bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between biaxial stress and free exciton transition in AlN epilayers
Authors: Pantha B. N. , Nepal N. , Al Tahtamouni T. M. , Nakarmi M. L. , Li J. , Lin J. Y. , Jiang H. X.
Published: September 2007

Photoluminescence (PL) spectroscopy and x-ray diffraction measurements were employed to study biaxial strain in AlN epilayers grown on different substrates. X-ray diffraction revealed that AlN epilayers grown on AlN bulk substrates (or homoepilayers) have the same lattice parameters as AlN bulk crystals and are almost strain-free. Compared to the free exciton (FX) transition in an AlN homoepilayer, the FX line was 31meV higher in AlN/sapphire due to a compressive strain and 55 (69)meV lower in AlN∕SiC (AlN∕Si) due to a tensile strain. A linear relationship between the FX transition energy peak position and in-plane stress was obtained, and a value of 45meV∕GPa for the linear coefficient of the stress-induced bandgap shift in AlN epilayers was deduced. The work here establishes PL as another simple and effective method for monitoring the biaxial stress in AlN epilayers.
Optical gain measurements in porous silicon planar waveguides codoped by erbium and ytterbium ions at 1.53μm
Authors: Najar Adel , Charrier Joël , Lorrain Nathalie , Haji Lazhar , Oueslati Mehrezi
Published: September 2007

The on-off optical gain measurements as a function of the pump power were performed on porous silicon planar waveguides codoped by erbium and ytterbium ions. These measurements were obtained for different ratios of Yb concentration to Er concentration. The highest value of the gain was reached when the Yb concentration is three times higher than that of Er at a moderate 980nm pump power value equal to 70mW. Optical losses measurements have been performed on these waveguides and were equal to 2.1dB∕cm and an internal gain of about 6.4dB∕cm was obtained.
Geomagnetic sensor based on giant magnetoelectric effect
Authors: Zhai Junyi , Dong Shuxiang , Xing Zengping , Li Jiefang , Viehland D.
Published: September 2007

Here, the authors report a new type of geomagnetic field sensor based on the giant magnetoelectric effect in Metglas/piezoelectric-fiber laminates that are wrapped with a coil. These sensors can measure quite precisely the value of both the Earth’s magnetic field and its inclination. The geomagnetic field sensor does not require a dc magnetic bias and is driven by a 10mA ac. Highly sensitive dc magnetic field variations of less than 10−9T and angular inclinations of ⩽10−5deg can be detected, potentially offering opportunities for a small global positioning device.
Anisotropy of light extraction from two-dimensional photonic crystal light-emitting diodes
Authors: Lai Chun-Feng , Kuo H. C. , Chao C. H. , Hsueh H. T. , Wang J.-F. T. , Yeh W. Y. , Chi J. Y.
Published: September 2007

Anisotropic light extraction of photonic crystal (PhC) light-emitting diodes in the azimuthal direction has been investigated with an annular structure of triangular PhC lattice. The optical images of the photoluminescence light extraction are obtained with laser excitation. For increasing lattice constant, sixfold symmetric patterns with varying numbers of petals in multiples of six are observed and analyzed. A map of the anisotropy for various lattice constants and numerical apertures is constructed. Several features of light propagations associated with the PhC are observed including the focusing and collimating behaviors.
Nonlinear transport below TC for lateral nanoconstrictions realized in a 100nm GaMnAs epifilm
Authors: Cho Sung Woon , Choi Hyung Kook , Lee Joon Sue , Jeong Diana , Kim Hyung Joon , Hwang Taesoon , Kim Kee Hoon , Park Yun Daniel
Published: September 2007

Electrical transport across lateral geometrical nanoconstrictions realized in 100nm thick GaMnAs epifilms is studied. The constrictions are patterned with the aid of chemical etching techniques, as opposed to plasma-assisted methods. Transport behavior across the constrictions, where domain walls can be formed and pinned, changes from Ohmic to non-Ohmic below temperatures corresponding to epifilm TC for junctions with high resistances. Magnetoresistance measurements across such junctions qualitatively show similar behavior to unpatterned epifilms attributable to anisotropic magnetoresistance. The experimental IV curves are in good agreement with theoretical models accounting for spin flop across a region of high resistance.
The effects of the in-plane momentum on the quantization of nanometer metal-oxide-semiconductor devices due to the difference between the effective masses of silicon and gate oxide
Authors: Mao Ling-Feng
Published: September 2007

By taking the coupling effects caused by the difference between the effective masses of silicon and gate oxide into consideration, the effects of in-plane momentum on the quantization in the electron motion perpendicular to the Si∕SiO2 interface of a nanometer metal-oxide-semiconductor device with p-type silicon substrate are described. The results show that the coupling, which largely affects the quantization of the perpendicular motion of channel electrons in the inversion layer, should be considered when the in-plane momentum of channel electrons is high.
Fabrication of complex nanoscale structures on various substrates
Authors: Han Kang-Soo , Hong Sung-Hoon , Lee Heon
Published: September 2007

Polymer based complex nanoscale structures were fabricated and transferred to various substrates using reverse nanoimprint lithography. To facilitate the fabrication and transference of the large area of the nanostructured layer to the substrates, a water-soluble polyvinyl alcohol mold was used. After generation and transference of the nanostructured layer, the polyvinyl alcohol mold was removed by dissolving in water. A residue-free, UV-curable, glue layer was formulated and used to bond the nanostructured layer onto the substrates. As a result, nanometer scale patterned polymer layers were bonded to various substrates and three-dimensional nanostructures were also fabricated by stacking of the layers.
Ammonia sensitivity of amorphous carbon film/silicon heterojunctions
Authors: Gao Xili , Xue Qingzhong , Hao Lanzhong , Zheng Qingbin , Li Qun
Published: September 2007

The amorphous carbon film/n-Si (a-C∕Si) junctions have been fabricated by magnetron sputtering. The results show that these junctions have good rectifying properties and high ammonia (NH3) gas sensitivity. For a given reverse bias voltage, the resistance of the junction can increase by 100 times rapidly when exposed to NH3 gas. This phenomenon may be attributed to the change of the space charge width of the junction, which is caused by the adsorption of NH3 gas molecules. This study shows that these a-C∕Si junctions have potential application as NH3 gas detect sensors.
Can fairy shrimps (Crustacea: Anostraca) structure zooplankton communities in temporary ponds?
Authors: Sánchez Beatriz , Angeler David G.
Published: September 2007

Predation and competition are recognised as strong community structuring forces, and these processes are often mediated by keystone species. However, the role of keystone species in the plankton of temporary wetlands has hardly been evaluated. In the present study, the potential structuring role of fairy shrimps (Anostraca, Branchiopoda) on temporary wetland zooplankton communities was assessed. Dry sediments were collected from randomly chosen temporary ponds in the Campo de Calatrava area (Central Spain), and these were rewetted in outdoor microcosms. Zooplankton community dynamics of three wetlands that lacked fairy shrimps (controls) were contrasted with three wetlands that contained Branchinecta orientalis (G. O. Sars) (treatment). ANOVA analyses showed no significant differences in zooplankton community metrics and in taxonomic groups between the controls and treatments. Analyses of similarity (ANOSIM) and similarity percentages (SIMPER) revealed significant differences and a high degree of community dissimilarity within and between treatment levels. The high degree of environmental variability between wetlands compromised the detection of the structuring role of fairy shrimps on zooplankton in the present study. Studies based on manipulative designs could be more appropriate to test for the keystone role of fairy shrimps in temporary wetland food webs. Replicated before-after control-impact (BACI) designs could be especially useful for understanding basic ecological processes and this knowledge could then be used for the development of sound management strategies of ecologically poorly understood temporary ponds.
A mouse model for nonsense mutation bypass therapy shows a dramatic multiday response to geneticin
Authors: Yang Chunmei , Feng Jinong , Song Wenjia , Wang Jicheng , Tsai Becky , Zhang Yunwu , Scaringe William A. , Hill Kathleen A. , Margaritis Paris , High Katherine A. , Sommer Steve S.
Published: September 2007

Aminoglycosides can bypass nonsense mutations and are the prototypic agents for translational bypass therapy (TBT). Initial results demonstrate the need for more potent drugs and an
in vivo
model system for quantitative assessment of TBT. Herein, we present an
in vivo
system for evaluating the efficacy of premature stop codon management therapies:
in vivo
quantitative stop codon management repli-sampling TBT efficacy assay (IQSCMaRTEA). Application of IQSCMaRTEA reveals that geneticin is much more efficacious
in vivo
than gentamicin. Treatment with geneticin elicits a multiday response, and residual
F9
antigen can be detected after 3 weeks. These data demonstrate the utility of IQSCMaRTEA for evaluating drugs that bypass nonsense mutations. In addition, IQSCMaRTEA may be helpful for testing inhibitors of nonsense-mediated decay, as stop codon management therapy will sometimes require inhibition of nonsense-mediated decay and translational bypass of the nonsense mutation. Furthermore, geneticin, its metabolites, or better tolerated analogues should be evaluated as a general treatment with multiday response for severe genetic disease caused by nonsense mutation.
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding
Authors: Daidone Isabella , Ulmschneider Martin B. , Di Nola Alfredo , Amadei Andrea , Smith Jeremy C.
Published: September 2007

Recent work has shown that the nature of hydration of pure hydrophobic surfaces changes with the length scale considered: water hydrogen-bonding networks adapt to small exposed hydrophobic species, hydrating or “wetting” them at relatively high densities, whereas larger hydrophobic areas are “dewetted” [Chandler D (2005),
Nature
29:640–647]. Here we determine whether this effect is also present in peptides by examining the folding of a β-hairpin (the 14-residue amyloidogenic prion protein H1 peptide), using microsecond time-scale molecular dynamics simulations. Two simulation models are compared, one explicitly including the water molecules, which may thus adapt locally to peptide configurations, and the other using a popular continuum approximation, the generalized Born/surface area implicit solvent model. The results obtained show that, in explicit solvent, peptide conformers with high solvent-accessible hydrophobic surface area indeed also have low hydration density around hydrophobic residues, whereas a concomitant higher hydration density around hydrophilic residues is observed. This dewetting effect stabilizes the fully folded β-hairpin state found experimentally. In contrast, the implicit solvent model destabilizes the fully folded hairpin, tending to cluster hydrophobic residues regardless of the size of the exposed hydrophobic surface. Furthermore, the rate of the conformational transitions in the implicit solvent simulation is almost doubled with respect to that of the explicit solvent. The results suggest that dehydration-driven solvent exposure of hydrophobic surfaces may be a significant factor determining peptide conformational equilibria.
Community-based conservation in a globalized world
Authors: Berkes Fikret
Published: September 2007

Communities have an important role to play in biodiversity conservation. However, community-based conservation as a panacea, like government-based conservation as a panacea, ignores the necessity of managing commons at multiple levels, with vertical and horizontal interplay among institutions. The study of conservation in a multilevel world can serve to inform an interdisciplinary science of conservation, consistent with the Convention on Biological Diversity, to establish partnerships and link biological conservation objectives with local development objectives. Improving the integration of conservation and development requires rethinking conservation by using a complexity perspective and the ability to deal with multiple objectives, use of partnerships and deliberative processes, and learning from commons research to develop diagnostic tools. Perceived this way, community-based conservation has a role to play in a broad pluralistic approach to biodiversity protection: it is governance that starts from the ground up and involves networks and linkages across various levels of organization. The shift of attention to processes at multiple levels fundamentally alters the way in which the governance of conservation development may be conceived and developed, using diagnostics within a pluralistic framework rather than a blueprint approach.
A diagnostic approach for going beyond panaceas
Authors: Ostrom Elinor
Published: September 2007

The articles in this special feature challenge the presumption that scholars can make simple, predictive models of social–ecological systems (SESs) and deduce universal solutions, panaceas, to problems of overuse or destruction of resources. Moving beyond panaceas to develop cumulative capacities to diagnose the problems and potentialities of linked SESs requires serious study of complex, multivariable, nonlinear, cross-scale, and changing systems. Many variables have been identified by researchers as affecting the patterns of interactions and outcomes observed in empirical studies of SESs. A step toward developing a diagnostic method is taken by organizing these variables in a nested, multitier framework. The framework enables scholars to organize analyses of how attributes of (i) a resource system (e.g., fishery, lake, grazing area), (ii) the resource units generated by that system (e.g., fish, water, fodder), (iii) the users of that system, and (iv) the governance system jointly affect and are indirectly affected by interactions and resulting outcomes achieved at a particular time and place. The framework also enables us to organize how these attributes may affect and be affected by larger socioeconomic, political, and ecological settings in which they are embedded, as well as smaller ones. The framework is intended to be a step toward building a strong interdisciplinary science of complex, multilevel systems that will enable future diagnosticians to match governance arrangements to specific problems embedded in a social–ecological context.
Beyond panaceas in water institutions
Authors: Meinzen-Dick Ruth
Published: September 2007

The past 50 years of water policy have seen alternating policies emphasize the state, user groups, or markets as essential for solving water-management problems. A closer look reveals that each of these solutions has worked in some places but failed in others, especially when policies attempted to spread them over too many countries and diverse situations. A study of the variable performances of user groups for canal irrigation in India illustrates the factors that affect institutional performance. Research that identifies the critical factors affecting irrigation institutions can lead to sustainable approaches that are adapted to specific contextual attributes.
Drivers of reforestation in human-dominated forests
Authors: Nagendra Harini
Published: September 2007

Tropical forest habitat continues to decline globally, with serious negative consequences for environmental sustainability. The small mountain country of Nepal provides an excellent context in which to examine trajectories of forest-cover change. Despite having experienced large-scale forest clearing in the past, significant reforestation has taken place in recent years. The range of biophysical and ecological environments and diversity of tenure arrangements provide us with a context with sufficient variation to be able to derive insight into the impact of a range of hypothesized drivers of forest change. This article draws on a dataset of 55 forests from the middle hills and Terai plains of Nepal to examine the factors associated with forest clearing or regeneration. Results affirm the central importance of tenure regimes and local monitoring for forest regrowth. In addition, user group size per unit of forest area is an important, independent explanator of forest change. These variables also can be associated with specific practices that further influence forest change such as the management of social conflict, adoption of new technologies to reduce pressure on the forest, and involvement of users in forest maintenance activities. Such large-N, comparative studies are essential if we are to derive more complex, nuanced, yet actionable frameworks that help us to plan better policies for the management of natural resources.
Solution structure of the A4 domain of factor XI sheds light on the mechanism of zymogen activation
Authors: Samuel Dharmaraj , Cheng Hong , Riley Paul W. , Canutescu Adrian A. , Nagaswami Chandrasekaran , Weisel John W. , Bu Zimei , Walsh Peter N. , Roder Heinrich
Published: September 2007

Factor XI (FXI) is a homodimeric blood coagulation protein. Each monomer comprises four tandem apple-domain repeats (A1–A4) and a serine protease domain. We report here the NMR solution structure of the A4 domain (residues 272–361), which mediates formation of the disulfide-linked FXI dimer. A4 exhibits characteristic features of the plasminogen apple nematode domain family, including a five-stranded β-sheet flanked by an α-helix on one side and a two-stranded β-sheet on the other. In addition, the solution structure reveals a second α-helix at the C terminus. Comparison with a recent crystal structure of full-length FXI, combined with molecular modeling, suggests that the C-terminal helix is formed only upon proteolytic activation. The newly formed helix disrupts interdomain contacts and reorients the catalytic domains, bringing the active sites into close proximity. This hypothesis is supported by small-angle x-ray scattering and electron microscopy data, which indicate that FXI activation is accompanied by a major change in shape. The results are consistent with biochemical evidence that activated FXI cleaves its substrate at two positions without release of an intermediate.
Metabolic rate does not calibrate the molecular clock
Authors: Lanfear Robert , Thomas Jessica A. , Welch John J. , Brey Thomas , Bromham Lindell
Published: September 2007

Rates of molecular evolution vary widely among lineages, but the causes of this variation remain poorly understood. It has been suggested that mass-specific metabolic rate may be one of the key factors determining the rate of molecular evolution, and that it can be used to derive “corrected” molecular clocks. However, previous studies have been hampered by a paucity of mass-specific metabolic rate data and have been largely limited to vertebrate taxa. Using mass-specific metabolic rate measurements and DNA sequence data for >300 metazoan species for 12 different genes, we find no evidence that mass-specific metabolic rate drives substitution rates. The mechanistic basis of the metabolic rate hypothesis is discussed in light of these findings.
Extracting the hierarchical organization of complex systems
Authors: Sales-Pardo Marta , Guimerà Roger , Moreira André A. , Amaral Luís A. Nunes
Published: September 2007

Extracting understanding from the growing “sea” of biological and socioeconomic data is one of the most pressing scientific challenges facing us. Here, we introduce and validate an unsupervised method for extracting the hierarchical organization of complex biological, social, and technological networks. We define an ensemble of hierarchically nested random graphs, which we use to validate the method. We then apply our method to real-world networks, including the air-transportation network, an electronic circuit, an e-mail exchange network, and metabolic networks. Our analysis of model and real networks demonstrates that our method extracts an accurate multiscale representation of a complex system.
A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration
Authors: Kanda Atsuhiro , Chen Wei , Othman Mohammad , Branham Kari E. H. , Brooks Matthew , Khanna Ritu , He Shirley , Lyons Robert , Abecasis Gonçalo R. , Swaroop Anand
Published: September 2007

Genetic variants at chromosomes 1q31-32 and 10q26 are strongly associated with susceptibility to age-related macular degeneration (AMD), a common blinding disease of the elderly. We demonstrate, by evaluating 45 tag SNPs spanning
HTRA1
,
PLEKHA1
, and predicted gene
LOC387715/ARMS2
, that rs10490924 SNP alone, or a variant in strong linkage disequilibrium, can explain the bulk of association between the 10q26 chromosomal region and AMD. A previously suggested causal SNP, rs11200638, and other examined SNPs in the region are only indirectly associated with the disease. Contrary to previous reports, we show that rs11200638 SNP has no significant impact on
HTRA1
promoter activity in three different cell lines, and
HTRA1
mRNA expression exhibits no significant change between control and AMD retinas. However, SNP rs10490924 shows the strongest association with AMD (
P
= 5.3 × 10
−30
), revealing an estimated relative risk of 2.66 for GT heterozygotes and 7.05 for TT homozygotes. The rs10490924 SNP results in nonsynonymous A69S alteration in the predicted protein LOC387715/ARMS2, which has a highly conserved ortholog in chimpanzee, but not in other vertebrate sequences. We demonstrate that
LOC387715/ARMS2
mRNA is detected in the human retina and various cell lines and encodes a 12-kDa protein, which localizes to the mitochondrial outer membrane when expressed in mammalian cells. We propose that rs10490924 represents a major susceptibility variant for AMD at 10q26. A likely biological mechanism is that the A69S change in the LOC387715/ARMS2 protein affects its presumptive function in mitochondria.
Wnt5a inhibits canonical Wnt signaling in hematopoietic stem cells and enhances repopulation
Authors: Nemeth Michael J. , Topol Lilia , Anderson Stacie M. , Yang Yingzi , Bodine David M.
Published: September 2007

The mechanisms that regulate hematopoietic stem cell (HSC) fate decisions between proliferation and multilineage differentiation are unclear. Members of the Wnt family of ligands that activate the canonical Wnt signaling pathway, which utilizes β-catenin to relay the signal, have been demonstrated to regulate HSC function. In this study, we examined the role of noncanonical Wnt signaling in regulating HSC fate. We observed that noncanonical Wnt5a inhibited Wnt3a-mediated canonical Wnt signaling in HSCs and suppressed Wnt3a-mediated alterations in gene expression associated with HSC differentiation, such as increased expression of
myc
. Wnt5a increased short- and long-term HSC repopulation by maintaining HSCs in a quiescent G
0
state. From these data, we propose that Wnt5a regulates hematopoiesis by the antagonism of the canonical Wnt pathway, resulting in a pool of quiescent HSCs.
Hybrid vigor between native and introduced salamanders raises new challenges for conservation
Authors: Fitzpatrick Benjamin M. , Shaffer H. Bradley
Published: September 2007

Hybridization between differentiated lineages can have many different consequences depending on fitness variation among hybrid offspring. When introduced organisms hybridize with natives, the ensuing evolutionary dynamics may substantially complicate conservation decisions. Understanding the fitness consequences of hybridization is an important first step in predicting its evolutionary outcome and conservation impact. Here, we measured natural selection caused by differential viability of hybrid larvae in wild populations where native California Tiger Salamanders (Ambystoma californiense) and introduced Barred Tiger Salamanders (Ambystoma tigrinum mavortium) have been hybridizing for 50–60 years. We found strong evidence of hybrid vigor; mixed-ancestry genotypes had higher survival rates than genotypes containing mostly native or mostly introduced alleles. Hybrid vigor may be caused by heterozygote advantage (overdominance) or recombinant hybrid vigor (due to epistasis or complementation). These genetic mechanisms are not mutually exclusive, and we find statistical support for both overdominant and recombinant contributions to hybrid vigor in larval tiger salamanders. Because recombinant homozygous genotypes can breed true, a single highly fit genotype with a mosaic of native and introduced alleles may eventually replace the historically pure California Tiger Salamander (listed as Threatened under the U.S. Endangered Species Act). The management implications of this outcome are complex: Genetically pure populations may not persist into the future, but average fitness and population viability of admixed California Tiger Salamanders may be enhanced. The ecological consequences for other native species are unknown.
Specific tumor suppressor function for E2F2 in Myc-induced T cell lymphomagenesis
Authors: Opavsky Rene , Tsai Shih-Yin , Guimond Martin , Arora Anjulie , Opavska Jana , Becknell Brian , Kaufmann Michael , Walton Nathaniel A. , Stephens Julie A. , Fernandez Soledad A. , Muthusamy Natarajan , Felsher Dean W. , Porcu Pierluigi , Caligiuri Michael A. , Leone Gustavo
Published: September 2007

Deregulation of the Myc pathway and deregulation of the Rb pathway are two of the most common abnormalities in human malignancies. Recent
in vitro
experiments suggest a complex cross-regulatory relationship between Myc and Rb that is mediated through the control of E2F. To evaluate the functional connection between Myc and E2Fs
in vivo
, we used a bitransgenic mouse model of Myc-induced T cell lymphomagenesis and analyzed tumor progression in mice deficient for
E2f1
,
E2f2
, or
E2f3
. Whereas the targeted inactivation of
E2f1
or
E2f3
had no significant effect on tumor progression, loss of
E2f2
accelerated lymphomagenesis. Interestingly, loss of a single copy of
E2f2
also accelerated tumorigenesis, albeit to a lesser extent, suggesting a haploinsufficient function for this locus. The combined ablation of
E2f1
or
E2f3
, along with
E2f2
, did not further accelerate tumorigenesis. Myc-overexpressing T cells were more resistant to apoptosis in the absence of
E2f2
, and the reintroduction of E2F2 into these tumor cells resulted in an increase of apoptosis and inhibition of tumorigenesis. These results identify the
E2f2
locus as a tumor suppressor through its ability to modulate apoptosis.
Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors
Authors: Kosinski Cynthia , Li Vivian S. W. , Chan Annie S. Y. , Zhang Ji , Ho Coral , Tsui Wai Yin , Chan Tsun Leung , Mifflin Randy C. , Powell Don W. , Yuen Siu Tsan , Leung Suet Yi , Chen Xin
Published: September 2007

Human colonic epithelial cell renewal, proliferation, and differentiation are stringently controlled by numerous regulatory pathways. To identify genetic programs of human colonic epithelial cell differentiation
in vivo
as well as candidate marker genes that define colonic epithelial stem/progenitor cells and the stem cell niche, we applied gene expression analysis of normal human colon tops and basal crypts by using expression microarrays with 30,000 genes. Nine hundred and sixty-nine cDNA clones were found to be differentially expressed between human colon crypts and tops. Pathway analysis revealed the differential expression of genes involved in cell cycle maintenance and apoptosis, as well as genes in bone morphogenetic protein (BMP), Notch, Wnt, EPH, and MYC signaling pathways. BMP antagonists gremlin 1, gremlin 2, and chordin-like 1 were found to be expressed by colon crypts.
In situ
hybridization and RT-PCR confirmed that these BMP antagonists are expressed by intestinal cryptal myofibroblasts and smooth muscle cells at the colon crypt.
In vitro
analysis demonstrated that gremlin 1 partially inhibits Caco-2 cell differentiation upon confluence and activates Wnt signaling in normal rat intestinal epithelial cells. Collectively, the expression data set provides a comprehensive picture of human colonic epithelial cell differentiation. Our study also suggests that BMP antagonists are candidate signaling components that make up the intestinal epithelial stem cell niche.
Structural determination of wild-type lactose permease
Authors: Guan Lan , Mirza Osman , Verner Gillian , Iwata So , Kaback H. Ronald
Published: September 2007

Here we describe an x-ray structure of wild-type lactose permease (LacY) from
Escherichia coli
determined by manipulating phospholipid content during crystallization. The structure exhibits the same global fold as the previous x-ray structures of a mutant that binds sugar but cannot catalyze translocation across the membrane. LacY is organized into two six-helix bundles with twofold pseudosymmetry separated by a large interior hydrophilic cavity open only to the cytoplasmic side and containing the side chains important for sugar and H
+
binding. To initiate transport, binding of sugar and/or an H
+
electrochemical gradient increases the probability of opening on the periplasmic side. Because the inward-facing conformation represents the lowest free-energy state, the rate-limiting step for transport may be the conformational change leading to the outward-facing conformation.
Financial risk‐taking on “Who Wants to Be a Millionaire”: A comparison between Austria, Germany, and Slovenia
Authors: Daghofer Fedor
Published: September 2007

The aim of the present study was to examine the impact of gender, age, education, and stake on financial risk‐taking in contestants on the television game show “Who Wants to Be a Millionaire.” According to the existing literature on the impact of demographic parameters on financial risk‐taking, it was expected that women should take less risks than men in the low‐stake condition of the game, older contestants should take less risks than their younger counterparts, and contestants with an academic degree should take more risks than contestants without an academic degree. It was also expected that the tendency towards voluntarily quitting the game should increase with increasing stake. In order to test the generality of the obtained results, the study was conducted in three European countries: Austria, Germany, and Slovenia. The total sample comprised 416 Austrian, 331 German, and 199 Slovenian contestants on the television game show “Who Wants to Be a Millionaire.” By means of meta‐analyses it was found that the most important predictor of voluntarily quitting the game was the stake, indicating that the tendency towards quitting the game voluntarily increased with increasing stake, and that in the low‐stake condition women were less inclined to take risks than men. No statistically significant impact of age and academic degree on financial risk‐taking was found. It was also found that older contestants received higher cash pay‐offs, compared to their younger counterparts. The findings accentuate the importance of comparing data from different countries for a better understanding of the sometimes varying results on financial risk‐taking.
Relations among self‐certainty, sense of control and quality of life
Authors: Wu Chia‐huei , Yao Grace
Published: September 2007

This article investigates the mediation effect of the sense of control on the relationship between self‐certainty and quality of life (QOL). In the first study, 101 students at National Taiwan University (NTU) completed a self‐certainty rating scale with respect to interpersonal traits of the general self and three role‐specific selves (son/daughter, sibling, and friend). They also filled out the WHOQOL‐BREF (World Health Organization Quality of Life questionnaire—brief version) Taiwan version to assess QOL. A two‐factor confirmatory factor analysis revealed that self‐certainty on interpersonal traits has a positive relationship with QOL. In the second study, 121 NTU students completed a self‐certainty rating scale with respect to personality traits of the general self and two role‐specific selves (son/daughter and friend), a control scale measuring sense of control, and the WHOQOL‐BREF Taiwan version assessing QOL. A two‐factor confirmatory factor analysis revealed that self‐certainty on personality traits has a positive relationship with QOL. In addition, a structural equation model revealed that the sense of self‐control mediated the positive relation between self‐certainty and QOL. The findings showed that people with higher self‐certainty had a higher sense of control and, hence, led a better life. The results also showed that the positive relationship between self‐certainty and QOL was stronger when self‐certainty was assessed with interpersonal traits than with personality traits. Implications of this study for self research and adjustment are discussed.
Ethnic Differences in the Predictors of Drug and Alcohol Abuse in Hospitalized Adolescents
Authors: Becker Daniel F. , Grilo Carlos M.
Published: September 2007

This study examined psychosocial correlates of drug and alcohol abuse in hospitalized adolescents and the extent to which these associations may be affected by ethnicity. Four hundred fifty‐eight psychiatric inpatients, ages 12–19, completed measures of psychological functioning, environmental stress, drug abuse, and alcohol abuse. Multiple regression analyses examined the joint and independent predictors of drug and alcohol abuse for European Americans, Latino Americans, and African Americans separately. Seven variables—age, depression, impulsivity, low self‐esteem, delinquent predisposition, low peer insecurity, and history of child abuse—jointly predicted drug abuse for all groups, and predicted alcohol abuse for European Americans and Latino Americans. However, several differences were noted with respect to which variables made independent contributions to the model. Such differences may reflect distinct risk factors for drug and alcohol abuse in these three ethnic groups and may also have implications for prevention and treatment programs.
Self‐Treatment of Opioid Withdrawal with a Dietary Supplement, Kratom
Authors: Boyer Edward W. , Babu Kavita M. , Macalino Grace E. , Compton Wilson
Published: September 2007

We examined the use of Kratom (Mitragyna sp.), a dietary supplement with mu‐opioid agonist activity, by members of a cybercommunity who self‐treat chronic pain with opioid analgesics from Internet pharmacies. Within one year, an increase in the number of mentions on http://Drugbuyers.com, a Web site that facilitates the online purchase of opioid analgesics, suggested that members began managing opioid withdrawal with Kratom. This study demonstrates the rapidity with which information on psychoactive substances disseminates through online communities and suggests that online surveillance may be important to the generation of effective opioid analgesic abuse prevention strategies.
Fathers Who Abuse Drugs and Their Adolescent Children: Longitudinal Predictors of Adolescent Aggression
Authors: Brook Judith S. , Duan Tao , Brook David W.
Published: September 2007

This longitudinal study examines the relationship between earlier paternal drug abuse, environmental factors, paternal child‐rearing practices, and adolescent vulnerable personality attributes and later adolescent aggressive behavior. Data were collected at two points in time, one year apart, via individual, structured interviews. Structural Equation Modeling (SEM) was used to assess the interrelationship of the earlier factors with respect to later adolescent aggression. Interviews took place in an inner‐city community, within the schools and the participants' homes. Participants included low‐income, predominantly African American and Hispanic adolescents (N = 296) whose fathers abused drugs. The fathers were recruited from drug‐abuse treatment programs in several U.S. cities. The outcome measure was adolescent aggressive behavior at Time 2 (T2). The findings showed that paternal drug abuse, environmental factors, and paternal child‐rearing practices were mediated by the adolescent's vulnerable personality attributes. The adolescent's vulnerable personality attributes were the most proximal constructs to later adolescent aggressive behavior. Both paternal drug abuse and environmental factors were mediated by paternal child‐rearing practices. The findings suggest that earlier environmental stresses, paternal drug abuse, paternal child‐rearing practices, and adolescent vulnerable personality attributes are associated with later adolescent aggression.
Research Network Involvement and Addiction Treatment Center Staff: Counselor Attitudes toward Buprenorphine
Authors: Knudsen Hannah K. , Ducharme Lori J. , Roman Paul M.
Published: September 2007

The National Institute on Drug Abuse's Clinical Trials Network (CTN) aims to improve addiction treatment in the United States in part through technology transfer. Given the importance of clinicians in the technology transfer process, this research compares 561 CTN‐affiliated and 1,745 non‐CTN counselors’ ratings of buprenorphine acceptability. CTN‐affiliated counselors reported significantly greater acceptability than non‐CTN counselors. This difference was not explained by controlling for counselor characteristics, but was completely attenuated by measures of buprenorphine‐specific training and buprenorphine implementation. These data suggest that the CTN's impact on counselor attitudes may be attributed to the greater exposure to buprenorphine received by CTN‐affiliated counselors.
Personality‐Guided Treatment for Alcohol Dependence: A Quasi‐Randomized Experiment
Authors: Nielsen Per , Røjskjær Steffen , Hesse Morten
Published: September 2007

Personality disorders are highly prevalent among alcohol‐dependent populations and result in a seriously elevated risk for non‐responding to treatment; therefore, they represent a major challenge for professionals providing treatment for alcohol dependence. Personality‐guided Treatment for Alcohol Dependence (PETAD), an approach that integrates cognitive therapy for addictive behaviors with strategic intervention for maladaptive personality features, may be helpful for patients with co‐morbid alcohol dependence and personality disorders. Clients admitted for inpatient treatment for alcohol dependence at Ringgaarden, Denmark (n = 108) were allocated to either standard inpatient treatment with cognitive therapy for alcohol dependence, or PETAD. Both treatments were manualized. Clients were followed up by mail at six months post‐treatment and administered the MCMI‐I and II and the SCL‐90 at intake, post‐treatment, and at follow‐up. PETAD was associated with better retention, longer time to first relapse, and less time spent drinking post‐treatment, although few differences reached statistical significance. Differences in results were mainly found in the subgroup with higher levels of PD. The study suggests that PETAD is a promising approach that warrants further study.
Is Hepatitis C Infection Associated with Increased Risk of Depression in Persons with Methamphetamine Dependence?
Authors: Vigil Ofilio , Woods Steven Paul , Moran Lisa M. , Letendre Scott L. , Young‐Casey Corinna , Grant Igor , Atkinson J. Hampton ,   the HIV Neurobehavioral Research Center (HNRC) Group
Published: September 2007

The abuse of methamphetamine (MA) has increased in the United States over the past 15 years and is associated with considerable negative social, psychological, and health effects, including symptoms of depression. Infection with the hepatitis C virus (HCV), which is independently associated with increased risk of depression, is common among MA users, possibly due to high rates of transmission risk behaviors in this cohort (eg, injection drug use). Given the prevalence of depression among HCV‐infected individuals and MA users separately, the current study aimed to determine whether HCV infection and MA dependence are associated with additive effects on depression. Focused psychiatric evaluations were conducted on 39 individuals with both MA dependence and HCV infection (MA + HCV +), 57 persons with only MA dependence (MA + HCV −), and a comparison sample of 46 participants with neither risk factor (MA − HCV −). Consistent with prior research, greater self‐reported symptoms of depression were observed in the MA + groups relative to MA − HCV − participants; however, there was no evidence to suggest an additive effect of HCV infection. Surprisingly, the prevalence of current and lifetime diagnoses of Major Depressive Disorder (MDD) did not differ across the study groups. Results from this study suggest that HCV infection does not confer an additive effect on the severity of depressive symptoms or the prevalence of major depression in persons with MA dependence.
New mangrove ecosystem data along the UAE coast using remote sensing
Authors: Habshi A. Al , Youssef T. , Aizpuru M. , Blasco F.
Published: September 2007

Characteristics of mangrove communities along the Gulf Coast of the UAE were explored using high-resolution satellite data Terra ASTER imageries in the common visible and near infra-red bands. Mangrove stands in three geographically distinctive sites, Khor Kalba, Khor Umm Al-Quwain and Al Dabbiya, were studied through spatial data and ground verification surveys. Mangroves in the UAE appear in patchy and scattered patterns, occupying about 40 km2 of the coastal zone, half of which are located in Abu Dhabi in sheltered lagoons. The remaining areas are linear communities fringing tidal waterways distributed along intertidal zones. Their distribution is limited however, by aridity and site topography.

Despite similarities in substrate conditions, differences in climatic and vegetation characteristics between the three sites indicate that growth conditions seem to be more favourable at Khor Kalba with the higher winter temperatures and higher annual rainfalls.

Nine main units were recognized on the colour composite image of the Terra ASTER space data; dense vegetation, scattered vegetation, algal deposits, dry sand, sabkhas, settlements, recent deposits and turbid water, shallow water and deep water. Radiance did not allow for the separation of mangrove areas from inland vegetation through the supervised classification. Confusion was also encountered between different soil classes (e.g. wet soils) and settlements or roads. It is concluded, therefore, that satellite data such as SPOT and Terra ASTER can be effectively analyzed through visual interpretations supported by local digital enhancement.
Crab induced salt marsh regeneration after the 1991 Gulf War oil spill
Authors: Barth Dr. Hans-Jörg
Published: September 2007

The 1991 Gulf War led to the largest oil spill in human history. Over 770 km of coastline from southern Kuwait to Abu Ali Island (Saudi Arabia) were smothered with oil and tar, erasing most of the local plant and animal communities. Salt marshes were most severely hit of the different coastal ecosystem types along the Saudi Arabian coast and are far from being completely restored several years later. Repeated monitoring from 1993 until 2004 revealed that, out of several processes, the re-colonisation by crabs is the most important one regarding the restoration of salt marsh ecosystems. The occurrence of crabs (mainly Nasima dotilliformis) is concentrated along tidal channels from where they slowly advance into the adjacent oiled sediment. These results support the statements made by others in the mid 1990's (i.e. Höpner) that the intertidal fauna is clearly the first to re-colonize the oil affected salt marshes (several years before any plant species return). Therefore the idea of digging an artificial network of channels into the salt marshes in order to accelerate the slow process of re-colonisation in greater distance to the channels seems to be the most promising melioration effort.
Subtidal crabs of the Iranian coast of the Persian Gulf: New collections and biogeographic considerations
Authors: Naderloo Reza , Sari Alireza
Published: September 2007

Benthic sampling was performed along all Iranian subtidal waters of the Persian Gulf during the years 2003 and 2004. A total of 56 species of crabs were caught from 174 stations using a trawler fishing net and Peterson grab. These species belong to 12 families, 15 subfamilies and 37 genera. The results of the present study revealed that families Portunidae, Leucosiidae and Pilumnidae have the highest species richness with 14, 13 and 13 species respectively.

Zoogeographical analysis shows that a high proportion (27%) of the Iranian subtidal crabs have world distribution in the Northern part of Indo-West Pacific region and only two endemic species were found.
Baseline ecological survey of Huwar Islands, The Kingdom of Bahrain
Authors: Zainal K. , Al-Sayed H. , Ghanem E. , Butti E. , Nasser H.
Published: September 2007

A baseline survey of macrobenthic fauna inhabiting shallow subtidal habitats was carried out around Huwar islands during two different cruises in May 2003. A total of 144 quadrats (0.25 m2), 48 subsurface seawater samples and replicate samples of sediments from 16 sites resulted in a collection of 119 species belonging to macrobenthos. Physicochemical parameters of the seawater namely depth (0.2 – 1.5 m), water temperature (28–32°C), pH (7.5–8.0), and dissolved oxygen (5.7–8.5 mg l−1) did not vary significantly between eastern and western shores. However, marked variation in salinity (46.5–54.5 ‰) and chlorophyll-a content of seawater (0.58–6.3 μ g l−1) were found. There was some indication that the eastern coast is more biologically diverse. Sediment organic content was slightly higher along the eastern coast. The substrate was typical of other areas around Bahrain and composed of sand, mud and harder encrustations. Grain size analysis indicated the dominance of fine to very fine sand fractions. Microbial indicators of seawater contamination were found in five of the sixteen sites and Enterococci were found at almost all sites with higher numbers recorded along the western coast. Similar results were found for Salmonella–Shigella counts. The total coliform count was over 100 Colony Forming Units with the exception of a few sites, and a considerable total vibrio count was also recorded. The island's coastal water was nevertheless considered relatively clean from pathogenic bacteria as compared to other areas around Bahrain. A monitoring of macrobenthos and pathogenic bacteria should be conducted in order to endure good water quality around Huwar. A survey of this sort requires dedicated time and resources in order to establish a monitoring program because of the fast rate in urban developments within this region.
Bacteria, Sex, and Systematics
Authors: Franklin L. R.
Published: September 2007

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard.