domain. The method is based on the phase shift of the forward voltage waveform with respect to that of the harmonically modulated forward current due to the sensitivity of the forward voltage to junction temperature. The phase shift was shown to exhibit dips at angular frequencies equal to inverse thermal time constants. Extraction of thermal time constants was demonstrated for common low-power and high-power LEDs. The measured thermal time constants (∼0.1–100 ms) were linked to heat flows between the LED components.
Degenerate doping induced metallic behaviors in ZnO nanobelts
Authors: Wan Qing , Huang Jin , Lu Aixia , Wang Taihong
Published: September 2008

The authors report the electrical transport properties of an individual degenerately In-doped ZnO (ZnO:In) nanobelts. The room temperature resistivity and electron concentration of the ZnO:In nanobelts are found to be 8.9×10−4 Ω cm and 1.17×1020 cm−3, respectively. The temperature dependent resistivity of the ZnO:In nanobelts agrees well with the Bloch–Grüneisen theory due to the electron-acoustic phonon scattering mechanism. A high failure-current density of 7.4×106 A/cm2 is measured because of the single-crystalline metallic structure.
Small scale lateral superlattices in two-dimensional electron gases prepared by diblock copolymer masks
Authors: Hugger S. , Heinzel T. , Thurn-Albrecht T.
Published: September 2008

A poly(styrene-block-methylmethacrylate) diblock copolymer in the hexagonal cylindrical phase has been used as a mask for preparing a periodic gate on top of a GaAs/AlxGa1−xAs heterostructure. A superlattice period of 43 nm could be imposed on the two-dimensional electron gas. Transport measurements show a characteristic positive magnetoresistance around zero magnetic field, which we interpret as a signature of electron motion guided by the superlattice potential.
GLD2 poly(A) polymerase is required for long-term memory
Authors: Kwak Jae Eun , Drier Eric , Barbee Scott A. , Ramaswami Mani , Yin Jerry C. P. , Wickens Marvin
Published: September 2008

The formation of long-term memory is believed to require translational control of localized mRNAs. In mammals, dendritic mRNAs are maintained in a repressed state and are activated upon repetitive stimulation. Several regulatory proteins required for translational control in early development are thought to be required for memory formation, suggesting similar molecular mechanisms. Here, using
Drosophila
, we identify the enzyme responsible for poly(A) elongation in the brain and demonstrate that its activity is required specifically for long-term memory. These findings provide strong evidence that cytoplasmic polyadenylation is critical for memory formation, and that GLD2 is the enzyme responsible.
A systematic methodology for proteome-wide identification of peptides inhibiting the proliferation and migration of endothelial cells
Authors: Karagiannis Emmanouil D. , Popel Aleksander S.
Published: September 2008

We introduce a systematic computational methodology based on bioinformatics that has enabled us to identify and classify >120 endogenous peptide inhibitors of endothelial cell proliferation and migration. These peptides are derived from members of the type IV collagen, thrombospondin, and CXC chemokine protein families, as well as somatotropin hormones, serpins, and various kringle-containing proteins. Their activity in suppressing the proliferation and migration of endothelial cellsin vitroprovides proof of principle for the validity of this computational method. Interestingly, some of the peptides are derived from proteins known to be proangiogenic. By performing receptor neutralization studies, we have identified receptors to which these peptides bind. On the basis of this receptor-binding information, we evaluated several examples of peptide-based combinatorial screening strategies. In some cases, this combinatorial screening identified strong synergism between peptides. The current work provides a guideline for a computational-based peptidomics approach for the discovery of endogenous bioactive peptides.
High Myc pathway activity and low stage of neuronal differentiation associate with poor outcome in neuroblastoma
Authors: Fredlund Erik , Ringnér Markus , Maris John M. , Påhlman Sven
Published: September 2008

The childhood cancer neuroblastoma arises in the developing sympathetic nervous system and is a genotypically and phenotypically heterogeneous disease. Prognostic markers of poor survival probability include amplification of the
MYCN
oncogene and an undifferentiated morphology. Whereas these features discriminate high- from low-risk patients with precision, identification of poor outcome low- and intermediate-risk patients is more challenging. In this study, we analyze two large neuroblastoma microarray datasets using
a priori
-defined gene expression signatures. We show that differential overexpression of Myc transcriptional targets and low expression of genes involved in sympathetic neuronal differentiation predicts relapse and death from disease. This was evident not only for high-risk patients but was also robust in identifying groups of poor prognosis patients who were otherwise judged to be at low- or intermediate-risk for adverse outcome. These data suggest that pathway-specific gene expression profiling might be useful in the clinic to adjust treatment strategies for children with neuroblastoma.
MAVS and MyD88 are essential for innate immunity but not cytotoxic T lymphocyte response against respiratory syncytial virus
Authors: Bhoj Vijay G. , Sun Qinmiao , Bhoj Elizabeth J. , Somers Cynthia , Chen Xiang , Torres Juan-Pablo , Mejias Asuncion , Gomez Ana M. , Jafri Hasan , Ramilo Octavio , Chen Zhijian J.
Published: September 2008

Infection by RNA viruses is detected by the host through Toll-like receptors or RIG-I-like receptors. Toll-like receptors and RIG-I-like receptors signal through the adaptors MyD88 and MAVS, respectively, to induce type I IFNs (IFN-I) and other antiviral molecules, which are thought to be essential for activating the adaptive immune system. We investigated the role of these adaptors in innate and adaptive immune responses against respiratory syncytial virus (RSV), a common human pathogen. Deletion ofMavsabolished the induction of IFN-I and other proinflammatory cytokines by RSV. Genome-wide expression profiling in the lung showed that the vast majority of RSV-induced genes depended on MAVS. AlthoughMyd88deficiency did not affect most RSV-induced genes, mice lacking both adaptors harbored a higher and more prolonged viral load and exhibited more severe pulmonary disease than those lacking either adaptor alone. Surprisingly,Myd88−/−Mavs−/−mice were able to activate a subset of pulmonary dendritic cells that traffic to the draining lymph node in response to RSV. These mice subsequently mounted a normal cytotoxic T-lymphocyte response and demonstrated delayed but effective viral clearance. These results provide an example of a normal and effective adaptive immune response in the absence of innate immunity mediated by MAVS and MyD88.
A porphyrin complex of Gold(I): (Phosphine)gold(I) azides as cation precursors
Authors: Partyka David V. , Robilotto Thomas J. , Zeller Matthias , Hunter Allen D. , Gray Thomas G.
Published: September 2008

A silver- and Brönsted acid-free protocol for generating the (tricyclohexylphosphine)gold(I) cation from the corresponding azide complexes is disclosed. The gold(I) cations so liberated are trapped by complexation with octaethylporphyrin. The first structurally authenticated gold(I) porphyrin complex crystallizes with formula C
72
H
112
Au
2
F
12
N
4
P
2
Sb
2
, space group
C
2/
c
,
a
= 21.388 (4),
b
= 19.679 (4),
c
= 19.231 (3) Å; β = 111.030 (3)°. Solution spectroscopic studies indicate that the di-gold complex fragments on dissolution in organic solvents. Approximate density-functional theory calculations find an electrostatic origin for the binding of two gold(I) centers to the unprotonated nitrogen atoms, despite greater orbital density on the porphyrin
meso
carbons.
Transcriptional impact of Aire varies with cell type
Authors: Guerau-de-Arellano Mireia , Mathis Diane , Benoist Christophe
Published: September 2008

Aire promotes T cell tolerance by inducing the expression of a broad swath of genes encoding peripheral tissue antigens (PTAs) in medullary epithelial cells (MECs) of the thymus. The exact mechanism used in inducing this ectopic transcription remains obscure. To address this issue, we generated transgenic mice expressing Aire in pancreatic islet β cells. Gene-expression profiling of such islets revealed that Aire can have a significant impact on transcription in these cells, mainly inducing, but also repressing, transcript levels in a manner comparable with its influence on MECs. The exact transcripts affected differed in MECs and β cells, with limited overlap between the two sets of Aire-modulated genes. We propose that Aire promotes ectopic gene expression by a generic mechanism that does not depend on any particular characteristics or transcription mechanisms operating in MECs, whereas the cellular environment does govern which genes are actually susceptible to Aire regulation.
Calculated interactions of a nitro group with aromatic rings of crystalline picryl bromide
Authors: Huang Lulu , Massa Lou , Karle Jerome
Published: September 2008

Several crystalline polymorphs have been discovered for picryl bromide. Among the several forces that control the formation of such polymorphs are the interactions among the nitro groups and phenyl rings of those crystals. Although there are >300 structures to be found in the Cambridge Structural Database displaying the nitro-phenyl interaction, nonetheless this interesting, and apparently important, interaction, seems not to have been discussed within any of the papers reporting the structures. In this article, quantum calculations are reported that assess the strength of these nitro-phenyl interactions within a crystal of picryl bromide. The rather flat molecules of picryl bromide are arranged in layered planes within the crystal, and we examine the attractive interactions that occur within a given plane, and between adjacent planes. Calculations of Hartree Fock and Møller Plesset perturbation theory carried to a second-order expansion are used. Both quantum mechanical approximations are implemented with 6–31G* basis functions.
Initial experience of 3-tesla apparent diffusion coefficient values in characterizing squamous cell carcinomas of the head and neck
Authors: Srinivasan A. , Dvorak R. , Rohrer S. , Mukherji S.K.
Published: September 2008

Background: With the increased clinical use of 3-Tesla (3T) magnets, it becomes important to identify the potential applications of advanced magnetic resonance (MR) imaging techniques such as diffusion-weighted imaging in head and neck pathologies.

Purpose: To establish the 3T apparent diffusion coefficient (ADC) values for normal neck structures, and to examine the utility of ADC values in distinguishing head and neck squamous cell carcinomas (HNSCC) from normal neck anatomy.

Material and Methods: 3T diffusion-weighted imaging was performed on 10 normal volunteers and 10 patients with known HNSCC. In the volunteers, mean ADC was calculated in the parotid gland, submandibular gland, base of the tongue, pterygoid muscle, masseter muscle, paraspinal muscles, true vocal cord, thyroid gland, thyroid cartilage, cricoid cartilage, and lymph nodes. The mean tumor ADC value was calculated from the 10 patients with HNSCC and compared with the normal ADC values from various neck structures.

Results: The mean ADC value measured in the HNSCC was 1.101 (±0.214)×10−3mm2/s. This was significantly lower than ADC values of paraspinal muscles, pterygoid muscle, masseter muscle, thyroid gland, and base of the tongue ( P=0.0006, 0.0002, 0.0001, 0.001, and 0.002, respectively). The tumor ADC values were not significantly different from ADC values of parotid and submandibular glands ( P=0.057 and 0.14, respectively).

Conclusion: 3T ADC values show potential for distinguishing HNSCC from normal extracranial head and neck structures.
More is Still not Better: Testing the Perturbation Model of Temporal Reference Memory across Different Modalities and Tasks
Authors: Ogden Ruth S. , Jones Luke A.
Published: September 2008

The ability of the perturbation model (Jones & Wearden, 2003) to account for reference memory function in a visual temporal generalization task and auditory and visual reproduction tasks was examined. In all tasks the number of presentations of the standard was manipulated (1, 3, or 5), and its effect on performance was compared. In visual temporal generalization the number of presentations of the standard did not affect the number of times the standard was correctly identified, nor did it affect the overall temporal generalization gradient. In auditory reproduction there was no effect of the number of times the standard was presented on mean reproductions. In visual reproduction mean reproductions were shorter when the standard was only presented once; however, this effect was reduced when a visual cue was provided before the first presentation of the standard. Whilst the results of all experiments are best accounted for by the perturbation model there appears to be some attentional benefit to multiple presentations of the standard in visual reproduction.
Short Article: The Hebb Repetition Effect as a Laboratory Analogue of Novel Word Learning
Authors: Szmalec Arnaud , Duyck Wouter , Vandierendonck André , Mata Ariadna Barberá , Page Mike P. A.
Published: September 2008

The present study tests the hypothesis that a common ordering mechanism underlies both short-term serial recall of verbal materials and the acquisition of novel long-term lexical representations, using the Hebb repetition effect. In the first experiment, participants recalled visually presented nonsense syllables following a typical Hebb effect learning protocol. Replicating the Hebb repetition effect, we observed improved recall for repeated sequences of syllables. In the second experiment, the same participants performed an auditory lexical decision task, which included nonwords that were constructed from the syllables used in the first experiment. We observed inhibited rejection of nonwords that were composed of the repeated Hebb sequences, compared to nonwords that were built from nonrepeated filler sequences. This suggests that a long-term phonological lexical representation developed during Hebb learning. Accordingly, the relation between immediate serial recall and word learning is made explicit by arguing that the Hebb repetition effect is a laboratory analogue of naturalistic vocabulary acquisition.
The regulatory framework for marine dredging indicators and their operational efficiency within the UK: a possible model for other nations?
Authors: Bayer Elizabeth , Barnes Richard A. , Rees Hubert L.
Published: September 2008

Bayer, E., Barnes, R. A., and Rees, H. L. 2008. The regulatory framework for marine dredging indicators and their operational efficiency within the UK: a possible model for other nations? – ICES Journal of Marine Science, 65: 1402–1406. The use of indicators within marine policy and legislation is a developing phenomenon worldwide. As governments begin to take a more holistic approach to marine management, it is inevitable that economic and social goals will increasingly become enshrined in environmental regulations. Consequently, it is imperative to reach an understanding as to how scientific, economic, and social goals are interconnected, and how they influence indicator development. Arguably, a more integrated framework is needed to provide policy-makers and legislators with a coherent approach to applying marine indicators within the context of sustainable development. We examine a variety of indicators used in support of the environmental management of the UK marine aggregate-extraction industry and discuss the current UK regulatory framework in relation to the requirements of two EC directives. Additionally, we explore the depth to which interfacing occurs between various policy goals (i.e. scientific, social, economic, and legal). The study highlights the importance of good communication between the various government agencies and disciplines to better achieve sustainable-development objectives. If effective interfacing can be achieved, with scientific aims properly embedded within policy and legislative agendas, then the UK could provide a useful regulatory model for other Member States.
NAI2 Is an Endoplasmic Reticulum Body Component That Enables ER Body Formation in Arabidopsis thaliana
Authors: Yamada Kenji , Nagano Atsushi J. , Nishina Momoko , Hara-Nishimura Ikuko , Nishimura Mikio
Published: September 2008

Plants develop various endoplasmic reticulum (ER)–derived structures, each of which has specific functions. The ER body found in Arabidopsis thaliana is a spindle-shaped structure that specifically accumulates high levels of PYK10/BGLU23, a β-glucosidase that bears an ER-retention signal. The molecular mechanisms underlying the formation of the ER body remain obscure. We isolated an ER body–deficient mutant in Arabidopsis seedlings that we termed nai2. The NAI2 gene (At3g15950) encodes a member of a unique protein family that is only found in the Brassicaceae. NAI2 localizes to the ER body, and a reduction in NAI2 gene expression elongates ER bodies and reduces their numbers. NAI2 deficiency does not affect PYK10 mRNA levels but reduces the level of PYK10 protein, which becomes uniformly diffused throughout the ER. NAI1, a transcription factor responsible for ER body formation, regulates NAI2 gene expression. These observations indicate that NAI2 is a key factor that enables ER body formation and the accumulation of PYK10 in ER bodies of Arabidopsis. Interestingly, ER body–like structures are also restricted to the Brassicales, including the Brassicaceae. NAI2 homologs may have evolved specifically in Brassicales for the purpose of producing ER body–like structures.
Determination of average carbon number of petroleum waxes by X-ray diffraction
Authors: Kumar Sanat , Srivastava S. P. , Khan H. U.
Published: September 2008

Eight petroleum waxes, both paraffin as well as microcrystalline, have been analysed by X-ray diffraction. The average carbon number has been estimated by the long-range ordering observed in the diffractograms of these waxes. The average carbon number has also been determined following the standard gas chromatographic (GC) method. The results obtained by X-ray diffractometry compare well with those obtained by the GC method. The former method also permits determination of the average carbon number of high melting point waxes, which is otherwise difficult using GC.
Three flavonoids targeting the β‐hydroxyacyl‐acyl carrier protein dehydratase from Helicobacter pylori: Crystal structure characterization with enzymatic inhibition assay
Authors: Zhang Liang , Kong Yunhua , Wu Dalei , Zhang Haitao , Wu Jian , Chen Jing , Ding Jianping , Hu Lihong , Jiang Hualiang , Shen Xu
Published: September 2008

Flavonoids are the major functional components of many herbal and insect preparations and demonstrate varied pharmacological functions including antibacterial activity. Here by enzymatic assay and crystal structure analysis, we studied the inhibition of three flavonoids (quercetin, apigenin, and (S)‐sakuranetin) against the β‐hydroxyacyl‐acyl carrier protein dehydratase from Helicobacter pylori (HpFabZ). These three flavonoids are all competitive inhibitors against HpFabZ by either binding to the entrance of substrate tunnel B (binding model A) or plugging into the tunnel C near the catalytic residues (binding model B) mainly by hydrophobic interaction and hydrogen‐bond pattern. Surrounded by hydrophobic residues of HpFabZ at both positions of models A and B, the methoxy group at C‐7 of (S)‐sakuranetin seems to play an important role for the inhibitor's binding to HpFabZ, partly responsible for the higher inhibitory activity of (S)‐sakuranetin than those of quercetin and apigenin against HpFabZ (IC50 in μM: (S)‐sakuranetin, 2.0 ± 0.1; quercetin: 39.3 ± 2.7; apigenin, 11.0 ± 2.5). Our work is expected to supply useful information for understanding the potential antibacterial mechanism of flavonoids.
Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases
Authors: Brucet Marina , Querol‐Audí Jordi , Bertlik Kamila , Lloberas Jorge , Fita Ignacio , Celada Antonio
Published: September 2008

TREX1 is the major exonuclease in mammalian cells, exhibiting the highest level of activity with a 3′→5′ activity. This exonuclease is responsible in humans for Aicardi‐Goutières syndrome and for an autosomal dominant retinal vasculopathy with cerebral leukodystrophy. In addition, this enzyme is associated with systemic lupus erythematosus. TREX1 belongs to the exonuclease DEDDh family, whose members display low levels of sequence identity, while possessing a common fold and active site organization. For these exonucleases, a catalytic mechanism has been proposed that involves two divalent metal ions bound to the DEDD motif. Here we studied the interaction of TREX1 with the monovalent cations lithium and sodium. We demonstrate that these metals inhibit the exonucleolytic activity of TREX1, as measured by the classical gel method, as well as by a new technique developed for monitoring the real‐time exonuclease reaction. The X‐ray structures of the enzyme in complex with these two cations and with a nucleotide, a product of the exonuclease reaction, were determined at 2.1 Å and 2.3 Å, respectively. A comparison with the structures of the active complexes (in the presence of magnesium or manganese) explains that the inhibition mechanism is caused by the noncatalytic metals competing with distinct affinities for the two metal‐binding sites and inducing subtle rearrangements in active centers. Our analysis also reveals that a histidine residue (His124), highly conserved in the DEDDh family, is involved in the activity of TREX1, as confirmed by mutational studies. Our results shed further light on the mechanism of activity of the DEDEh family of exonucleases.
Refolding and simultaneous purification by three‐phase partitioning of recombinant proteins from inclusion bodies
Authors: Raghava Smita , Barua Bipasha , Singh Pradeep K. , Das Mili , Madan Lalima , Bhattacharyya Sanchari , Bajaj Kanika , Gopal B. , Varadarajan Raghavan , Gupta Munishwar N.
Published: September 2008

Many recombinant eukaryotic proteins tend to form insoluble aggregates called inclusion bodies, especially when expressed in Escherichia coli. We report the first application of the technique of three‐phase partitioning (TPP) to obtain correctly refolded active proteins from solubilized inclusion bodies. TPP was used for refolding 12 different proteins overexpressed in E. coli. In each case, the protein refolded by TPP gave either higher refolding yield than the earlier reported method or succeeded where earlier efforts have failed. TPP‐refolded proteins were characterized and compared to conventionally purified proteins in terms of their spectral characteristics and/or biological activity. The methodology is scaleable and parallelizable and does not require subsequent concentration steps. This approach may serve as a useful complement to existing refolding strategies of diverse proteins from inclusion bodies.
Preventing serpin aggregation: The molecular mechanism of citrate action upon antitrypsin unfolding
Authors: Pearce Mary C. , Morton Craig J. , Feil Susanne C. , Hansen Guido , Adams Julian J. , Parker Michael W. , Bottomley Stephen P.
Published: September 2008

The aggregation of antitrypsin into polymers is one of the causes of neonatal hepatitis, cirrhosis, and emphysema. A similar reaction resulting in disease can occur in other human serpins, and collectively they are known as the serpinopathies. One possible therapeutic strategy involves inhibiting the conformational changes involved in antitrypsin aggregation. The citrate ion has previously been shown to prevent antitrypsin aggregation and maintain the protein in an active conformation; its mechanism of action, however, is unknown. Here we demonstrate that the citrate ion prevents the initial misfolding of the native state to a polymerogenic intermediate in a concentration‐dependent manner. Furthermore, we have solved the crystal structure of citrate bound to antitrypsin and show that a single citrate molecule binds in a pocket between the A and B β‐sheets, a region known to be important in maintaining antitrypsin stability.
The effects of macromolecular crowding on the mechanical stability of protein molecules
Authors: Yuan Jian‐Min , Chyan Chia‐Lin , Zhou Huan‐Xiang , Chung Tse‐Yu , Peng Haibo , Ping Guanghui , Yang Guoliang
Published: September 2008

Macromolecular crowding, a common phenomenon in the cellular environments, can significantly affect the thermodynamic and kinetic properties of proteins. A single‐molecule method based on atomic force microscopy (AFM) was used to investigate the effects of macromolecular crowding on the forces required to unfold individual protein molecules. It was found that the mechanical stability of ubiquitin molecules was enhanced by macromolecular crowding from added dextran molecules. The average unfolding force increased from 210 pN in the absence of dextran to 234 pN in the presence of 300 g/L dextran at a pulling speed of 0.25 μm/sec. A theoretical model, accounting for the effects of macromolecular crowding on the native and transition states of the protein molecule by applying the scaled‐particle theory, was used to quantitatively explain the crowding‐induced increase in the unfolding force. The experimental results and interpretation presented could have wide implications for the many proteins that experience mechanical stresses and perform mechanical functions in the crowded environment of the cell.
Taking the stress out of blood collection: comparison of field blood‐sampling techniques for analysis of baseline corticosterone
Authors: Arnold Jennifer M. , Oswald Stephen A. , Voigt Christian C. , Palme Rupert , Braasch Alexander , Bauch Christina , Becker Peter H.
Published: September 2008

Many ecological studies use stress hormones to assess the condition, health or disturbance levels of wild organisms. Common blood sampling protocols for this research involve trapping individuals and taking blood within three minutes to obtain a “baseline” for analysis of stress hormones (“conventional method”). In some situations it may be difficult to get an accurate measure of baseline values; therefore, alternative sampling techniques may be preferable. We compared corticosterone levels in samples taken via a newly developed, minimally invasive blood sampling technique with corticosterone levels in blood taken via the conventional method. We collected samples from incubating adult common terns Sterna hirundo via blood sucking bugs (Heteroptera, Triatominae) contained in “dummy eggs” (“bug method”) and compared measured corticosterone concentrations to concentrations in blood taken from the same birds using the conventional method. We found no significant differences in mean or variance of baseline corticosterone levels between samples collected via the different methods. This suggests that the bug method offers a viable alternative for hormone sampling.
Cloacal microbial communities of female spotted towheesPipilo maculatus: microgeographic variation and individual sources of variability
Authors: Klomp Jennifer E. , Murphy Michael T. , Smith Sarah Bartos , McKay Jenny E. , Ferrera Isabella , Reysenbach Anna‐Louise
Published: September 2008

We used Polymerase Chain Reaction (PCR) amplification of 16S rRNA genes and Denaturing Gradient Gel Electrophoresis (DGGE) to describe the microbial communities present in the cloacae of spotted towheesPipilo maculatus. Our goals were to quantify bacterial diversity of breeding females, describe microgeographic variation of cloacal communities in a network of four urban parks in Portland, OR, and evaluate the degree to which microbial species richness varied with individual female characteristics (age, size, and condition). We detected 57 Operational Taxonomic Units (OTUs) in 46 towhees, but most OTUs showed a relatively low prevalence. Discriminant function analysis correctly classified 69.6% of towhees to their park of origin based on the presence or absence of five OTUs. Parks thus had unique “microbial signatures”. The presence or absence of specific OTUs was not associated with a female's age, but a general linear models analysis established that OTU richness was greatest among females with short tails, narrow bills, and with the exception of one individual, among relatively heavy birds. We speculate that the microgeographic differences in cloacal microbial community structure may exist due to differences in anthropogenic influences among parks. The explanations for the negative relationship between microbial richness and flight feather length, but positive relationship between microbial richness and body condition are unclear, but may reflect the different time frames over which feather growth and body mass are determined.
Molecular phylogenetics and diversification within one of the most geographically variable bird species complexesPachycephala pectoralis/melanura
Authors: Jønsson Knud A. , Bowie Rauri C. K. , Moyle Robert G. , Christidis Les , Filardi Christopher E. , Norman Janette A. , Fjeldså Jon
Published: September 2008

The golden‐mangrove whistler complexPachycephala pectoralis/melanurais, with 66 named populations, described as the most complex avian example of geographic variation in the World. It represents a well‐known example of niche differentiation where one speciesP. pectoralisis found on faunistically rich larger islands (and mainland) and the otherP. melanurais confined to adjacent, faunistically poor islets. Except for a comparison of some Solomon Island populations, the relationships among these taxa have not been tested using molecular data. Here we combine a dense taxon sampling (22 populations of 12 named taxa distributed east of New Guinea and in Australia), with molecular data (two nuclear and two mitochondrial markers) to unravel more of the evolutionary history behind the golden whistler complex. In particular we examine relationships betweenPachycephala melanura, and the very similar‐lookingP. citreogaster(Bismarcks Islands) andP. pectoralis(Australia). We demonstrate that a well‐supported group of golden whistlers inhabit the Bismarck Islands and that several small islets in the immediate vicinity are inhabited by another monophyletic group consisting ofP. melanura, mangrove golden whistler.
Independent evolutionary reductions of the phallus in basal birds
Authors: Brennan Patricia L. R. , Birkhead Tim R. , Zyskowski Kristof , Van Der Waag Jessica , Prum Richard O.
Published: September 2008

Despite a long history of anatomical studies in birds, the genitalia of most avian species remain undescribed. Birds are the only vertebrate taxon with internal fertilization where an intromittent phallus has been lost in most species. Studying the anatomical transitions of the avian phallus in those species where it is still present, allows us to test evolutionary hypotheses of why the phallus was lost in the ancestor of modern birds. As part of an anatomical survey of the evolution of avian phallus morphology, we have examined some avian species whose genitalia have not been described. Previously, there were only two known events of phallus reduction in birds: one transition from intromittent to non‐intromittent in the Galliformes, and a complete loss of phallic structures in the ancestor of Neoaves. Here we report three additional cases of phallus reduction in birds: a transition from intromittent to non‐intromittent phallus in Tinamiformes (Crypturellus, Tinamidae), the presence of a non‐intromittent phallus inAlectura(Megapodidae), and a complete loss of the phallus inLeipoa(Megapodidae). In addition, we report on the unique morphology of theCrypturellusnon‐intromittent phallus. These new records of phallus reduction highlight the dynamic nature of phallus evolution in birds. Our findings provide evidence against the hypothesis that the phallus in birds is maintained to insure paternity in taxa with exclusive male parental care, since both groups where we report phallus reduction provide predominately male‐only care.
Irritable bowel syndrome and dyspepsia among women veterans: prevalence and association with psychological distress
Authors: SAVAS L. S. , WHITE D. L. , WIEMAN M. , DACI K. , FITZGERALD S. , LADAY SMITH S. , TAN G. , GRAHAM D. P. , CULLY J. A. , EL‐SERAG H. B.
Published: September 2008

Background  The burden of functional GI disorders and their associations with psychological distress in women veterans is unclear.

Aim  To examine 1‐year prevalence of irritable bowel syndrome (IBS) and dyspepsia symptoms and their associations with anxiety, depression and post‐traumatic stress disorder (PTSD) among women veterans receiving primary care at a Veteran Affairs Medical Center Women’s Clinic.

Methods  Irritable bowel syndrome, dyspepsia and psychological distress were assessed using the validated self‐administered Bowel Disorder Questionnaire, the Beck Depression and Anxiety Inventories, as well as the Mississippi Scale for Combat‐Related Post‐Traumatic Stress Disorder Questionnaire.

Results  We enrolled 248 women (84% participation rate). Ninety‐three (38%) reported IBS and 51 (21%) dyspepsia symptoms. Women with IBS and dyspepsia reported higher mean scores of anxiety (IBS: 24 vs. 12, P < 0.0005 and dyspepsia: 26 vs. 12, P < 0.0005), depression (IBS: 22 vs. 11, P = 0.0005 and dyspepsia: 23 vs. 11, P < 0.0005) and PTSD (IBS: 87 vs. 69, P < 0.001 and dyspepsia: 86 vs. 69, P < 0.0005). Age‐ and ethnicity‐adjusted logistic regression analyses showed a 3‐ to 46‐fold increase in odds of IBS and dyspepsia among women with anxiety, depression or PTSD.

Conclusion  Women veterans have high prevalence of IBS and dyspepsia symptoms, both of which are highly associated with presence of depression, anxiety and PTSD.
The challenge of respiratory virus infections in hematopoietic cell transplant recipients
Authors: Boeckh Michael
Published: September 2008

Respiratory virus infections in hematopoietic cell transplant (HCT) recipients are a major cause of morbidity and mortality. While respiratory syncytial virus (RSV), human metapneumonvirus, parainfluenzaviruses, and influenza viruses are well known for their potential to cause fatal pneumonia, information has only recently emerged regarding the significance of the newly discovered viruses, such as human coronaviruses NL63 and HKU1, and human bocavirus. Lymphopenia seems to be the most important risk factor for progression to lower respiratory tract disease. Airflow obstruction is another complication of respiratory virus infections after HCT, and data to date indicate this complication may occur following parainfluenza virus and RSV infection. Infection control procedures are key for prevention. Unfortunately, there are no randomized treatment studies, which make the interpretation of the literature on interventions difficult. This article reviews the spectrum of pathogens, epidemiology, risk factors and clinical manifestations of infection, as well as recent advances in diagnostic and clinical management.
Patterns of entry to community‐based services for families with children with developmental disabilities: implications for social work practice
Authors: Hiebert‐Murphy Diane , Trute Barry , Wright Alexandra
Published: September 2008

The purpose of the present study was to understand, from parents' perspectives, the process of entry to community‐based services for children with developmental disabilities and to explore the relationship between patterns of entry and parent‐reported needs and priorities for service. Qualitative interviews were conducted with 43 mothers and 29 fathers of children with developmental disabilities approximately 6 months after the families entered community‐based childhood disability support services in Manitoba, Canada. Analysis of the coded interview data resulted in the identification of three process factors influential in the entry of families to community‐based support services: recognition of problems in child development, formal diagnosis of child disability and linkage between diagnostic services and the community‐based support system. Analysis of these processes identified four patterns of service entry associated with differing family needs for service: early entry, prompt entry, delayed entry and atypical entry. The results can be understood as a typology useful for social workers in the assessment of family needs and priorities at the point of entry to community‐based services.
Thiazolidinediones and antiblastics in primary human anaplastic thyroid cancer cells
Authors: Antonelli Alessandro , Ferrari Silvia Martina , Fallahi Poupak , Berti Piero , Materazzi Gabriele , Minuto Michele , Giannini Riccardo , Marchetti Ivo , Barani Lucio , Basolo Fulvio , Ferrannini Ele , Miccoli Paolo
Published: September 2008

Objective  No study has evaluated the antiproliferative effects of thiazolidinediones and antiblastics in ‘primary cultured human anaplastic thyroid cancer cells’.

Design  Primary anaplastic cells proliferation was evaluated after incubation with increasing concentrations of rosiglitazone or pioglitazone or antiblastics (bleomycin, cisplatin, gemcitabine) by a proliferation assay (WST‐1‐tetrazolium reaction) and cell counting.

Measurements and results  A reduction of proliferation by thiazolidinediones at 1 h (from the start of tetrazolium reaction) [of 11% and 25%, with rosiglitazone, 10 or 20 (P = 0·0001) µM, respectively; of 7% and 17%, with pioglitazone, 10 or 20 (P = 0·0125) µM, respectively], and at 2 h [of 14% and 24%, with rosiglitazone, 10 (P = 0·0043) or 20 (P < 0·0001) µM, respectively; of 9% and 21%, with pioglitazone, 10 (P = 0·0397) or 20 (P = 0·0001) µM, respectively] was shown. No significant thiazolidinediones effect was observed in normal thyroid follicular cells. Bleomycin, cisplatin and gemcitabine significantly (P < 0·0001) inhibited (> 50%) anaplastic cells proliferation. Cell counting confirmed the above mentioned results. Inhibition of proliferation was similar in tumours with or without V600EBRAF mutation, both for thiazolidinediones and antiblastics.

Conclusions  Thiazolidinediones exert an antiproliferative effect in primary cultured human anaplastic carcinoma cells in vitro, such as antiblastics.
Iodine status in pregnancy: role of dietary habits and geographical origin
Authors: Mian Caterina , Vitaliano Pantaleo , Pozza Dina , Barollo Susi , Pitton Mariangela , Callegari Giovanna , Di Gianantonio Elena , Casaro Anna , Acamulli Davide N , Busnardo Benedetto , Mantero Franco , Girelli Maria Elisa
Published: September 2008

Objectives  A study was conducted on iodine status during pregnancy and its dependence on dietary habits, racial and geographical origin, and time since arrival in Italy.

Design and methods  We enrolled 322 consecutive pregnant women: 217 Italians, 62 Eastern Europeans and 43 from Northern and Central Africa. All women completed a food frequency questionnaire on their dietary habits. The urinary iodide concentration (UIC) was determined in spot morning urine samples.

Results  In the group as a whole, the median UIC was 83 µg/l; the UIC was < 50 in 33% and of 150 µg/l or more in 27%; it was significantly lower in Africans and Eastern Europeans than in Italians (medians 45 and 46 vs. 100 µg/l, respectively, P = 0·005). For the foreign women, there was a significant correlation between UIC and time since arrival in Italy (r = 0·22, P = 0·02). A significant link emerged between UIC and cow's milk intake (P = 0·0001). Iodine supplements were used by 40% of the women, and UIC were higher in those who did so than in those who did not (median 103 vs. 75 µg/l, P = 0·03), particularly if the latter did not drink milk (median 98 vs. 42 µg/l, P = 0·01). Multivariate analysis showed that milk was the only variable influencing UIC (OR 1·29, P = 0·0005).

Conclusions  (i) Iodine levels are too low among pregnant women in our region, and particularly in foreign women. (ii) Cow's milk intake is their main source of iodine. (iii) Iodine supplementation is mandatory during pregnancy, particularly for women do not drink milk.
Surface–subsurface water exchange rates along alluvial river reaches control the thermal patterns in an Alpine river network
Authors: ACUÑA V. , TOCKNER K.
Published: September 2008

1. Water temperature is a key characteristic of stream ecosystems that is gaining scientific and managerial relevance as maximum temperatures in aquatic ecosystems increase worldwide.

2. To assess the effect of surface–subsurface water exchange on stream water temperature patterns, four alluvial reaches in the Tagliamento River basin (NE Italy), constrained by geomorphic knickpoints at the upper and lower end, and two to four hyporheic flowpaths within each reach, were continuously studied during summer 2007 and winter 2007–08. Water temperature was continuously monitored at the upstream and downstream knickpoints of the floodplains, as well as at discrete upwelling areas within each reach. Discharge and vertical hydraulic gradient were measured along the alluvial reaches, and the residence time and chemistry of upwelling water were assessed four times during the study.

3. Discharge variation along the study reaches revealed that massive hyporheic exchange occurred in all sites, ranging from 21% in reach 2–52% in reach 1. End member mixing analysis showed little influence of ground water, as almost all upwelling water was freshly infiltrated hyporheic water. Importantly, hyporheic exchange flows shaped surface temperature at the upwelling locations in all study reaches, providing potential thermal refugia for aquatic biota. At sites with highest hyporheic flow rates, net temperature change was also reflected at the floodplain scale.

4. The magnitude of the thermal change along a hyporheic flowpath was not related to the flowpath length but to the estimated222Rn water age. Reduction in the diel thermal amplitude by hyporheic flows rather than net temperature change, reduced temperature extremes. Therefore, restoration activities to create thermal refugia should consider the role of hyporheic flows and enhance the exchange between surface and hyporheic waters.