bluuebunny/crossref_metadata_2025 huggingface dataset:
Self‐organised patchiness and scale‐dependent bio‐geomorphic feedbacks in aquatic river vegetation
Authors: Schoelynck Jonas , de Groote Toon , Bal Kris , Vandenbruwaene Wouter , Meire Patrick , Temmerman Stijn
Published: November 2011

Spatial self‐organisation of ecosystems is the process by which large‐scale ordered spatial patterns emerge from disordered initial conditions through local feedbacks between organisms and their environment. Such process is considered important for ecosystem functioning, providing increased productivity, resistance and resilience against environmental change. Although spatial self‐organisation has been found for an increasing number of ecosystems, it has never been shown so far for aquatic river vegetation. Here we explore the existence of spatial self‐organisation of freshwater macrophyte patches in a typical lowland river (Belgium), showing that the underlying mechanisms for pattern formation are scale‐dependent feedbacks between plant growth, water flow and local river bed erosion and sedimentation. The mapping of vegetation patches showed that the frequency distribution of patch sizes is governed by a power‐law function, suggesting that the patches are self‐organised. Scale‐dependent feedbacks, likely to lead to this self‐organised pattern, were demonstrated with a mimic experiment. Both positive and negative feedbacks on plants were confirmed by a transplantation experiment. Placing vegetation patch mimics in the river showed experimentally that on a short range (within and behind the mimics) flow reduction and increased sedimentation occurred, while on a larger range (next to patches) the flow was accelerated and decreased sedimentation took place. By transplanting macrophytes within, next to and further away from existing patches, it was proven that the conditions within the patches favoured the survival and growth of transplants (i.e. short‐range positive feedback), while the conditions just next to patches led to decreased survival and growth (i.e. long‐range negative feedback).
Gene expression analysis of an epidermolysis bullosa simplex Dowling‐Meara cell line by subtractive hybridization: recapitulation of cellular differentiation, migration and wound healing
Authors: Wagner Martin , Hintner Helmut , Bauer Johann W. , Onder Kamil
Published: November 2011

Abstract: An intact keratin 5/keratin 14 intermediate filament cytoskeleton is vital for the integrity of basal keratinocytes and for the development and maintenance of epidermal structures. In patients with epidermolysis bullosa simplex Dowling‐Meara (EBS‐DM), heterozygous mutations in the keratin 14 gene in keratinocytes cause a cytoskeletal collapse leading to fragile cells susceptible to cellular stress. The primary aim of this work was to extend analysis of differentially expressed genes in an EBS‐DM model cell line to obtain insights into the molecular consequences resulting from the keratin 14 mutation. In a first step, suppression subtractive hybridization (SSH), a powerful technology to enrich for differentially expressed genes, was used to identify genes whose up‐regulation may be a direct or indirect result of the keratin 14 mutation, R125P. We discovered 55 candidate genes (SSH genes) that were further analysed by RTq‐PCR. Of the 55 SSH genes, 14 (25.45%) were found to be congruently up‐regulated. Bioinformatic analysis revealed significant enrichment of genes regulating epidermal development, migration, apoptosis and wound healing.
Loss of claudin‐1 in lipopolysaccharide‐treated periodontal epithelium
Authors: Fujita T. , Firth J. D. , Kittaka M. , Ekuni D. , Kurihara H. , Putnins E. E.
Published: November 2011

Fujita T, Firth JD, Kittaka M, Ekuni D, Kurihara H, Putnins EE. Loss of claudin‐1 in lipopolysaccharide‐treated periodontal epithelium. J Periodont Res 2012; 47: 222–227. © 2011 John Wiley & Sons A/S

Background and Objective:  The epithelial barrier is a critical component of innate immunity and provides protection against microbial invasion. Claudin‐1, a tight junction protein, is known to contribute to the epithelial cell barrier. An experimentally induced rat periodontal disease model was used to study the effects of lipopolysaccharide (LPS) on the expression of tight junction‐associated molecule genes in the junctional epithelium.

Material and Methods:  LPS was applied for 8 wk in the gingival sulcus, and junctional epithelium was collected by laser‐capture microdissection and subjected to microarray analysis.

Results:  Microarray analysis identified that expression of the claudin‐1 gene was decreased in the epithelium by chronic LPS challenge. Immunohistochemical analysis confirmed the expression of claudin‐1 protein in junctional epithelium and that 8 wk of chronic LPS topical application significantly reduced claudin‐1 expression. The effect of LPS on claudin‐1 protein expression was validated using a porcine junctional epithelial cell culture Transwell model. The epithelial barrier, as measured using transmembrane resistance, was significantly reduced after 3 wk of LPS challenge and this was associated with a decreased level of expression of claudin‐1 protein.

Conclusion:  These results confirm that the initiation of experimental periodontal disease is associated with reduction in the expression of claudin‐1 gene and protein. This decreased level of a critical tight junction protein may result in the disruption of barrier function and may play an important role in the initiation of periodontal disease.
Oral malodorous compound causes caspase‐8 and ‐9 mediated programmed cell death in osteoblasts
Authors: Aoyama I. , Calenic B. , Imai T. , Ii H. , Yaegaki K.
Published: November 2011

Aoyama I, Calenic B, Imai T, Ii H, Yaegaki K. Oral malodorous compound causes caspase‐8 and ‐9 mediated programmed cell death in osteoblasts. J Periodont Res 2012; 47: 365–373. © 2011 John Wiley & Sons A/S

Background and Objective:  Hydrogen sulfide (H2S) is one of two volatile sulfur compounds that are known to be the main cause of oral malodor; the other is methyl mercaptan. Other known volatiles existing in mouth air do not contribute significantly to oral malodor originating in the oral cavity. Hydrogen sulfide is also known to be an etiological factor in periodontal disease. However, the effects of H2S on alveolar bone remain unclear. The objectives of this study were to determine the apoptotic effects of H2S on osteoblasts and to verify the apoptotic molecular pathways.

Material and Methods:  A clonal murine calvaria cell line was incubated with 50 ng/mL of H2S. To detect apoptosis, the cells were analysed by flow cytometry and ELISA. Mitochondrial membrane depolarization was assessed using flow cytometry as well. ELISA was used to evaluate the release of cytochrome c into the cytosol and to assess Fas ligand, p53, tumor necrosis factor α, interleukin IL1‐α IL‐β, IL‐2, IL‐4, IL‐10, interferon‐γ, granulocyte‐colony stimulating factor and granulocyte‐macrophage colony stimulating factor. Caspase‐3, ‐8 and ‐9 activities were estimated. Expression of BAX and Bcl‐2 was assessed by real‐time quantitative RT‐PCR. DNA fragmentation was detected by single‐cell gel electrophoresis. Fas receptors were evaluated by western blotting.

Results:  After H2S incubation, apoptotic levels increased significantly in a time‐dependent manner. Mitochondrial membrane depolarization, the release of cytochrome c, p53 and caspase‐3, ‐8 and ‐9 and DNA fragmentation were all significantly greater. BAX gene activity was upregulated, whereas Bcl‐2 remained low. Fas ligand/Fas receptor, tumor necrosis factor α and other cytokines were not increased to a significant degree.

Conclusion:  At less‐than‐pathological concentrations in gingival crevicular fluid, H2S induces apoptosis in osteoblasts. The molecular mechanisms underlying the apoptotic process include p53, a mitochondrial pathway and caspase‐8 activation.
Vegetation recovery of gypsum quarries: short‐term sowing response to different soil treatments
Authors: Ballesteros Miguel , Cañadas Eva M. , Foronda Ana , Fernández‐Ondoño Emilia , Peñas Julio , Lorite Juan
Published: November 2011

Question

How does the sowing of native species under different soil treatments contribute to the recovery of gypsum habitats affected by quarrying in Mediterranean environments?

Location

Mediterranean gypsum outcrops in Granada (SE Spain; 37º2′ N, 3º45′ W).

Methods

We conducted an experimental sowing of native perennial species from gypsum habitats (both gypsophiles and gypsovags) considering two factors: bedding materials and surface treatments. For bedding material we used: gypsum spoil, topsoil addition on gypsum spoil, raw gypsum and topsoil removal. The surface treatments were: control, sowing, sowing plus organic matter and sowing plus an organic blanket. There were five replicates per combination treatment (80 plots in total, of 25 m2 each). The sowing was performed in Nov 2009. All subplots were monitored to estimate density, richness, survival, growth of seedlings and herbaceous biomass, in two monitoring periods (Jul and Oct).

Results

No gypsophiles or gypsovags were found in the control plots (no sowing or surface treatment), and therefore natural succession proved ineffective in the first year. In contrast, sowing was very satisfactory, especially on gypsum spoil, where mean density was of more than 15 individuals m−2. This result is noteworthy as this material remains after the end of gypsum mining activity. Spreading topsoil over gypsum spoil proved to be no more positive, since it provided not only seeds of target species but also of competitor species. Also, with regard to herbaceous species, this treatment produced a highly significant increase of biomass. The organic blanket increased plant density, whereas the addition of organic matter had significant positive effects on survival and growth of the seedlings. The global high survival rate is remarkable, especially for the gypsum spoil treatment.

Conclusions

We highlight the importance of implementing recovery measures in gypsum habitats. An appropriate selection of seed mixture and density, as well as the use of gypsum spoil (the most favourable bedding material, according the results), is sufficient to ensure presence of the key species. Both technical solutions tested, organic blanket installation and organic matter addition, improved the results in terms of density, survival and growth of the seedlings.
Short‐term changes caused by fire and mowing in Brazilian Campos grasslands with different long‐term fire histories
Authors: Fidelis Alessandra , Blanco Carolina C. , Müller Sandra C. , Pillar Valério D. , Pfadenhauer Jörg
Published: November 2011

Questions

What are the main short‐term changes in vegetation structure after fire and mowing in Campos grasslands? Are there differences in functional vegetation group responses between sites with diverse fire histories and different treatments (fire and mowing)?

Location

Subtropical grasslands in Porto Alegre, Brazil, 30 °03′ S, 51 °07′ W.

Methods

In two sites with different fire histories: FB – frequently burned grasslands and E – exclusion of fire for 6 yr, seven pairs of plots were examined. In each pair, fire and mowing treatments were established. Bare soil and litter cover were estimated. Vegetation relevés were conducted, plants identified, their cover estimated and stems counted (except for graminoids). Later, plants were grouped according to their functional group (graminoids, forbs and shrubs) for statistical analyses. Observations were conducted 30, 90 and 360 d after treatments.

Results

Burned plots always showed a higher percentage of bare soil, whilst mowed plots had higher litter cover. Fire enhanced graminoid and forb cover, but did not affect shrubs. Species turnover was very high, mainly in burned plots in site FB and in mowed plots in site E. Species diversity in burned plots was the same in sites FB and E 1 yr after treatments, contrary to our hypothesis. However, in mowed plots, the number of species tended to decrease 1 yr after treatments for both sites FB and E.

Conclusions

The most important short‐term effect was the removal of litter and consequent opening of gaps, mostly by fire. This stimulated vegetation regeneration and provided microsites for the establishment of new species. However, fire did not enhance plant diversity, as we had hypothesized. Moreover, the disturbance history of sites should be considered, since vegetation in these sites responded differently to fire and mowing.
Caring for smiles – a new educational resource for oral health training in care homes
Authors: Welsh Sheila , Edwards Maura , Hunter Laura
Published: November 2011

doi: 10.1111/j.1741‐2358.2011.00457.x
 
Caring for smiles – a new educational resource for oral health training in care homes
Identification of two new phylogenetically distant phytoplasmas from Senna surattensis plants exhibiting stem fasciation and shoot proliferation symptoms
Authors: Wu W. , Cai H. , Wei W. , Davis R.E. , Lee I.‐M. , Chen H. , Zhao Y.
Published: November 2011

Sunshine trees (Senna surattensis) exhibiting unusual stem fasciation symptoms were observed in Yunnan, China. Morphological abnormalities of the affected plants included enlargement and flattening of stems and excessive proliferation of shoots. An electron microscopic investigation revealed presence of single membrane bound mycoplasma‐like bodies in sieve elements of symptomatic plants. With DNA templates extracted from diseased plants and phytoplasma universal primers P1/P7 and P1A/R16S‐SR, nested polymerase chain reactions produced amplicons of 1.5 kb. Subsequent restriction fragment polymorphism and nucleotide sequence analyses of the amplicons indicated that the diseased plants were infected by distinct phytoplasmas affiliated with two phylogenetically distant taxa classified in two 16Sr groups (16SrXII and 16SrV). This is the first report that sunshine tree is a natural host of two evolutionarily divergent phytoplasmas and the first report that a ‘Candidatus Phytoplasma australiense’‐related strain is present in China. The findings signal a significant expansion of both geographical distribution and host range of 16SrXII and 16SrV phytoplasmas.
The Impact of Annual and Seasonal Rainfall Patterns on Growth and Phenology of Emergent Tree Species in Southeastern Amazonia, Brazil
Authors: Grogan James , Schulze Mark
Published: November 2011

Understanding tree growth in response to rainfall distribution is critical to predicting forest and species population responses to climate change. We investigated inter‐annual and seasonal variation in stem diameter by three emergent tree species in a seasonally dry tropical forest in southeast Pará, Brazil. Annual diameter growth rates bySwietenia macrophyllademonstrated strong positive correlation with annual rainfall totals during 1997–2009;Hymenaea courbarilgrowth rates demonstrated weak positive correlation, whereasParkia pendulaexhibited weak negative correlation. For bothSwieteniaandHymenaea, annual diameter growth rates correlated positively and significantly with rainfall totals during the first 6 mo of the growing year (July to December). Vernier dendrometer bands monitored at 4‐wk intervals during 3–5 yr confirmed strong seasonal effects on stem diameter expansion. Individuals of all three species expanded in unison during wet season months and were static or even contracted during dry season months. Stems of the deciduousSwieteniacontracted as crowns were shed during the early dry season, expanded slightly as new crowns were flushed, and then contracted further during 3–5 wk flowering periods in the late dry season by newly mature crowns. The three species’ physiographic distribution patterns at the study site may partially underlie observed differences in annual and seasonal growth. With most global circulation models predicting conditions becoming gradually drier in southeast Amazonia over the coming decades, species such asSwieteniathat perform best on the ‘wet end’ of current conditions may experience reduced growth rates. However, population viability will not necessarily be threatened if life history and ecophysiological responses to changing conditions are compensatory.
Cocaine‐related oronasal communication and hard palate destruction
Authors: Silvestre Francisco Javier , Salort‐Llorca Cesar , Mínguez‐Serra Maria Paz , Silvestre‐Rangil Javier
Published: November 2011

Four cases of midpalatal perforation in cocaine abusers are presented. Other potential etiological processes are discussed to establish an adequate differential diagnosis. These patients were treated at our department, due to the drawback promoted by the establishment of oronasal communication that was provided after an accurate diagnosis. Histopathological evaluation of the lesion margins were conducted in two of the four cases, and yielded no evidence of vasculitis or active cocaine abuse. Therapeutic approach consisted of reconstructive surgeries and/or sealing prostheses. Histological assessment of oronasal communication margins could be useful in establishing the persistence of active addiction, and also as a complementary tool for planning possible treatment.
Heterogeneous patterns of availability for detection during visual surveys: spatiotemporal variation in sea turtle dive–surfacing behaviour on a feeding ground
Authors: Thomson Jordan A. , Cooper Andrew B. , Burkholder Derek A. , Heithaus Michael R. , Dill Lawrence M.
Published: November 2011

1. During aerial or boat‐based surveys for large‐bodied diving taxa (e.g. marine mammals and marine turtles), a proportion of animals present will be missed because they are submerged and out of view, leading to ‘availability bias’ in abundance indices. Information on dive–surfacing patterns can improve corrections for availability bias. However, as dive data are typically limited, availability correction factors are often based on poorly resolved dive and surface times, and diving heterogeneity is not considered.

2. We collected dive records for green turtlesChelonia mydas,Linnaeus 1758, and loggerhead turtlesCaretta caretta, Linnaeus 1758, on a foraging ground in Shark Bay, Western Australia to quantify dive–surfacing patterns and assess potential correlations with easily measured environmental features: habitat depth and water temperature. Bayesian regression models were used to predict dive and surface interval durations across temperature–depth gradients and assess their uncertainty. We used these predictions to quantify variation in availability correction factors, which were multipliers designed, in this case, to adjust surface sightings data to incorporate diving animals.

3. Dive and surface interval durations for both species varied positively with depth and negatively with temperature, consistent witha prioriexpectations, although temperature effects were not always significant. Dive metrics were predictable, although uncertainty increased in deeper habitat with few observed dives.

4. Availability correction factors were highly heterogeneous, with larger corrections necessary in colder, deeper conditions (long‐diving, infrequent surfacing behaviour) and smaller corrections required in warmer, shallower conditions (short‐diving, frequent‐surfacing behaviour).

5. Predictable variation in the diving behaviour of chelonid sea turtles across environmental gradients on a foraging ground reveals that site‐specific knowledge of dive–surfacing patterns can be important to mitigate the effects of availability bias during population surveys. Accounting for such trends may improve the reliability of ecological inferences (e.g. spatiotemporal distribution trends) and the efficacy of applications (e.g. conservation planning) based on survey data.
Pharmacokinetics and tissue distribution profile of icariin propylene glycol-liposome intraperitoneal injection in mice
Authors: Yang Wei , Yu Xi-Chong , Chen Xing-Yan , Zhang Lu , Lu Cui-Tao , Zhao Ying-Zheng
Published: November 2011

Objectives

The pharmacokinetics and tissue distribution of icariin propylene glycol-liposome suspension (ICA-PG-liposomes) have been investigated.

Methods

ICA-PG-liposomes or ICA-PG-solution were prepared and intraperitoneally injected to mice. Morphology and size distribution of ICA-PG-liposomes were observed by transmission electron microscopy (TEM) and laser particle sizer. Plasma and tissues were collected at different times after intraperitoneal injection and icariin concentrations were determined by HPLC.

Key findings

From TEM, ICA-PG-liposomes showed spherical vesicles with a mean particle size of 182.4 nm. The encapsulation efficiency of ICA-PG-liposomes reached 92.6%. Pharmacokinetics of ICA-PG-liposomes displayed the three open compartments model. ICA-PG-liposomes enhanced icariin absorption from the abdominal cavity, prolonged mean retention time (MRT(0-t)), increased area under curve (AUC(0-t)) and maximum concentration in plasma. Compared with ICA-PG-solution, ICA-PG-liposomes resulted in larger amounts of icariin being distributed into spleen (60.38% total icariin), liver (16.68%), lung (6.21%), kidney (4.64%), heart (1.43%) and brain (1.83%). AUC(0-t) values in most tissues (except lung) of mice administered ICA-PG-liposomes were higher than those administered ICA-PG-solution, while Clearance in most tissues (except brain and lung) decreased. The MRT(0-t) values of ICA-PG-liposomes in all tissues and half lives of most tissues (except brain) were prolonged. From Targeted efficiency and relative uptake data, the spleen was the target tissue of the ICA-PG-liposomes.

Conclusions

ICA-PG-liposomes changed the pharmacokinetic behaviour and enhanced icariin distribution in tissues. With nanometer size, high encapsulation efficiency and improved pharmacokinetics, ICA-PG-liposomes might be developed as promising carriers for icariin injection.
Comparison of sildenafil with strontium fructose diphosphate in improving erectile dysfunction against upregulated cavernosal NADPH oxidase, protein kinase Cε, and endothelin system in diabetic rats
Authors: Xu Ming , Tang Yi-Qun , Dai De-Zai , Zheng Yu-Feng , Cheng Yu-Si , Zhang Qi , Dai Yin
Published: November 2011

Objectives

Phosphodiesterase type 5 inhibitors are potent in relieving erectile dysfunction (ED), however, they are less satisfactory in diabetic patients, probably due to the pro-inflammatory biomarkers caused by diabetes. Therefore, it was interesting to compare the effects of sildenafil with strontium fructose 1,6-diphosphate (FDP-Sr) on cavernosal vascular activity and expressions of pro-inflammatory biomarkers in diabetic rats.

Methods

Male Sprague-Dawley rats were injected with streptozocin (60 mg/kg, i.p.) to develop diabetes. The animals were diabetic for eight weeks with sildenafil (12 mg/kg per day) or FDP-Sr (200 mg/kg per day) being administered for the last four of those eight weeks.

Key findings

Sildenafil was more effective in relieving reduced vascular dilatation (relevant to ED), but less in attenuating over-expressions of NADPH oxidase p22, p47 and p67 subunits, and ETA/BR (endothelin receptor type A and type B) in the diabetic cavernosum. In contrast, FDP-Sr was less effective in improving ED, but more effective in normalizing the abnormal NADPH oxidase and ETA/BR.

Conclusions

The activated NADPH oxidase and upregulated ETAR and ETBR due to diabetic lesions played a minor or moderate role in ED. By offering extra ATP, FPD-Sr suppressed these abnormalities, however, sildenafil did not. A combined therapy of sildenafil with FDP-Sr may be more effective in relieving ED in diabetic patients through normalizing pro-inflammatory cytokines and improving the nitric oxide/cGMP pathway in the cavernosum.
Solvation in hydrofluoroalkanes: how can ethanol help?
Authors: Conti Denise S , Grashik Jordan , Yang Lin , Wu Libo , da Rocha Sandro R P
Published: November 2011

Objectives

The goal of this work was to evaluate the ability of ethanol mixed with hydrofluoroalkanes (HFAs) to improve solvation of moieties of relevance to pressurized metered-dose inhalers (pMDIs).

Methods

Chemical force microscopy was used to measure the adhesion force (Fad) between alkyl-based, ether-based and ester-based moieties (C8/C8, COC/COC and COOC/COOC interactions) in 2H,3H-perfluoropentane (HPFP)/ethanol mixtures. HPFP is a liquid that mimics propellant HFAs. The Fad results are thus a measure of solvation in HFAs. Johnson–Kendall–Roberts (JKR) theory was used to model the results.

Key findings

The Fad normalized by the tip radius of curvature (Fad/R) decreased upon the addition of ethanol, suggesting its ability to enhance the solvent environment. At 15% (v/v) ethanol, the Fad/R was reduced 34% for the alkyl, 63% for the ether, and down 67% for the ester tails. Thus, the solvation could be ranked as: ester > ether > alkyl. JKR theory was a reasonable model for the Fad/R.

Conclusions

Ethanol, within the concentration range of interest in commercial pMDIs, provided limited enhancement in solvation of alkyl moieties. On the other hand, the cosolvent significantly enhanced solvation of ether-based and ester-based moieties, thus suggesting its potential for formulations containing amphiphiles with such groups.
NSAIDs: take with food or after fasting?
Authors: Rainsford Kim D , Bjarnason Ingvar
Published: November 2011

Objective

Published and regulatory advice is to take NSAIDs with fluids and/or food irrespective whether NSAIDs are taken over the counter or long-term. The basis for this recommendation is not clear and we sought to establish the reasons for it through a search of published literature and personal files.

Results

Results from experimental animals show that fasting increases the gastric side effects of NSAIDs while food increases small bowel damage, but this has not been tested in humans. The possible effects of food in modifying the gastric damage caused by NSAIDs are complex, as food quantity and composition modify the responses substantially. Food usually delays peak levels of NSAIDs (and hence onset of action) without affecting total bioavailability. This may not be important when a steady state is achieved, but rapid onset of action is highly relevant for over-the-counter use of NSAIDs. The safety of over-the-counter use of ibuprofen and naproxen appears to be excellent and comparable with paracetamol.

Conclusion

The rapid onset of action of NSAIDs is most important during over-the-counter use, in which case it may be more appropriate to take the drugs on a fasting stomach.
New Correlative Models for Fully Developed Turbulent Heat and Mass Transfer in Circular and Noncircular Ducts
Authors: Duan Zhipeng
Published: November 2011

Fully developed turbulent flow in noncircular ducts is examined, and simple models are proposed to predict the friction, heat and mass transfer in most common noncircular channels. It is found that the square root of cross-sectional area is the relatively more appropriate length scale to use in defining the dimensionless parameters to ensure similarity between the circular and most noncircular ducts. By using the dimensionless parameters based on the square root of cross-sectional area, it is demonstrated that the circular tube relations may be applied to most noncircular ducts eliminating large errors in estimation. As turbulent transport phenomena are inherently complex and there, currently, is no extensive experimental data for turbulent heat and mass transfer in noncircular ducts, the simple models are valuable in spite of their limitations.
Three-dimensional proximity effect correction for large-scale uniform patterns
Authors: Dai Q. , Lee S.-Y. , Lee S.-H. , Kim B.-G. , Cho H.-K.
Published: November 2011

One of the major limiting factors in electron beam (e-beam) lithography is the geometric distortion of written features due to electron scattering, which is known as the proximity effect. A conventional approach to the proximity effect correction (PEC) is, through 2D simulation, to determine the dose distribution and/or shape modification for each feature in a circuit pattern such that the written pattern is as close to the target pattern as possible. Earlier, it was shown that the 3D PEC, which considers the variation of exposure along the resist-depth dimension, would be necessary for the feature size well below 100 nm. Also, a feature-by-feature correction procedure is too time-consuming to be practical, especially for the 3D PEC of large-scale patterns. In this paper, a new method for the 3D PEC is proposed, which adopts 3D resist profile (instead of 2D exposure distribution) in optimization, but avoids the intensive computation by employing a critical-location-based correction procedure. The proposed method achieves 3D resist profiles closer to the target ones, compared to 2D PEC. The simulation results show that the proposed method has a potential to provide a practical and effective alternative to the conventional approach.
Scanning proximal probe lithography for sub-10 nm resolution on calix[4]resorcinarene
Authors: Kaestner Marcus , Rangelow Ivo W.
Published: November 2011

The use of molecular resist in scanning proximal probe lithography (SPPL) offers a novel and promising maskless lithographic method with sub-10 nm resolution. Here, the authors present their investigation of the patterning capabilities of C-Methylcalix[4]resorcinarene at ambient conditions using SPPL. The STM-based setup operates in constant-current Fowler–Nordheim regime and results in positive-tone self-developing phenomena. The lithographic operation is performed at currents in the range of pico-ampere, writing speeds of 1–10 μm/s, and bias voltages ranging from 20 up to 70 V. Currently, the authors have achieved feature sizes from 7 nm to micrometers depending on the applied exposure parameters. The direct patterning process shows high reproducibility and reliability over this large feature range.
The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution
Authors: Ben-Shem Adam , Garreau de Loubresse Nicolas , Melnikov Sergey , Jenner Lasse , Yusupova Gulnara , Yusupov Marat
Published: November 2011

A close-up view of the ribosome’s 79 proteins and 5500 RNA nucleotides.
Host Proteasomal Degradation Generates Amino Acids Essential for Intracellular Bacterial Growth
Authors: Price Christopher T. D. , Al-Quadan Tasneem , Santic Marina , Rosenshine Ilan , Abu Kwaik Yousef
Published: November 2011

The bacterial pathogen
Legionella pneumophila
ensures amino acid supplies by promoting degradation of target host proteins.
Calibrating the End-Permian Mass Extinction
Authors: Shen Shu-zhong , Crowley James L. , Wang Yue , Bowring Samuel A. , Erwin Douglas H. , Sadler Peter M. , Cao Chang-qun , Rothman Daniel H. , Henderson Charles M. , Ramezani Jahandar , Zhang Hua , Shen Yanan , Wang Xiang-dong , Wang Wei , Mu Lin , Li Wen-zhong , Tang Yue-gang , Liu Xiao-lei , Liu Lu-jun , Zeng Yong , Jiang Yao-fa , Jin Yu-gan
Published: November 2011

High-precision geochronologic dating constrains probable causes of Earth's largest mass extinction.
HIDDEN SYMMETRIES IN A GAUGE-COVARIANT APPROACH, HAMILTONIAN REDUCTION AND OXIDATION
Authors: VISINESCU MIHAI
Published: November 2011

Hidden symmetries in a covariant Hamiltonian formulation are investigated involving gauge covariant equations of motion. The special role of the Stäckel–Killing tensors is pointed out. A reduction procedure is used to reduce the original phase space to another one in which the symmetries are divided out. The reverse of the reduction procedure is done by stages performing the unfolding of the gauge transformation followed by the Eisenhart lift in connection with scalar potentials.
NONCOMMUTATIVE SPACE CORRECTIONS ON THE KLEIN–GORDON AND DIRAC OSCILLATORS SPECTRA
Authors: MALUF ROBERTO V.
Published: November 2011

We consider the influence of a noncommutative space on the Klein–Gordon and the Dirac oscillators. The nonrelativistic limit is taken and the θ-modified Hamiltonians are determined. The corrections of these Hamiltonians on the energy levels are evaluated in first-order perturbation theory. It is observed a total lifting of the degeneracy to the considered levels. Such effects are similar to the Zeeman splitting in a commutative space.
ELASTIC SURFACE PLASMON POLARITON SCATTERING: NEAR- AND FAR-FIELD INTERACTIONS
Authors: SEGOVIA PAULINA , COELLO VICTOR
Published: November 2011

Using a vectorial dipolar model for multiple surface plasmon-polariton (SPP) scattering, we investigate propagation and elastic (in-plane) scattering of SPP's excited in the wavelength range of 543–633nm at random nanostructured gold surfaces. The model makes use of a composed analytic Green dyadic which takes into account near- and far-field regions, with the latter being approximated by the part describing the scattering via excitation of SPP. Simultaneous SPP excitation and in-plane propagation inside square-random arrays of nanoparticles were observed with different density of particles, demonstrating the feasibility of the suggested approach. The composed Green dyadic represents an improvement of previous SPP simulations for random nanoparticles arrays since it permits SPP scattering simulations for more realistic systems with relatively large number of close, or even in contact, nanoparticles. Our results suggest that this numerical approach is quite promising for the quantitative description of light-SPP coupling and associated processes such as weak and strong SPP localization.
Enteral bile acid treatment improves parenteral nutrition-related liver disease and intestinal mucosal atrophy in neonatal pigs
Authors: Jain Ajay Kumar , Stoll Barbara , Burrin Douglas G. , Holst Jens J. , Moore David D.
Published: November 2011

Total parenteral nutrition (TPN) is essential for patients with impaired gut function but leads to parenteral nutrition-associated liver disease (PNALD). TPN disrupts the normal enterohepatic circulation of bile acids, and we hypothesized that it would decrease intestinal expression of the newly described metabolic hormone fibroblast growth factor-19 (FGF19) and also glucagon-like peptides-1 and -2 (GLP-1 and GLP-2). We tested the effects of restoring bile acids by treating a neonatal piglet PNALD model with chenodeoxycholic acid (CDCA). Neonatal pigs received enteral feeding (EN), TPN, or TPN + CDCA for 14 days, and responses were assessed by serum markers, histology, and levels of key regulatory peptides. Cholestasis and steatosis were demonstrated in the TPN group relative to EN controls by elevated levels of serum total and direct bilirubin and also bile acids and liver triglyceride (TG) content. CDCA treatment improved direct bilirubin levels by almost fourfold compared with the TPN group and also normalized serum bile acids and liver TG. FGF19, GLP-1, and GLP-2 were decreased in plasma of the TPN group compared with the EN group but were all induced by CDCA treatment. Intestinal mucosal growth marked by weight and villus/crypt ratio was significantly reduced in the TPN group compared with the EN group, and CDCA treatment increased both parameters. These results suggest that decreased circulating FGF19 during TPN may contribute to PNALD. Moreover, we show that enteral CDCA not only resolves PNALD but acts as a potent intestinal trophic agent and secretagogue for GLP-2.
Mechanisms of systemic vasodilation by lysozyme-c in septic shock
Authors: Gotes Jose , Kasian Krika , Jacobs Hans , Cheng Zhao-Qin , Mink Steven N.
Published: November 2011

In septic shock (SS), cardiovascular collapse is caused by the release of inflammatory mediators. We previously found that lysozyme-c (Lzm-S), released from leukocytes, contributed to systemic vasodilation in a canine model of SS. We then delineated the pathway by which this occurs in a canine carotid artery organ bath preparation (CAP). We showed that Lzm-S could intrinsically generate hydrogen peroxide (H2O2) and that H2O2subsequently reacted with endogenous catalase to form compound I, an oxidized form of catalase. In turn, compound I led to an increase in cyclic guanosine 3′,5′-monophosphate to produce vasodilation. However, it was not clear from previous studies whether it is necessary for Lzm-S to bind to the vasculature to cause vasodilation or, alternatively, whether the generation of H2O2by Lzm-S in the surrounding medium is all that is required. We examined this question in the present study in which we used multiple preparations. In a partitioned CAP, we found that when we added Lzm-S to a partitioned space in which a semipermeable membrane prevented diffusion of Lzm-S to the carotid artery tissue, vasodilation still occurred because of diffusion of H2O2. On the other hand, we found that Lzm-S could accumulate within the vascular smooth muscle layer (VSML) after 7 h of SS in a canine model. We also determined that when Lzm-S was located in close proximity to vascular smooth muscle cells, it could generate H2O2to produce lengthening in a human cell culture preparation. We conclude that there are two mechanisms by which Lzm-S can cause vasodilation in SS. In one instance, H2O2generated by Lzm-S in plasma diffuses to the VSML to cause vasodilation. In a second mechanism, Lzm-S directly binds to the VSML, where it generates H2O2to produce vasodilation.
Spaceflight regulates ryanodine receptor subtype 1 in portal vein myocytes in the opposite way of hypertension
Authors: Dabertrand Fabrice , Porte Yves , Macrez Nathalie , Morel Jean-Luc
Published: November 2011

Gravity has a structural role for living systems. Tissue development, architecture, and organization are modified when the gravity vector is changed. In particular, microgravity induces a redistribution of blood volume and thus pressure in the astronaut body, abolishing an upright blood pressure gradient, inducing orthostatic hypotension. The present study was designed to investigate whether isolated vascular smooth muscle cells are directly sensitive to altered gravitational forces and, second, whether sustained blood pressure changes act on the same molecular target. Exposure to microgravity during 8 days in the International Space Station induced the decrease of ryanodine receptor subtype 1 expression in primary cultured myocytes from rat hepatic portal vein. Identical results were found in portal vein from mice exposed to microgravity during an 8-day shuttle spaceflight. To evaluate the functional consequences of this physiological adaptation, we have compared evoked calcium signals obtained in myocytes from hindlimb unloaded rats, in which the shift of blood pressure mimics the one produced by the microgravity, with those obtained in myocytes from rats injected with antisense oligonucleotide directed against ryanodine receptor subtype 1. In both conditions, calcium signals implicating calcium-induced calcium release were significantly decreased. In contrast, in spontaneous hypertensive rat, an increase in ryanodine receptor subtype 1 expression was observed as well as the calcium-induced calcium release mechanism. Taken together, our results shown that myocytes were directly sensitive to gravity level and that they adapt their calcium signaling pathways to pressure by the regulation of the ryanodine receptor subtype 1 expression.
Middle cerebral artery alterations in a rat chronic hypoperfusion model
Authors: Márquez-Martín Ana , Jiménez-Altayó Francesc , Dantas Ana P. , Caracuel Laura , Planas Anna M. , Vila Elisabet
Published: November 2011

Chronic cerebral hypoperfusion (CHP) induces microvascular changes that could contribute to the progression of vascular cognitive impairment and dementia in the aging brain. This study aimed to analyze the effects of CHP on structural, mechanical, and myogenic properties of the middle cerebral artery (MCA) after bilateral common carotid artery occlusion (BCCAO) in adult male Wistar rats. Sham animals underwent a similar surgical procedure without carotid artery (CA) ligation. After 15 days of occlusion, MCA and CA were dissected and MCA structural, mechanical, and myogenic properties were assessed by pressure myography. Collagen I/III expression was determined by immunofluorescence in MCA and CA and by Western blot in CA. mRNA levels for 1A1, 1A2, and 3A1 collagen subunits were quantified by quantitative real-time PCR in CA. Matrix metalloproteinase (MMP-1, MMP-2, MMP-9, and MMP-13) and hypoxia-inducible factor-1α (HIF-1α) protein expression were determined in CA by Western blot. BCCAO diminished cross-sectional area, wall thickness, and wall-to-lumen ratio. Nevertheless, whereas wall stress was increased, stiffness was not modified and myogenic response was diminished. Hypoperfusion triggered HIF-1α expression. Collagen I/III protein expression diminished in MCA and CA after BCCAO, despite increased mRNA levels for 1A1 and 3A1 collagen subunits. Therefore, the reduced collagen expression might be due to proteolytic degradation, since the expression of MMP-1 and MMP-9 increased in the CA. These data suggest that BCCAO induces hypotrophic remodeling by a mechanism that involves a reduction of collagen I/III in association with increased MMP-1 and MMP-9 and that decreases myogenic tone in major arteries supplying the brain.
Effects of whole body vibration on motor unit recruitment and threshold
Authors: Pollock Ross D. , Woledge Roger C. , Martin Finbarr C. , Newham Di J.
Published: November 2011

Whole body vibration (WBV) has been suggested to elicit reflex muscle contractions but this has never been verified. We recorded from 32 single motor units (MU) in the vastus lateralis of 7 healthy subjects (34 ± 15.4 yr) during five 1-min bouts of WBV (30 Hz, 3 mm peak to peak), and the vibration waveform was also recorded. Recruitment thresholds were recorded from 38 MUs before and after WBV. The phase angle distribution of all MUs during WBV was nonuniform ( P < 0.001) and displayed a prominent peak phase angle of firing. There was a strong linear relationship ( r = −0.68, P < 0.001) between the change in recruitment threshold after WBV and average recruitment threshold; the lowest threshold MUs increased recruitment threshold ( P = 0.008) while reductions were observed in the higher threshold units ( P = 0.031). We investigated one possible cause of changed thresholds. Presynaptic inhibition in the soleus was measured in 8 healthy subjects (29 ± 4.6 yr). A total of 30 H-reflexes (stimulation intensity 30% Mmax) were recorded before and after WBV: 15 conditioned by prior stimulation (60 ms) of the antagonist and 15 unconditioned. There were no significant changes in the relationship between the conditioned and unconditioned responses. The consistent phase angle at which each MU fired during WBV indicates the presence of reflex muscle activity similar to the tonic vibration reflex. The varying response in high- and low-threshold MUs may be due to the different contributions of the mono- and polysynaptic pathways but not presynaptic inhibition.
Mesenchymal Stromal Cell Mutations and Wound Healing Contribute to the Etiology of Desmoid Tumors
Authors: Carothers Adelaide M. , Rizvi Hira , Hasson Rian M. , Heit Yvonne I. , Davids Jennifer S. , Bertagnolli Monica M. , Cho Nancy L.
Published: November 2011

Desmoid tumors are nonmalignant neoplasms of mesenchymal origin that mainly contain fibroblast lineage cells. These tumors often occur in patients with familial adenomatous polyposis (FAP) coli who have germ line mutations in the APC gene. Given emerging data that has implicated multipotent mesencyhmal stromal cells (MSC) in the origin of mesenchymal tumors, we hypothesized that desmoid tumors may arise in patients with FAP after MSCs acquire somatic mutations during the proliferative phase of wound healing. To test this idea, we examined 16 desmoid tumors from FAP-associated and sporadic cases, finding that all 16 of 16 tumors expressed stem cell markers, whereas matching normal stromal tissues were uniformly negative. Desmoid tumors also contained a subclass of fibrocytes linked to wound healing, angiogenesis, and fibrosis. Using an MSC cell line derived from an FAP-associated desmoid tumor, we confirmed an expected loss in the expression of adenomatous polyposis coli (APC) and the transcriptional repressor BMI-1 while documenting the coexpression of markers for chondrocytes, adipocytes, and osteocytes. Together, our findings argue that desmoid tumors result from the growth of MSCs in a wound healing setting that is associated with deregulated Wnt signaling due to APC loss. The differentiation potential of these MSCs combined with expression of BMI-1, a transcriptional repressor downstream of Hedgehog and Notch signaling, suggests that desmoid tumors may respond to therapies targeting these pathways. Cancer Res; 72(1); 346–55. ©2011 AACR.
Lymphatic Invasion Is Independently Prognostic of Metastasis in Primary Cutaneous Melanoma
Authors: Xu Xiaowei , Chen Lianjun , Guerry DuPont , Dawson Peter R. , Hwang Wei-ting , VanBelle Patricia , Elder David E. , Zhang Paul J. , Ming Michael E. , Schuchter Lynn , Gimotty Phyllis A.
Published: November 2011

Purpose: Lymphatic invasion (LI) in primary cutaneous melanomas was recently found to be common. In this study, we evaluated LI as an independent prognostic factor.

Experimental Design: This study included 251 patients with vertical growth phase (VGP) primary cutaneous melanomas who had paraffin-fixed lesional tissue and were in a prospective cohort seen between 1972 and 1991, had no clinical evidence of regional nodal disease at diagnosis, and had at least ten years of follow-up. Dual immunohistochemical staining was used to detect lymphatic endothelium (podoplanin) and melanoma cells (S-100). Multivariate logistic regression for ten-year metastasis was used to define independent prognostic factors, and a prognostic tree was developed to characterize and discriminate risk groups. Kaplan–Meier disease-free survival curves for those with and without LI within current American Joint Committee on Cancer stages were compared using the log-rank statistic.

Results: LI was observed in 43% (108 of 251) of the study melanomas. The multivariate model for ten-year metastasis identified four independent prognostic factors: tumor thickness, mitotic rate, LI, and anatomic site. The prognostic tree identified a group of patients with thin (≤1 mm thick) melanomas and poor prognosis: stage IB melanomas with LI. Survival curves for time to first metastasis showed significantly poorer prognosis for patients with LI compared with those without it for both stages IB and IIA.

Conclusions: LI is common across the range of tumor thicknesses in primary VGP melanomas. It is an independent prognostic factor and significantly increases the risk of metastasis in patients in clinical stages IB and IIA. Clin Cancer Res; 18(1); 229–37. ©2011 AACR.
S100A8 and S100A9 in Cardiovascular Biology and Disease
Authors: Averill Michelle M. , Kerkhoff Claus , Bornfeldt Karin E.
Published: November 2011

There is recent and widespread interest in the damage-associated molecular pattern molecules S100A8 and S100A9 in cardiovascular science. These proteins have a number of interesting features and functions. For example, S100A8 and S100A9 (S100A8/A9) have both intracellular and extracellular actions, they are abundantly expressed in inflammatory and autoimmune states, primarily by myeloid cells but also by other vascular cells, and they modulate inflammatory processes, in part through Toll-like receptor 4 and the receptor for advanced glycation end products. S100A8/A9 also have anti-inflammatory and immune regulatory actions. Furthermore, increased plasma levels of S100A8/A9 predict cardiovascular events in humans, and deletion of these proteins partly protects
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mice from atherosclerosis. Understanding the roles of S100A8 and S100A9 in vascular cell types and the mechanisms whereby these proteins mediate their biological effects may offer new therapeutic strategies to prevent, treat, and predict cardiovascular diseases.