bluuebunny/crossref_metadata_2025 huggingface dataset:
An ab initio investigation of boron nanotube in ringlike cluster form
Authors: Tian Fu-Yang , Wang Yuan-Xu , Lo V. C. , Sheng Jiang
Published: March 2010

Four types of boron nanotubes (BNTs) in the form of double-ring basic units are theoretically predicted. The structure, stability, and electronic properties of these stable BNTs are investigated by the first-principles calculations. The BNT formed by the basic unit with one hole every six atoms on each ring is found to be more stable than those with other three types of basic units. By increasing diameter for boron ring, the stability is enhanced. The density of state demonstrates that BNTs formed by these basic units are metallic.
Exchange bias by implantation of O ions into Co thin films
Authors: Demeter J. , Meersschaut J. , Almeida F. , Brems S. , Van Haesendonck C. , Teichert A. , Steitz R. , Temst K. , Vantomme A.
Published: March 2010

An original approach for the formation of an exchange bias system is presented. Alternative to surface oxidation or deposition for the formation of Co/CoO bilayer exchange bias systems, implantation of oxygen ions into Co films is applied. The implantation results in the formation of CoxOy embedded in a Co matrix. Comparison with noble gas implantation unambiguously demonstrates that the observed exchange bias effect is induced by the implanted oxygen. Opposed to bilayers formed by surface oxidation, the implantation results in a different morphology of the interface between Co and CoxOy and also gives rise to a radically different magnetization reversal mechanism.
Microwave characterization of Purcell enhancement in a microcavity laser
Authors: Then H. W. , Wu C. H. , Feng M. , Holonyak N.
Published: March 2010

A sensitive microwave method is described to study the optical frequency response of a microcavity laser, demonstrating that a quantum-well vertical cavity surface-emitting laser (∼3 μm aperture, ITH=180 μA) can exhibit almost single mode operation (nearly threshold free), and an electron-hole spontaneous lifetime Purcell enhancement of 2.08 times. The microwavemeasurement method employing electrical-to-optical conversion, and distinct separation of electrical input and optical output, is more revealing than photoluminescence decay experiments (and the inconvenient overlap of optical input and output).
Electrically surface-driven switchable wettability of liquid crystal/polymer composite film
Authors: Chiu Ya-Ping , Shen Cheng-Yu , Wang Wen-Ching , Chu Ting-Yu , Lin Yi-Hsin
Published: March 2010

This study demonstrates the electrical control of the surface wettability of liquid crystal and polymer composite film. The application of external voltages significantly affects the surface wettability of the film. This study uses atomic force microscopy to quantitatively characterize the fundamental mechanism responsible for the structurally driven changes in surface properties at various applied voltages. The surface wettability transitions of the film are electrically driven, as shown by reorganized liquid crystal molecules. Measurements of the voltage-dependent surface wettability of the composite film suggest approaches to supporting control applications of future electro-optical nanotechnology devices.
The Problem with Zoning: Nonlinear Effects of Interactions between Location Preferences and Externalities on Land Use and Utility
Authors: Zellner Moira L , Riolo Rick L , Rand William , Brown Daniel G , Page Scott E , Fernandez Luis E
Published: March 2010

An important debate in the literature on exurban sprawl is whether low-density development results from residential demand, as operationalized by developers, or from exclusionary zoning policies. Central to this debate is the purpose of zoning, which could alternatively be a mechanism to increase the utility of residents by separating land uses and reducing spillover effects of development, or an obstacle to market mechanisms that would otherwise allow the realization of residential preferences. To shed light on this debate, we developed an agent-based model of land-use change to study how the combined effects of zoning-enforcement levels, density preferences, preference heterogeneity, and negative externalities from development affect exurban development and the utility of residents. Our computational experiments show that sprawl is not inevitable, even when most of the population prefers low densities. The presence of negative externalities consistently encourage sprawl while decreasing average utility and flattening the utility distribution. Zoning can reduce sprawl by concentrating development in specific areas, but in doing so decreases average utility and increases inequality. Zoning does not internalize externalities; instead, it contains externalities in areas of different development density so that residents bear the burden of the external effects of the density they prefer. Effects vary with residential preference distributions and levels of zoning enforcement. These initial investigations can help inform policy makers about the conditions under which zoning enforcement is preferable to free-market development and vice versa. Future work will focus on the environmental impacts of different settlement patterns and the role land-use and market-based policies play in this relationship.
Integrated Multihazard Mapping
Authors: Tate Eric , Cutter Susan L , Berry Melissa
Published: March 2010

A primary goal of the US Disaster Mitigation Act of 2000 is to slow the increase in disaster losses by emphasizing a proactive approach focusing on predisaster hazard mitigation, rather than postdisaster relief. The legislation requires local communities to produce hazard-mitigation plans that include multihazard maps, signifying a de facto prioritization of mitigation dollars on the basis of areas with the greatest vulnerability. However, there is little formal or practical guidance for communities on how to produce such maps. We propose a methodology for hazard-vulnerability assessments using multihazard mapping, where hazard frequency is a measure of risk, historical dollar losses are a proxy for infrastructure impact or exposure, and the Social Vulnerability Index (SoVI) evaluates human vulnerability. Using a test case of one county, Charleston, South Carolina, a geographic information system spatially combined these dimensions of vulnerability across multiple hazards. The resulting maps provide a tool for hazard-mitigation planning, which contains an initial screening element to highlight zones of highest multihazard vulnerability. The approach helps to generate a view of not just what is at risk, but who is at risk, and where, thus enhancing the implementation of targeted impact-reduction strategies.
The effect of Cylindrocarpon destructans on the growth of Eucalyptus regnans seedlings in air-dried and undried forest soil
Authors: Iles T. M. , Ashton D. H. , Kelliher K. J. , Keane P. J.
Published: March 2010

The growth of Eucalyptus regnans F.Muell. (mountain ash) seedlings is poor in natural forest soil, where purple coloration of the foliage indicates P deficiency and where the fungus Cylindrocarpon destructans (Zinsm.) Scholten is commonly isolated from the roots of the seedlings. When forest soil is air-dried, P acquisiton and growth of seedlings are markedly improved, although the degree of growth stimulation varies considerably at different times, as does the frequency of occurrence of C. destructans on the roots. C. destructans has been implicated as a possible reason for suppressed growth of seedlings in undried natural soil. To find out whether C. destructans contributes to growth inhibition of E. regnans seedlings in undried forest soil, the effect of three isolates of C. destructans on the root growth of E. regnans seedlings was tested in Petri dish experiments in vitro and the effect of C. destructans inoculation on seedling growth both in air-dried and undried forest soil was tested in pot experiments. The frequency of occurrence of C. destructans on the roots varied at different times, and was not consistently higher in undried than in air-dried soil, even though the growth of the seedlings was always poor in undried soil compared with that in air-dried soil. In vitro, C. destructans decreased the root growth significantly and caused blackening of root tips. This effect was removed by adding natural air-dried or undried soil. In pot experiments using undried forest soil, there was no evidence of either direct toxic effect or any other adverse effect on the roots when soil was inoculated with this fungus, even when the growth of the seedlings was reduced to ~1/2 of that in uninoculated undried soil. In air-dried soil, inoculation with the fungus did not significantly reduce seedling growth. Although potentially pathogenic and able to cause blackening of root tips, C. destructans is unlikely to be the main reason for poor seedling growth in undried forest soil. It appears to be antagonistic rather than pathogenic, suppressing seedling growth only under unfavourable conditions, such as in undried soil, possibly by competing for limited nutrients, or by suppressing other beneficial micro-organisms. The results are discussed in the context of field conditions.
Claying and deep ripping can increase crop yields and profits on water repellent sands with marginal fertility in southern Western Australia
Authors: Hall D. J. M. , Jones H. R. , Crabtree W. L. , Daniels T. L.
Published: March 2010

Sandplain soils on the south coast of Western Australia have multiple limitations to crop production that include water repellence, low water and nutrient retention, subsoil acidity, and high soil strength. Crops on sandplain soils achieve, on average, almost 85% of their rainfall-limited yield potential; however, where there are multiple limitations the corresponding value is often <50% in any given year. Previous research has shown the value of applying clay-rich subsoil (‘claying’) to ameliorate water repellent soils and improve nutrient retention. Other studies have shown that deep ripping is effective in reducing compaction in sandplain soils. This paper quantifies the effects of 5 subsoil clay rates (0, 50, 100, 200, and 300 t/ha), with and without deep ripping to 0.5m, on soil properties, crop growth, and profitability in a replicated field experiment.
Crop yields were increased by 0.3–0.6 t/ha as result of added clay. The clay content of the surface soil required to alleviate water repellence and achieve the highest yield increases was 3–6% in soils with ~1% organic carbon. Longer term effects of claying included increased soil organic carbon by 0.2%, pH by 0.6 units, potassium by 47 mg/kg, soil strength by 250 kPa, and cation exchange capacity by 1.3 cmolc/kg to a depth of 0.1 m. However, changes in plant-available water (mm/m) were inconsistent between the clay treatments. Deep ripping to 0.5 m increased crop yields by 0.1–0.5 t/ha. These crop yield responses were still evident 3 years after the ripping treatment had been applied. Soil strength measurements indicate that re-compaction of the ripped treatments had occurred to a depth of 0.2 m in the second year following ripping. Crop responses to claying and deep ripping were additive. Claying and deep ripping, while almost doubling yields, achieved only 50–70% of the rainfall-limited yield potential on these marginally fertile soils. The highest clay rates (>3–6%) had cumulative discounted cash returns $AU100–200/ha higher than the unclayed ‘control’ treatment and $300/ha higher than the lowest clay rates. For most of the clay treatments, deep ripping increased discounted returns between 2005 and 2007 by $80–120/ha.
A numerical study of slope and fuel structure effects on coupled wildfire behaviour
Authors: Linn Rodman R. , Winterkamp Judith L. , Weise David R. , Edminster Carleton
Published: March 2010

Slope and fuel structure are commonly accepted as major factors affecting the way wildfires behave. However, it is possible that slope affects fire differently depending on the fuel bed. Six FIRETEC simulations using three different fuel beds on flat and upslope topography were used to examine this possibility. Fuel beds resembling grass, chaparral, and ponderosa pine forests were created in such a way that there were two specific locations with identical local fuel beds located around them. These fuel beds were each used for a flat-terrain simulation and an idealised-hill simulation in order to isolate the impacts of the topography without the complications of having different local fuels. In these simulations, fuel bed characteristics have a significant effect on the spread rate and perimeter shape of the fires on both flat ground and on the idealised smooth hill topography. The analysis showed that these simulated fires evolved as they travelled between the locations even on flat ground, and the accelerations and decelerations that affect the fire occurred at different times and at different rates depending on the fuel bed. The results of these simulations and analyses indicate that though some general principles are true for all fuel beds, there are differences in the way that fires react to non-homogeneous topographies depending on the fuel bed.
Experimental measurements during combustion of moist individual foliage samples
Authors: Pickett Brent M. , Isackson Carl , Wunder Rebecca , Fletcher Thomas H. , Butler Bret W. , Weise David R.
Published: March 2010

Individual samples of high moisture fuels from the western and southern United States and humidified aspen excelsior were burned over a flat-flame burner at 987° ± 12°C and 10 ± 0.5 mol% O2. Time-dependent mass and temperature profiles of these samples were obtained and analysed. It was observed that significant amounts of moisture remained in the individual samples after ignition occurred. Temperature histories showed a plateau at 200°–300°C at the leaf perimeter rather than at 100°C, with a plateau of 140°C for the leaf interior. Implications are that classical combustion models should be altered to reflect the behaviour of moisture in high moisture (live) samples. Mass release rates were determined at ignition and maximum flame height; these appeared to vary due to surface area and perimeter, but no significant correlation was found for all species.
Scaling of morphogen gradients by an expansion-repression integral feedback control
Authors: Ben-Zvi Danny , Barkai Naama
Published: March 2010

Despite substantial size variations, proportions of the developing body plan are maintained with a remarkable precision. Little is known about the mechanisms that ensure this adaptation (scaling) of pattern with size. Most models of patterning by morphogen gradients do not support scaling. In contrast, we show that scaling arises naturally in a general feedback topology, in which the range of the morphogen gradient increases with the abundance of some diffusible molecule, whose production, in turn, is repressed by morphogen signaling. We term this mechanism “expansion–repression” and show that it can function within a wide range of biological scenarios. The expansion-repression scaling mechanism is analogous to an integral-feedback controller, a key concept in engineering that is likely to be instrumental also in maintaining biological homeostasis.
How different is translated Chinese from native Chinese?
Authors: Xiao Richard
Published: March 2010

Corpus-based translation studies focus on translation as a product by comparing comparable corpora of translational and non-translational texts. A number of distinctive features of translational English in relation to native English have been uncovered. Nevertheless, research of this area has so far been confined largely to translational English translated from closely related European languages. If the features of translational language that have been reported on the basis of translated English are to be generalized as ‘translation universals’, it is of vital importance to find supporting evidence from non-European languages. Clearly, evidence from “genetically” distinct language pairs such as English and Chinese is arguably more convincing, if not indispensable. This article explores potential features of translational Chinese on the basis of two balanced monolingual comparable corpora of translated and native Mandarin Chinese. The implications of the study for translation universal hypotheses are also discussed.
Deixis, gesture, and cognition in spatial Frame of Reference typology
Authors: Danziger Eve
Published: March 2010

The three Frames of Reference recognized in the current inventory of spatial-language types are differentiated by their placement of the Anchor from which the vector of search space from Ground to Figure is calculated (Levinson 1996). In certain well-recognized examples, Anchor merges with Ground. The existing analysis treats this merged component as analytically Ground rather than Anchor; its location in or out of the speech situation is therefore taken to be independent of the Frame of Reference typology. Instead, I treat this component as analytically Anchor, making its speech-situation status criterial to the typology. Four, not three, Frames of Reference now appear. The fourth, “Direct” frame, distinguishes binary locutions with a speech participant as Ground/Anchor (e.g. ‘in front of you’) from “Object-Centered” binary locutions in which Ground/Anchor is not a speech participant ( e.g. ‘in front of the kettle’). This four-frame analysis corresponds better than does the three-frame one to the logic of rotation sensitivity which has been used to show Whorfian parallels between language and conceptualization across cultures. I close by discussing the application of Frame of Reference typology to pointing gestures, and show how recognition of the fourth frame of reference allows us to bring discussion of these, and of the linguistic demonstratives and locatives with which they so frequently co-occur, fully within the Frame of Reference typology.
Regulation of Lens Gap Junctions by Transforming Growth Factor Beta
Authors: Boswell Bruce A. , VanSlyke Judy K. , Musil Linda S.
Published: March 2010

Gap junction–mediated intercellular communication (GJIC) is essential for the proper function of many organs, including the lens. GJIC in lens epithelial cells is increased by FGF in a concentration-dependent process that has been linked to the intralenticular gradient of GJIC required for lens transparency. Unlike FGF, elevated levels of TGF-β are associated with lens dysfunction. We show that TGF–β1 or -2 up-regulates dye coupling in serum-free primary cultures of chick lens epithelial cells (dissociated cell-derived monolayer cultures [DCDMLs]) via a mechanism distinct from that utilized by other growth factors. Remarkably, the ability of TGF-β and of FGF to up-regulate GJIC is abolished if DCDMLs are simultaneously exposed to both factors despite undiminished cell–cell contact. This reduction in dye coupling is attributable to an inhibition of gap junction assembly. Connexin 45.6, 43, and 56–containing gap junctions are restored, and intercellular dye coupling is increased, if the activity of p38 kinase is blocked. Our data reveal a new type of cross-talk between the FGF and TGF-β pathways, as well as a novel role for TGF-β and p38 kinase in the regulation of GJIC. They also provide an explanation for how pathologically increased TGF-β signaling could contribute to cataract formation.
SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology
Authors: Kang Bo-Yeong , Ko Song , Kim Dae-Won
Published: March 2010

Summary: Despite the importance of using the semantic distance to improve the performance of conventional expression-based clustering, there are few freely available software that provides a clustering algorithm using the ontology-based semantic distances as prior knowledge. Here, we present the SICAGO (SemI-supervised Cluster Analysis using semantic distance between gene pairs in Gene Ontology) system that helps to discover the groups of genes more effectively using prior knowledge extracted from Gene Ontology.

Availability:  http://ai.cau.ac.kr/sicago.html

Contact:  dwkim@cau.ac.kr
Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification of Ipomoea mauritiana Jacq (Convolvulaceae)
Authors: Devaiah Kambiranda , Balasubramani Subramani Paranthaman , Venkatasubramanian Padma
Published: March 2010

Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation of Chyavanaprash. Tubers of Ipomoea mauritiana Jacq. (Convolvulaceae), Pueraria tuberosa (Roxb. ex Willd.) DC (Fabaceae), Adenia hondala (Gaertn.) de Wilde (Passifloraceae) and pith of Cycas circinalis L. (Cycadaceae) are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA‐based markers have been developed to distinguish I. mauritiana from the other Vidari candidates. A putative 600‐bp polymorphic sequence, specific to I. mauritiana was identified using randomly amplified polymorphic DNA (RAPD) technique. Furthermore, sequence characterized amplified region (SCAR) primers (IM1F and IM1R) were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323‐bp amplicon in authentic I. mauritiana and not in the allied species.
Bio‐Prospecting of a Few Brown Seaweeds for Their Cytotoxic and Antioxidant Activities
Authors: Vinayak Rashmi C. , Sabu A. S. , Chatterji Anil
Published: March 2010

Methanolic extracts (MEs) of seven brown seaweeds occurring in the Indian coastal waters were screened for their cytotoxic and antioxidant properties following various assays. The methanolic extracts of seaweeds in the order of Dictyopteris australis > Spatoglossum variabile > Stoechospermum marginatum > Spatoglossum aspermum showed significant cytotoxic activity. A very high DPPH radical scavenging activity was exhibited by the methanolic extracts prepared from St. marginatum, Padina tetrastromatica, Dictyopteris delicatula and S. aspermum. The total phenolic content of the MEs varied from 13.19 ± 0.32 to 25.29 ± 0.445 gallic acid equivalents (mg g−1 of methanolic extract). The reducing power assay indicated a dose dependency, at concentrations of 0.1, 0.5 and 1.0 and 2.0 mg mL−1 of MEs and decreased in the following order: Butylated hydroxy toluene > P. tetrastromatica > D. delicatula > S. aspermum > S. variabile > S. marginatum > D. australis > S. marginatum. Furthermore, D. australis, S. aspermum, S. variabile and S. marginatum demonstrated good metal ion chelating properties. All the above evidences suggest that, the antioxidant compounds found in brown seaweeds scavenge free radicals through effective intervention. This decisively promotes them as a potential source of natural antioxidants.
Myostatin activation in patients with advanced heart failure and after mechanical unloading
Authors: George Isaac , Bish Lawrence T. , Kamalakkannan Gayathri , Petrilli Christopher M. , Oz Mehmet C. , Naka Yoshifumi , Lee Sweeney H. , Maybaum Simon
Published: March 2010

Aims

Myostatin inhibits myoblast differentiation/proliferation and may play a role in heart failure (HF) and reverse remodelling after left ventricular assist device (LVAD) support. This study sought to characterize myostatin expression and activation in advanced HF before and after LVAD support.

Methods and results

Left ventricular tissue pairs were collected at LVAD implantation (core) and at cardiac transplantation/LVAD explantation in patients with advanced ischaemic (ICM—ischaemic cardiomyopathy) and non‐ischaemic (DCM—dilated cardiomyopathy) HF. Normal cardiac tissue (control) was obtained from hearts not placed for transplantation. Serum was collected independently from patients with stable DCM HF and from healthy controls. Full‐length and cleaved propeptide myostatin levels were quantified by western blot analysis. Dilated cardiomyopathy propeptide levels at core were significantly higher than control and significantly increased after LVAD support. Ischaemic cardiomyopathy propeptide levels were higher than control, but did not change after LVAD support. No changes in full‐length levels were seen. Serum myostatin levels were significantly higher in DCM HF patients than in healthy controls.

Conclusion

This is the first clinical evidence that myostatin activation is increased in HF. Myostatin may affect cardiac hypertrophy and may mediate regression of cellular hypertrophy after mechanical unloading.
Does cognitive impairment predict poor self‐care in patients with heart failure?
Authors: Cameron Jan , Worrall‐Carter Linda , Page Karen , Riegel Barbara , Lo Sing Kai , Stewart Simon
Published: March 2010

Aims

Cognitive impairment occurs often in patients with chronic heart failure (CHF) and may contribute to sub‐optimal self‐care. This study aimed to test the impact of cognitive impairment on self‐care.

Methods and results

In 93 consecutive patients hospitalized with CHF, self‐care (Self‐Care of Heart Failure Index) was assessed. Multiple regression analysis was used to test a model of variables hypothesized to predict self‐care maintenance, management, and confidence. Variables in the model were mild cognitive impairment (MCI; Mini‐Mental State Exam and Montreal Cognitive Assessment), depressive symptoms (Cardiac Depression Scale), age, gender, social isolation, education level, new diagnosis, and co‐morbid illnesses. Sixty‐eight patients (75%) were coded as having MCI and had significantly lower self‐care management (η2= 0.07, P < 0.01) and self‐confidence scores (η2= 0.05, P < 0.05). In multivariate analysis, MCI, co‐morbidity index, and NYHA class III or IV explained 20% of the variance in self‐care management (P < 0.01); MCI made the largest contribution explaining 9% of the variance. Increasing age and symptoms of depression explained 13% of the variance in self‐care confidence scores (P < 0.01).

Conclusion

Cognitive impairment, a hidden co‐morbidity, may impede patients' ability to make appropriate self‐care decisions. Screening for MCI may alert health professionals to those at greater risk of failed self‐care.
Differentiation of Mycoplasma gallisepticum strains using PCR and high-resolution melting curve analysis
Authors: Ghorashi Seyed A. , Noormohammadi Amir H. , Markham Philip F.
Published: March 2010

Mycoplasma gallisepticum (MG) is an economically important pathogen of poultry worldwide, causing chronic respiratory disease in chickens and turkeys. Differentiation of MG strains is critical, especially in countries where poultry flocks are vaccinated with live vaccines. In this study, oligonucleotide primers were designed based on a region preceding the trinucleotide repeat of a member of the vlhA gene family, and amplicons of 145–352 bp were generated from cultures of 10 different MG strains, including the ts-11, F and 6/85 vaccine strains. High-resolution melting (HRM) curve analysis of the resultant amplicons could differentiate all MG strains. Analysis of the nucleotide sequences of the amplicons from each strain revealed that each melting curve profile related to a unique DNA sequence. The HRM curve profiles (for ts-11) remained consistent after at least five passages under laboratory conditions. PCR-HRM curve analysis of 33 DNA extracts derived from respiratory swabs, or mycoplasma cultures grown from respiratory swabs, of ts-11-vaccinated commercial or specific pathogen-free chickens identified all these specimens, according to their sequences, as ts-11. The potential of the PCR-HRM curve analysis was also shown in the genotyping of 30 additional MG isolates from Europe, the USA and Israel. The results presented in this study indicate that PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping of MG isolates/strains using both MG cultures and clinical swabs.
Regulatory divergence in Drosophila revealed by mRNA-seq
Authors: McManus C. Joel , Coolon Joseph D. , Duff Michael O. , Eipper-Mains Jodi , Graveley Brenton R. , Wittkopp Patricia J.
Published: March 2010

The regulation of gene expression is critical for organismal function and is an important source of phenotypic diversity between species. Understanding the genetic and molecular mechanisms responsible for regulatory divergence is therefore expected to provide insight into evolutionary change. Using deep sequencing, we quantified total and allele-specific mRNA expression levels genome-wide in two closely related Drosophila species (D. melanogaster and D. sechellia) and their F1 hybrids. We show that 78% of expressed genes have divergent expression between species, and that cis- and trans-regulatory divergence affects 51% and 66% of expressed genes, respectively, with 35% of genes showing evidence of both. This is a relatively larger contribution of trans-regulatory divergence than was expected based on prior studies, and may result from the unique demographic history of D. sechellia. Genes with antagonistic cis- and trans-regulatory changes were more likely to be misexpressed in hybrids, consistent with the idea that such regulatory changes contribute to hybrid incompatibilities. In addition, cis-regulatory differences contributed more to divergent expression of genes that showed additive rather than nonadditive inheritance. A correlation between sequence similarity and the conservation of cis-regulatory activity was also observed that appears to be a general feature of regulatory evolution. Finally, we examined regulatory divergence that may have contributed to the evolution of a specific trait—divergent feeding behavior in D. sechellia. Overall, this study illustrates the power of mRNA sequencing for investigating regulatory evolution, provides novel insight into the evolution of gene expression in Drosophila, and reveals general trends that are likely to extend to other species.
F-Box Proteins FKF1 and LKP2 Act in Concert with ZEITLUPE to Control Arabidopsis Clock Progression
Authors: Baudry Antoine , Ito Shogo , Song Young Hun , Strait Alexander A. , Kiba Takatoshi , Lu Sheen , Henriques Rossana , Pruneda-Paz José L. , Chua Nam-Hai , Tobin Elaine M. , Kay Steve A. , Imaizumi Takato
Published: March 2010

Regulation of protein turnover mediated by ZEITLUPE (ZTL) constitutes an important mechanism of the circadian clock in Arabidopsis thaliana. Here, we report that FLAVIN BINDING, KELCH REPEAT, F-BOX1 (FKF1) and LOV KELCH PROTEIN2 (LKP2) play similar roles to ZTL in the circadian clock when ZTL is absent. In contrast with subtle circadian clock defects in fkf1, the clock in ztl fkf1 has a considerably longer period than in ztl. In ztl fkf1 lkp2, several clock parameters were even more severely affected than in ztl fkf1. Although LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) expression levels are lower in ztl than in the wild type, introducing both fkf1 and lkp2 mutations into the ztl mutant dramatically diminished LHY expression without further affecting CCA1 expression. This demonstrates different contributions of ZTL, FKF1, and LKP2 in the regulation of LHY and CCA1 expression. In addition, FKF1 and LKP2 also interacted with TIMING OF CAB EXPRESSION1 (TOC1) and PSEUDO-RESPONSE REGULATOR5 (PRR5), and both proteins were further stabilized in ztl fkf1 and ztl fkf1 lkp2 compared with in ztl. Our results indicate that ZTL, FKF1, and LKP2 together regulate TOC1 and PRR5 degradation and are major contributors to determining the period of circadian oscillation and enhancing robustness.
Nestedness versus modularity in ecological networks: two sides of the same coin?
Authors: Fortuna Miguel A. , Stouffer Daniel B. , Olesen Jens M. , Jordano Pedro , Mouillot David , Krasnov Boris R. , Poulin Robert , Bascompte Jordi
Published: March 2010

1. Understanding the structure of ecological networks is a crucial task for interpreting community and ecosystem responses to global change.

2. Despite the recent interest in this subject, almost all studies have focused exclusively on one specific network property. The question remains as to what extent different network properties are related and how understanding this relationship can advance our comprehension of the mechanisms behind these patterns.

3. Here, we analysed the relationship between nestedness and modularity, two frequently studied network properties, for a large data set of 95 ecological communities including both plant–animal mutualistic and host–parasite networks.

4. We found that the correlation between nestedness and modularity for a population of random matrices generated from the real communities decreases significantly in magnitude and sign with increasing connectance independent of the network type. At low connectivities, networks that are highly nested also tend to be highly modular; the reverse happens at high connectivities.

5. The above result is qualitatively robust when different null models are used to infer network structure, but, at a finer scale, quantitative differences exist. We observed an important interaction between the network structure pattern and the null model used to detect it.

6. A better understanding of the relationship between nestedness and modularity is important given their potential implications on the dynamics and stability of ecological communities.
Response of somatic embryos of Scots pine to fungal cell wall elicitors
Authors: Lu J. , Aronen T. , Pappinen A. , Asiegbu F. O.
Published: March 2010

Fungal cell wall elicitors have notable effects on germination of pine seeds, defence response and many other aspects of metabolic processes. In this study, we investigated morphological, physiological and molecular response of somatic embryos of Scots pine to fungal cell wall elicitors from ectomycorrhizal fungusSuillus bovinus, pathogenic fungusHeterobasidion annosumor weak Scots pine pathogen (Heterobasidion parviporum). Results from the embryo rooting experiment indicated that the genotypic origin of the conifer tree and the source of the elicitors affected the root development. Elicitors from eitherS. bovinusorH. parviporumincreased the root formation but increased concentration of elicitors fromH. annosumdecreased the rooting and survival rate of the embryos. At the molecular level, altered transcript changes were observed among genes encoding proteins involved in cell division, cell wall modification, and stress following exposure of embryos to elicitors. Increased levels of actin and peroxidase gene expression were detected at 7 days after exposure toS. bovinusorH. parviporumelicitors.H. annosumelicitors provoked significant induction of the ethylene synthesis genePsACS‐1. Generally the gene expression patterns at early stages observed in the subset of genes investigated after treatment withH. parviporumelicitor were found to be similar to that documented forS. bovinus.In contrast, somatic embryos exposed toH. annosumelicitor had different patterns of regulation marked by delayed response, and in some cases gradual degradation and death of the embryos were observed.
Colonoscopy as an adjunctive method for the diagnosis of irritable bowel syndrome: Focus on pain perception
Authors: Kim Eun Soo , Cheon Jae Hee , Park Jae Jun , Moon Chang Mo , Hong Sung Pil , Kim Tae Il , Kim Won Ho
Published: March 2010

Background and Aim:  Visceral hypersensitivity is an important component of the pathophysiology of irritable bowel syndrome (IBS). In the present study, we investigated differences in pain perception during colonoscopy between IBS patients and non‐IBS patients. We further assessed the sensitivity, specificity, and predictive values of pain scores to diagnose IBS.

Methods:  Patients who underwent colonoscopy for the evaluation of gastrointestinal symptoms or for screening purposes were included. All patients completed Rome III criteria questionnaires and reported pain scores on 0–100‐mm visual analog scales after colonoscopy. The patients were divided into three groups: (i) IBS; (ii) other functional gastrointestinal disorders (FGID), including functional bloating, functional diarrhea, and functional constipation; and (iii) healthy controls.

Results:  A total of 217 patients were included. The pain scores (median, interquartile range) of IBS patients (52, 34–71) were higher than those of the healthy controls (22, 12–35) or other FGID patients (18, 10–29) (P < 0.001). Upper gastrointestinal symptoms were observed more often in the IBS group than in the non‐IBS group (83.2% vs 34.5%, P < 0.001). At the pain score level of 31, the sensitivity, specificity, positive predictive value, and negative predictive value for IBS diagnosis were 86.1%, 75.9%, 75.7%, and 86.3%, respectively.

Conclusions:  The degree of pain perception during colonoscopy was higher in IBS patients than in non‐IBS patients. We concluded that colonoscopy can be useful in identifying IBS patients, with the additional benefit of excluding organic disorders of the lower gastrointestinal tract.
Media Violence Associations with the Form and Function of Aggression among Elementary School Children
Authors: Gentile Douglas A. , Mathieson Lindsay C. , Crick Nicki R.
Published: March 2010

Although the association between media violence exposure (MVE) and physical aggression (PA) has been well studied, few studies have examined the link between MVE and other subtypes of aggression. The purpose of this study was to examine the relation between MVE and reactive and proactive subtypes of both PA and relational aggression (RA). Six hundred and forty‐one third to fifth grade students reported on their exposure to media violence. RA and PA were assessed by peers and teachers. Reactive and proactive subtypes of RA and PA were assessed by teacher reports. Findings revealed a significant positive association between MVE and overall PA and RA. The relation with RA was stronger for girls than for boys. When predicting the functional subtypes of aggression, higher MVE was associated with lower reactive RA, higher proactive RA, and higher reactive PA, and MVE was unrelated to proactive PA. The implications of the findings for future research are discussed.
The Essence of Linkage‐based Imprinting Detection: Comparing Power, Type 1 Error, and the Effects of Confounders in Two Different Analysis Approaches
Authors: Greenberg David A. , Monti Maria Cristina , Feenstra Bjarke , Zhang Junying , Hodge Susan E.
Published: March 2010

Imprinting is critical to understanding disease expression. It can be detected using linkage information, but the effects of potential confounders (heterogeneity, sex‐specific penetrance, and sex‐biased ascertainment) have not been explored. We examine power and confounders in two imprinting detection approaches, and we explore imprinting‐linkage interaction.

One method (PP) models imprinting by maximising lod scores w.r.t. parent‐specific penetrances. The second (DRF) approximates imprinting by maximising lods over differential male‐female recombination fractions. We compared power, type 1 error, and confounder effects in these two methods, using computer‐simulated data. We varied heterogeneity, penetrance, family and dataset size, and confounders that might mimic imprinting.

Without heterogeneity, PP had more imprinting‐detecting power than DRF. PP's power increased when parental affectedness status was ignored, but decreased with heterogeneity. With heterogeneity, type 1 error increased dramatically for both methods. However, DRF's power also increased under heterogeneity, more than was attributable to inflated type 1 error.

Sex‐specific penetrance could increase false positives for PP but not for DRF. False positives did not increase on ascertainment through an affected “mother”. For PP, non‐penetrant individuals increased information, arguing against using affecteds‐only methods.

The high type 1 error levels under some circumstances means these methods must be used cautiously.
Women's Organisations and the Politics of Gender in Cuba's Urban Insurrection (1952–1958)
Authors: CHASE MICHELLE
Published: March 2010

This article sheds new light on Cuba's urban insurrection to oust Fulgencio Batista by focusing on two all‐women's anti‐Batista groups. It charts the origins and developments of the groups, explores their conceptions about the importance of women's political action and examines the impact that participating in the insurrection had on group members. The article complicates long‐standing assumptions about women's low levels of participation in the insurrection and the absence of demands for gender equity among those who did participate by noting that some older women militants had histories with the feminist movement of the 1930s, and that many younger women were forced by the circumstances of the insurrection to confront and challenge contemporary gender norms.
Dopamine D1receptor‐mediated enhancement of NMDA receptor trafficking requires rapid PKC‐dependent synaptic insertion in the prefrontal neurons
Authors: Li Yan‐Chun , Liu Gang , Hu Jian‐Li , Gao Wen‐Jun , Huang Yue‐Qiao
Published: March 2010

J. Neurochem.(2010)114, 62–73.

Understanding the interaction between dopamine and glutamate, particularly the interaction of dopamine and NMDA receptors, may enable a more rational approach to the treatment of schizophrenia, drug addiction, and other psychiatric disorders. We show that, in prefrontal cortical neurons, dopamine D1‐induced enhancement of NMDA receptor function depends on rapid insertion of new NMDA receptor 2B subunits on the synaptic surface. Protein kinase A (PKA) inhibitor, but not protein kinase C (PKC) inhibitor, completely blocked dopamine D1agonist SKF‐81297‐induced increase of the total expression of NMDA receptors. Furthermore, SKF‐81297 failed to alter the surface expression and synaptic insertion of NMDA receptors in the presence of PKA inhibitor, phospholipase C inhibitor, PKC inhibitor, or Src family kinase inhibitor. Our data suggest that D1‐mediated enhancement of NMDA current depends on the NMDA receptor trafficking through rapid synaptic insertion and both PKA and PKC signaling pathways play important roles in the regulatory process. Although both PKA and PKC mediate the D1‐induced enhancement of NMDA receptors, the phospholipase C‐PKC‐Src pathway is only required for surface expression and new synaptic insertion of NMDA receptors.
Induction of amyloid precursor protein by the neurotoxic peptide, amyloid‐beta 25–35, causes retinal ganglion cell death
Authors: Tsuruma Kazuhiro , Tanaka Yuka , Shimazawa Masamitsu , Hara Hideaki
Published: March 2010

J. Neurochem. (2010) 113, 1545–1564.

Patients with Alzheimer’s disease (AD) show a significantly increased incidence of glaucoma. AD is also associated with the occurrence of the neurotoxic peptide amyloid beta (Aβ). Therefore, we investigated whether Aβ is associated with retinal cell death in a retinal ganglion cell line (RGC‐5). Treatment with Aβ25–35, a neurotoxic fragment of Aβ, induced cell death in RGC‐5 in both a concentration‐ and time‐dependent manner. The amount of amyloid precursor protein was increased by treatment of RGC‐5 and primary culture of mouse cortical neurons with fibril Aβ25–35 and Aβ1–42, which is a putative physiological neurotoxic fragment of Aβ present in AD. Amyloid precursor protein knockdown inhibited the cell death induced by Aβ25–35. Treatment with Aβ25–35 increased the amount of intracellular Aβ1–40 and Aβ1–42, while β‐ and γ‐secretase inhibitors reduced cell death. Thus, the regulation of Aβ can be viewed as a new therapeutic target for glaucoma, especially in patients with coincident AD.
Neurites regrowth of cortical neurons by GSK3β inhibition independently of Nogo receptor 1
Authors: Seira Oscar , Gavín Rosalina , Gil Vanessa , Llorens Franc , Rangel Alejandra , Soriano Eduardo , Del Río José Antonio
Published: March 2010

J. Neurochem. (2010) 113, 1644–1658.

Lesioned axons do not regenerate in the adult mammalian CNS, owing to the over‐expression of inhibitory molecules such as myelin‐derived proteins or chondroitin sulphate proteoglycans. In order to overcome axon inhibition, strategies based on extrinsic and intrinsic treatments have been developed. For myelin‐associated inhibition, blockage with NEP1–40, receptor bodies or IN‐1 antibodies has been used. In addition, endogenous blockage of cell signalling mechanisms induced by myelin‐associated proteins is a potential tool for overcoming axon inhibitory signals. We examined the participation of glycogen synthase kinase 3β (GSK3β) and extracellular‐related kinase (ERK) 1/2 in axon regeneration failure in lesioned cortical neurons. We also investigated whether pharmacological blockage of GSK3β and ERK1/2 activities facilitates regeneration after myelin‐directed inhibition in two models: (i) cerebellar granule cells and (ii) lesioned entorhino‐hippocampal pathway in slice cultures, and whether the regenerative effects are mediated by Nogo Receptor 1 (NgR1). We demonstrate that, in contrast to ERK1/2 inhibition, the pharmacological treatment of GSK3β inhibition strongly facilitated regrowth of cerebellar granule neurons over myelin independently of NgR1. Finally, these regenerative effects were corroborated in the lesioned entorhino‐hippocampal pathway in NgR1−/− mutant mice. These results provide new findings for the development of new assays and strategies to enhance axon regeneration in injured cortical connections.
Insights into GPCR pharmacology from the measurement of changes in intracellular cyclic AMP; advantages and pitfalls of differing methodologies
Authors: Hill Stephen J , Williams Christine , May Lauren T
Published: March 2010

It is clear that the G protein‐coupled receptor family play a key role in the pharmaceutical industry, with a significant proportion of approved drugs targeting this protein class. While our growing understanding of the complexity of G protein‐coupled receptor pharmacology is playing a key role in the future success of these endeavours, with allosteric mechanisms now well integrated into the industrial community and G protein‐independent signalling mechanisms establishing themselves as novel phenomenon to be exploited, it is still possible to underestimate the complexity of G protein signal transduction mechanisms and the impact that inappropriate study of these mechanisms can have on data interpretation. In this manuscript we review different approaches to measuring the cAMP signal transduction pathway, with particular emphasis on key parameters influencing the data quality and biological relevance.
Acurhagin‐C, an ECD disintegrin, inhibits integrin αvβ3‐mediated human endothelial cell functions by inducing apoptosis via caspase‐3 activation
Authors: Wang Wen‐Jeng
Published: March 2010

Background and purpose:  Acurhagin, a member of versatile metalloproteinase disintegrins from Agkistrodon acutus venom, has been identified as a platelet aggregation inhibitor, previously. Here, acurhagin‐C, the C‐terminal Glu‐Cys‐Asp (ECD)‐containing fragment of acurhagin, was evaluated for its biological activities and potential applications in anti‐angiogenic therapy.

Experimental approach:  Human umbilical vein endothelial cells (HUVECs) were treated with acurhagin‐C to assay effects on viability, apoptosis, adhesion, migration, invasion, proliferation and angiogenesis. The recognition site and signalling involved for the interactions of acurhagin‐C with HUVEC were determined using flow cytometric, electrophoresis and immunoblotting analyses.

Key results:  Acurhagin‐C decreased viability and induced apoptosis in HUVEC. It also dose‐dependently inhibited HUVEC adhesion to immobilized extracellular matrices fibronectin, collagen I and vitronectin with respective IC50 values of approximately 0.6, 0.3 and 0.1 µM. Acurhagin‐C prevented migration and invasion of HUVEC through vitronectin‐ and Matrigel‐coated barriers respectively. Furthermore, acurhagin‐C attenuated fibroblast growth factor‐2‐primed angiogenesis both in vitro and in vivo, and specifically blocked the binding of anti‐αvβ3 monoclonal antibody 23C6 to HUVEC in an ECD‐dependent manner. However, purified αvβ3 also dose‐dependently bound to immobilized acurhagin and acurhagin‐C with a saturable pattern. Interference with integrin αvβ3‐mediated functions and promotion of caspase‐3 activation by acurhagin‐C affected morphology of HUVEC and induced apoptosis.

Conclusions and implications:  Acurhagin‐C elicited endothelial anoikis via disruption of αvβ3/focal adhesion kinase/phosphatidylinositol 3‐kinase/Akt survival cascade and subsequent initiation of the procaspase‐3 apoptotic signalling pathway.