bluuebunny/crossref_metadata_2025 huggingface dataset:
Tunneled superficial inferior epigastric artery (SIEA) myocutaneous/vascularized femur chimeric flaps: A model to study the role of vascularized bone marrow in composite allografts
Authors: Mundinger Gerhard S. , Kelamis Joseph A. , Kim Soon H. , Magarakis Michael , Jones Luke S. , Ha Jinny S. , Rodriguez Eduardo D.
Published: November 2011

The role of vascularized bone marrow in promoting composite allograft survival can be assessed by intrinsically chimeric flaps. In this study, we introduce a significant modification to a previously described rat model of combined superficial inferior epigastric artery (SIEA) myocutaneous/vascularized femur transplantation. We previously noted autocannibalization in orthotopic myocutaneous SIEA allotransplants, which complicated clinical and histologic evaluation of rejection. We therefore designed syngeneic experiments in eight Lewis (RTl1) rat pairs to explore the feasibility of tunneling the SIEA component of chimeric SIEA myocutaneous/vascularized femur flaps to the recipient dorsum. Vascularized SIEA myocutaneous/femur transplants survived in their entirety to POD 63 study endpoint with patent anastomoses in seven of eight (87.5%) transplants as confirmed clinically, histologically, and via near‐infrared fluorescent angiography. Tunneling of the SIEA component of SIEA myocutaneous/vascularized femur flaps to the recipient dorsum can be achieved with high success rate and acceptable operative times, and is a technically easy method to study the role of vascularized bone marrow in composite allografts. This modification facilitates SIEA component monitoring, removes it from constant contact with cage bedding, and places it in a location where autocannibalization is unlikely. © 2011 Wiley Periodicals, Inc. Microsurgery, 2012.
Prediction of time‐to‐exhaustion in the first dorsal interosseous muscle from early changes in surface electromyography parameters
Authors: Bouillard Killian , Frère Julien , Hug François , GuÉvel Arnaud
Published: November 2011

Introduction: In this study we evaluated the precision of the time‐to‐exhaustion (Tlim) prediction from the early changes in surface electromyography (sEMG) of the first dorsal interosseous muscle. Methods: Thirty subjects performed an index finger isometric abduction at 35% of maximal voluntary contraction (MVC) until exhaustion. Ten participants performed the same exercise at 50% MVC 1 week later. Changes in sEMG parameters across time were modeled using the area‐ratio and the linear regression slope. Tlim was plotted as a function of each of these indices of change, and the coefficient of determination (R2) was determined. Results: Null to moderate R2 (0.22 and 0.56 at 35% and 50% MVC, respectively) values were calculated. The best Tlim estimation led to a high prediction error (21.6 ± 15.0% of Tlim for the 50% MVC task). Conclusions: Although the prediction of time‐to‐exhaustion is an appealing research topic, these results suggest that it cannot be done solely from sEMG. Muscle Nerve 45: 835–840, 2012
Optical and electrical characteristics of Mn‐doped InN grown by plasma‐assisted molecular beam epitaxy
Authors: Chai Jessica H. , Song Young‐Wook , Reeves Roger J. , Durbin Steven M.
Published: November 2011

With the material quality of undoped indium nitride significantly improved, attention has more recently turned towards achieving control of the electrical properties of this infrared bandgap semiconductor. Of the candidate acceptors, only Mg has been reported in detail, primarily as it is the acceptor of choice for GaN and GaInN. There are several other possibilities, however, which may be worth considering. In this paper, we describe the in situ doping of InN using Mn in a plasma‐assisted molecular beam epitaxy process. Evidence of surfactant behaviour is observed in both in situ reflection high‐enegy electron diffraction (RHEED) and ex situ scanning electron microscopy (SEM). Although electrical measurements are difficult to interpret due to the presence of an electron accumulation layer on the surface, photoluminescence (PL) measurements reveal a number of low‐energy features previously unreported in this material, and may be correlated to Mn forming a deep acceptor.
Structural properties of AlN films deposited by plasma‐enhanced atomic layer deposition at different growth temperatures
Authors: Alevli Mustafa , Ozgit Cagla , Donmez Inci , Biyikli Necmi
Published: November 2011

Crystalline aluminum nitride (AlN) films have been prepared by plasma‐enhanced atomic layer deposition (PEALD) within the temperature range from 100 to 500 °C. A self‐limiting, constant growth rate per cycle temperature window (100–200 °C) was established which is the major characteristic of an ALD process. At higher temperatures (>225 °C), deposition rate increased with temperature. Chemical composition, crystallinity, surface morphology, mass density, and spectral refractive index were studied for AlN films. X‐ray photoelectron spectroscopy (XPS) analyses indicated that besides main AlN bond, the films contained AlON, AlO complexes, and AlAl metallic aluminum bonds as well. Crystalline hexagonal AlN films were obtained at remarkably low growth temperatures. The mass density increased from 2.65 to 2.96 g/cm3 and refractive index of the films increased from 1.88 to 2.08 at 533 nm for film growth temperatures of 100 and 500 °C, respectively.
Metal‐sulfide assisted rapid crystallization of highly (001)‐textured tungsten disulphide (WS2) films on metallic back contacts
Authors: Brunken Stephan , Mientus Rainald , Ellmer Klaus
Published: November 2011

Highly (001)‐textured, photoactive WS2 films, which could be deposited before only on insulating substrates, have been prepared on polycrystalline metal layers, which can be used as back contacts for electronic WS2 devices, for instance for thin film solar cells. The WS2 films were prepared by the amorphous‐solid‐liquid‐crystalline‐solid (aSLcS) crystallization process from a Ni–S eutectic. However, normal polycrystalline metallic films can not be used as back contact layers, caused by the diffusion of the thin metal promoter (Ni) into the back contact layer, before a nickel–sulfur eutectic can be formed. Preventing the diffusion of the metal promoter into the back contact allows using the well‐known metal‐promoter assisted crystallization to grow photoactive films on different back contacts, like TiN:O. Additionally, WS2 films on tungsten layers could be grown by Ni‐induced sulfidation of W films. Based on these experiments the model of the rapid nickel sulfide induced crystallization was modified: Ni assists the growth of WS2 crystallites already at temperatures between 500 and 600 °C leading to WS2 films with differently oriented crystallites. At temperatures above the Ni–S eutectic temperature (637 °C) liquid NiSx droplets induce, as reported earlier, a rapid recrystallization, which leads to WS2 films with strong (001) orientation.
Drug–drug Interactions between Ketoconazole and Berberine in Rats: Pharmacokinetic Effects Benefit Pharmacodynamic Synergism
Authors: Zhou Yanmi , He Ping , Liu Aiming , Zhang Lixin , Liu Yunde , Dai Renke
Published: November 2011

Ketoconazole (KTZ), a clinical antifungal agent, is a known inhibitor of CYP3A and permeability glycoprotein (P‐gp). Berberine (BBR), a natural plant‐derived product used for gastroenteritis, is a substrate of P‐gp. Recently, a synergistic antifungal effect of KTZ combined with BBR has been revealed. In this study, we performed both in vivo and in vitro experiments to explore whether pharmacokinetic interactions between KTZ and BBR would benefit their phamacodynamic synergism. After oral co‐administration of 10 mg/kg KTZ with 60 mg/kg BBR, the average area under the curve (AUC) and the maximum concentration (Cmax) for KTZ increased to 215% and 449% (p < 0.05), respectively, in male rats and 157% and 172% (p < 0.05), respectively, in female rats, compared with those administered KTZ alone. Area under the curve and Cmax for BBR increased to 173% and 142%, respectively, compared with those administered BBR alone. After intravenous co‐administration of 0.5 mg/kg KTZ and 0.8 mg/kg BBR, the pharmacokinetic properties of KTZ remained the same, but AUC of BBR increased to 254% (p < 0.05) compared with those administered BBR alone. In rat liver microsomes, inhibitory concentration (IC)50 of BBR inhibiting KTZ depletion was determined to be 103 µ m. These resulting pharmacokinetic interactions may benefit their pharmacodynamic synergism to a certain extent. Copyright © 2011 John Wiley & Sons, Ltd.
Betulinic Acid has an Inhibitory Effect on Pancreatic Lipase and Induces Adipocyte Lipolysis
Authors: Kim Junghyun , Lee Young Seub , Kim Chan‐Sik , Kim Jin Sook
Published: November 2011

Betulinic acid is a pentacyclic triterpenic acid that exists naturally in many kinds of food and has many biological functions. The present study investigated the antiobesity properties of betulinic acid and possible mechanisms by which betulinic acid functions. To examine the antilipase function of betulinic acid, the ability of betulinic acid to inhibit pancreatic lipase activity in vitro and to prevent the elevation of plasma triacylglycerol levels was tested after oral administration of a lipid emulsion in rats. In addition, the lipolytic effects of betulinic acid were assayed in rat adipose tissues. The activity of cAMP‐dependent phosphodiesterase was also measured in vitro. Betulinic acid inhibited pancreatic lipase activity in a dose‐dependent manner at concentrations of 1.5–100 µ m (IC50 value of 21.10 µ m) and prevented the elevation of plasma triacylglycerol levels 2 h after oral administration of the lipid emulsion at a dose of 100 mg/kg. In addition, betulinic acid had a strong lipolytic effect, which was mediated by cAMP‐dependent phosphodiesterase inhibition. In conclusion, betulinic acid may exert antiobesity effects by directly inhibiting pancreatic lipase, which would prevent the absorption of lipid from the small intestine. In addition, it was found that betulinic acid may further accelerate fat mobilization by enhancing the levels of lipolysis in adipose tissues. Copyright © 2011 John Wiley & Sons, Ltd.
Assimilation of GBVTD‐retrieved winds from single‐Doppler radar for short‐term forecasting of super typhoon Saomai (0608) at landfall
Authors: Zhao Kun , Xue Ming , Lee Wen‐Chau
Published: November 2011

A single‐Doppler wind retrieval method called the Ground‐Based Velocity‐Track Display technique (GBVTD) has been developed in recent years to retrieve horizontal circulations of tropical cyclones. The technique is able to retrieve axisymmetric tangential and radial winds, asymmetric tangential winds for wave numbers 1–3, and along‐beam mean winds in tropical cyclones. It has been successfully applied to tropical cyclone monitoring and warning. This study explores, for the first time, the assimilation of GBVTD‐retrieved winds into a tropical cyclone prediction model, and examines its impact relative to that of directly assimilated radial velocity data. super typhoon Saomai (2006), the most intense landfalling typhoon ever recorded in China, is chosen as the test case, and data from the coastal operational radar at Wenzhou, China, are used. The ARPS 3DVAR system is used to assimilate either the radial velocity data directly or the GBVTD‐retrieved winds, at 30 min intervals for 2 hours.

The assimilation of the GBVTD‐retrieved winds results in much improved structure and intensity analyses of Saomai compared to those in the Japan Meteorological Agency mesoscale reanalysis and compared to the analysis assimilating radial velocity (Vr) data directly. The ability of the GBVTD method in providing wind information covering the full circle of the inner‐core circulation is the primary reason for its superior performance over direct assimilation of Vr data; for the latter, the azimuthal data coverage is often incomplete. With the improved initial conditions, the subsequent forecasts of typhoon intensity, track and precipitation are also improved. The improvements to both track and intensity predictions persist over a 12‐hour forecast period, which is mostly after landfall. Subjective and quantitative evaluations of the precipitation and circulation patterns show consistent results. A further sensitivity experiment shows that the axisymmetric wind component in the GBVTD retrieval has the dominant impact on the prediction. Copyright © 2011 Royal Meteorological Society
Surgeon radiation exposure in cone beam computed tomography‐based, image‐guided spinal surgery
Authors: Nottmeier Eric W. , Bowman Cammi , Nelson Kevin L.
Published: November 2011

Background

Radiation exposure to the surgeon is a concern in spinal surgery, especially with the increasing popularity of minimally invasive spinal surgery techniques. Three‐dimensional (3D) image guidance used in conjunction with cone beam computed tomography (cbCT) has a theoretical advantage of decreased radiation exposure to the surgeon and operating room (OR) staff. Radiation scatter to the environment immediately surrounding a CT scanner during acquisition of a CT scan is a known entity. This in vivo study measures the radiation exposure to the surgeon when using cbCT registration in 3D image‐guided spinal surgery.

Methods

Two badge dosimeters were worn by the surgeon (EWN), one on the right waistband of the surgeon's scrubs and the other located over the thyroid area during 25 consecutive spinal surgery cases in which cbCT was used in conjunction with 3D image guidance. No lead protection was worn by the surgeon. The cbCT device was used for registration of the anatomy and to confirm adequate instrumentation placement. The surgeon stood behind a clear lead shield in the same location during every spin of the cbCT device. After the 25th case, the badge dosimeters were sent to the radiology department for analysis.

Results

Overall, 63 cbCT spins were accomplished in 25 patients. A total of 228 screws were placed into spinal levels spanning from C2 to the ileum. No complications resulted from instrumentation placement or the use of image guidance.Analysis of both badge dosimeters revealed 0 millirem (mRem) exposure.

Conclusions

Our study demonstrates that no radiation exposure to the surgeon occurs in cbCT‐based, 3D image‐guided spinal surgery procedures. Additionally, radiation scatter does not result in surgeon radiation exposure during patient registration if the surgeon stands behind a lead shield 10 feet from the cbCT device and not in direct line with the opening of the cbCT tube. Copyright © 2011 John Wiley & Sons, Ltd.
Voltammetry of the liposoluble vitamins (A, D, E and K) in organic solvents
Authors: Webster Richard D.
Published: November 2011

A review summarizing the voltammetric literature of the liposoluble vitamins A, D, E and K in organic solvents containing supporting electrolyte is presented. Electrochemical studies that were performed by attaching the vitamins to electrode surfaces and performing voltammetric scans in aqueous solutions are also summarized. Vitamins A (retinol and retinal) and D (cholecaliferol and ergocalciferol) undergo chemically irreversible voltammetric oxidation processes in organic solvents to form complicated or unknown compounds that cannot be electrochemically converted back to the starting materials. In contrast to vitamins A and D, vitamins E and K undergo chemically reversible electron‐transfer processes that are often coupled to proton‐transfer reactions. Vitamin E (a phenol) is voltammetrically oxidized in aprotic organic solvents in a −2e‐/−H+process to form a diamagnetic cation, which is unusually long‐lived compared to the analogous cations produced during the oxidation of other phenols. In an aqueous environment, vitamin E is electrochemically oxidized to the hydroquinone in a chemically irreversible −2e‐process. In low moisture content aprotic solvents, vitamin K (a quinone) is reduced in two one‐electron chemically reversible steps to form first a radical anion (semiquinone, atE1) and then at more negative potentials a dianion is formed (atE2). The dianion is especially prone to strong hydrogen‐bonding interactions with trace water present in the organic solvents, resulting in a shift in the formal reduction potential ofE2to more positive potentials as more water is added to the solvent.DOI 10.1002/tcr.201100005
Transition‐metal‐catalyzed aminations and aziridinations of CH and CC bonds with iminoiodinanes
Authors: Chang Joyce Wei Wei , Ton Thi My Uyen , Chan Philip Wai Hong
Published: November 2011

Catalytic insertion or addition of a metal‐imido/nitrene species, generated from reaction of a transition‐metal catalyst with iminoiodanes, to CH and CC bonds offers a convenient and atom economical method for the synthesis of nitrogen‐containing compounds. Following this groundbreaking discovery during the second half of the last century, the field has received an immense amount of attention with a myriad of impressive metal‐mediated methods for the synthesis of amines and aziridines having been developed. This review will cover the significant progress made in improving the efficiency, versatility and stereocontrol of this important reaction. This will include the various iminoiodanes, their in situ formation, and metal catalysts that could be employed and new ligands, both chiral and non‐chiral, which have been designed, as well as the application of this functional group transformation to natural product synthesis and the preparation of bioactive compounds of current therapeutic interest. DOI 10.1002/tcr.201100018
Rice in Thailand: The Archaeobotanical Contribution
Authors: Castillo Cristina
Published: November 2011

There are few archaeological projects incorporating archaeobotanical sampling and even fewer published archaeobotanical studies in Thailand. Available data show that rice was the ubiquitous cereal in prehistory and particularly during the Metal/Iron Age. This either signifies the importance of rice as a crop or signals a preservation bias; both topics are considered in this paper. The site Khao Sam Kaeo in Peninsular Thailand (ca. 400–100 BCE) is strategically located between the Indian Ocean and the South China Sea providing evidence of Indian, Han Chinese and locally produced cultural material. The archaeobotanical assemblage attests to South Asian and East Asian influence as well: the mungbean and horsegram of Indian origin and the northern Chinese cereal foxtail millet. But the site has also yielded the greatest amount of rice from Thai archaeology and provides information on the domestication of rice and the cultivation practices during this Late Prehistoric period.
Developing highly complex distributed systems: a software engineering perspective
Authors: Autili Marco , Inverardi Paola , Pelliccione Patrizio , Tivoli Massimo
Published: November 2011

What is a highly complex distributed system in the future era? What are the needs that may drive the development of such systems? And what is their life cycle? Is there any new challenge for Software Engineering (SE)? In this paper, we try to provide a partial answer to the above questions by characterizing few application domains that we consider of raising interest in the next years. Our thesis is that there is a need to rethink the whole software process for such systems. The traditional boundaries between static and dynamic activities disappear and development support mingles with run time support thus invading the middleware territory.
Assessing fetal response to maternal speech using a noninvasive functional brain imaging technique
Authors: Jardri Renaud , Houfflin‐Debarge Véronique , Delion Pierre , Pruvo Jean‐Pierre , Thomas Pierre , Pins Delphine
Published: November 2011

Evidence for cortical sensory activation in the human fetus at the beginning of the third trimester of pregnancy was provided in a recent imaging study. Although hearing is functional before birth, it is not clear whether recognition of the mother's voice is learned in utero or rapidly following delivery. We developed an original fMRI procedure that allows for the specific exploration of fetal brain response to auditory stimuli. This procedure provides the first in vivo evidence for the development of maternal voice recognition in utero between 33 and 34 weeks of gestation. This methodology could have crucial implications in the study of fetal cognition.
Boundary-layer-separation-driven vortex shedding beneath internal solitary waves of depression
Authors: Aghsaee Payam , Boegman Leon , Diamessis Peter J. , Lamb Kevin G.
Published: November 2011

We investigate global instability and vortex shedding in the separated laminar boundary layer beneath internal solitary waves (ISWs) of depression in a two-layer stratified fluid by performing high-resolution two-dimensional direct numerical simulations. The simulations were conducted with waves propagating over a flat bottom and shoaling over relatively mild $(S= 0. 05)$ and steep $(S= 0. 1)$ slopes. Over a flat bottom, the potential for vortex shedding is shown to be directly dependent on wave amplitude, for a particular stratification, owing to increase of the adverse pressure gradient ($\mathrm{d} P/ \mathrm{d} x\gt 0$ for leftward propagating waves) beneath the trailing edge of larger amplitude waves. The generated eddies can ascend from the bottom boundary to as high as 33 % of the total depth in two-dimensional simulations. Over sloping boundaries, global instability occurs beneath all waves as they steepen. For the slopes considered, vortex shedding begins before wave breaking and the vortices, shed from the bottom boundary, can reach the pycnocline, modifying the wave breaking mechanism. Combining the results over flat and sloping boundaries, a unified criterion for vortex shedding in arbitrary two-layer continuous stratifications is proposed, which depends on the momentum-thickness Reynolds number and the non-dimensionalized ISW-induced pressure gradient at the point of separation. The criterion is generalized to a form that may be readily computed from field data and compared to published laboratory experiments and field observations. During vortex shedding events, the bed shear stress, vertical velocity and near-bed Reynolds stress were elevated, in agreement with laboratory observations during re-suspension events, indicating that boundary layer instability is an important mechanism leading to sediment re-suspension.
The UK great bustard Otis tarda reintroduction trial: a 5-year progress report
Authors: Burnside Robert J. , Carter Ian , Dawes Alasdair , Waters David , Lock Leigh , Goriup Paul , Székely Tamás
Published: November 2011

The great bustard Otis tarda became extinct in the UK during the 19th century due to a combination of factors, including hunting, egg collection and changes in agriculture. In 2003 a 10-year licence was granted to begin a trial to reintroduce the species back to the UK. Here we report on the first 5 years of the trial and assess the progress made towards establishing a founder population. From April 2004 to September 2009 a total of 102 great bustard chicks were imported from Russia and 86 released on Salisbury Plain. Monitoring showed that post-release survival was 18% in the first year following release, and that mortality of released bustards was mainly attributable to predation and collisions. Estimated adult survival was 74%, although the sample size was small. All known surviving great bustards are faithful to the surroundings of the release site, returning throughout the year. A lek has been established where males have been observed displaying to females. The first nesting attempt was in 2007, and in 2009 two females aged 3 and 4 years successfully nested, fledging one chick each. Models incorporating the new demographic estimates suggest that at the end of the 10-year trial period the project can expect to have 8–26 adults as a founder population.
Review of doctoral research in English language education in the Philippines, Singapore and Malaysia (2007–2010)
Authors: Rubdy Rani , Tupas T. Ruanni F. , Villareal Corazon D. , David Maya Khemlani , Dumanig Francisco Perlas
Published: November 2011

This review highlights recent doctoral research in English language education and related areas completed between 2007 and 2010 in three countries in Southeast Asia: Singapore, Malaysia and the Philippines. Out of sixty dissertations initially chosen from major universities in these countries, five from the Philippines, four from Malaysia and three from Singapore were selected for review, the selection being based mainly on their quality of work and representation of key areas of intellectual work in the field in these countries. This review shows how the shared postcolonial identities of these countries and their unique sociohistorical locations help explain the coalescing and diverging agendas and trajectories in English language education doctoral research in the region. Much of the work affirms the dominant intellectual position of the West as the producer of knowledge, so there is a need to reposition the intellectual stance of research in English language education in the region within and emerging from its multilingual but unequally globalizing landscapes. Thus, there is an urgent need for more nuanced attention to socio-cultural factors that impact on English language education in the three countries under review, which, in turn, can help scholars produce new knowledge that can contribute to academic conversations in the field.
Modelling the impact of extended vaccination strategies on the epidemiology of pertussis
Authors: ROZENBAUM M. H. , De VRIES R. , LE H. H. , POSTMA M. J.
Published: November 2011

The aim of this study was to investigate the optimal pertussis booster vaccination strategy for The Netherlands. A realistic age-structured deterministic model was designed. Assuming a steady-state situation and correcting for underreporting, the model was calibrated using notification data from the period 1996–2000. Several sensitivity analyses were performed to explore the impact of different assumptions for parameters surrounded by uncertainty (e.g. duration of protection after natural infection, underreporting factors, and transmission probabilities). The optimal age of an additional booster dose is in the range of 10–15 years, and implementation of this booster dose will reduce both symptomatic and asymptomatic infections, although the incidence of symptomatic infections in older age groups will increase. The impact of the different assumptions used in the model was in general limited. We conclude that over a wide range of assumptions, an additional booster dose can reduce the incidence of pertussis in the population.
ON THE DETERMINANTS OF TOTAL FACTOR PRODUCTIVITY GROWTH: EVIDENCE FROM SPANISH MANUFACTURING FIRMS
Authors: Castiglionesi Fabio , Ornaghi Carmine
Published: November 2011

This paper explores the main determinants of productivity growth. The analysis is performed using Spanish firm-level data. We define a framework where the relative magnitudes of alternative, but not exclusive, sources of technical change are simultaneously estimated. Our main finding is that the average total factor productivity (TFP) growth is fully explained by embodied technical progress (i.e., either new capital goods or human capital). Our results contradict the existence of a positive contribution of economywide neutral technological progress in determining average TFP growth. They also leave little room for large, unpriced effects external to the firm, both at the aggregate and at the industry level. We find evidence of firm-specific learning by doing, short-lived and due to adoption of new processes.
Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter
Authors: Oakley Brian B , Carbonero Franck , Dowd Scot E , Hawkins Robert J , Purdy Kevin J
Published: November 2011

Understanding the ecological principles underlying the structure and function of microbial communities remains an important goal for microbial ecology. We examined two biogeochemically important taxa, the sulfate-reducing bacterial genus, Desulfobulbus, and the methanogenic archaeal genus, Methanosaeta, to compare and contrast niche partitioning by these two taxa that are ecologically linked as anaerobic terminal oxidizers of organic material. An observational approach utilizing functional gene pyrosequencing was combined with a community-based reciprocal incubation experiment and characterization of a novel Desulfobulbus isolate. To analyze the pyrosequencing data, we constructed a data analysis pipeline, which we validated with several control data sets. For both taxa, particular genotypes were clearly associated with certain portions of an estuarine gradient, consistent with habitat or niche partitioning. Methanosaeta genotypes were generally divided between those found almost exclusively in the marine habitat (∼30% of operational taxonomic units (OTUs)), and those which were ubiquitously distributed across all or most of the estuary (∼70% of OTUs). In contrast to this relatively monotonic distribution, for Desulfobulbus, there were many more genotypes, and their distributions represented a wide range of inferred niche widths from specialist genotypes found only at a single site, to ubiquitous or generalist genotypes found in all 10 sites examined along the full estuarine gradient. Incubation experiments clearly showed that, for both taxa, communities from opposite ends of the estuary did not come to resemble one another, regardless of the chemical environment. Growth of a Desulfobulbus isolated into pure culture indicated that the potential niche of this organism is significantly larger than the realized niche. We concluded that niche partitioning can be an important force structuring microbial populations, with biotic and abiotic components having very different effects depending on the physiology and ecology of each taxon.
Epigenetics—an emerging and highly promising source of new drug targets
Authors: Carey Nessa
Published: November 2011

Epigenetic modifications to DNA and its associated histone proteins are major influences on gene expression. This regulatory process is disrupted in cancer and a range of chronic human diseases, and provides attractive new intervention points and targets for drug discovery.
Bidirectional transport of organelles: unity and struggle of opposing motors
Authors: Bryantseva Sofiya A. , Zhapparova Olga N.
Published: November 2011

Bidirectional transport along microtubules is ensured by opposing motor proteins: cytoplasmic dynein that drives cargo to the minus‐ends and various kinesins that generally move to the plus‐ends of microtubules. Regulation of motor proteins that are simultaneously bound to the same organelle is required to maintain directional transport and prevent pausing of cargo pulled away by motors of opposite polarity. Debates of the recent decade have been focused on two possible mechanisms of such regulation: (i) coordination, which implies that only one type of motors is active at a given time, and (ii) tug‐of‐war, which assumes that both motors are active at the same time and that direction of transport depends on the outcome of motor's confrontation. The initial idea of coordination has been challenged by observations of simultaneous activity of plus‐ and minus‐end‐directed motors applied to the same cargo. Analysis of the available data indicates that coordination and tug‐of‐war theories rather complement than contradict each other: cargo interacts with two teams of active motors, the resulting direction and the winner team are determined by coordination complexes, but the activity of the loser team is never completely inhibited and remains at some background level. Such persisting activity might enhance the overall efficiency of transport by increasing processivity or helping to overcome the obstacles on microtubule track.
The impact of sexually transmissible infection programs in remote Aboriginal communities in Australia: a systematic review
Authors: Guy Rebecca , Ward James S. , Smith Kirsty S. , Su Jiunn-Yih , Huang Rae-Lin , Tangey Annie , Skov Steven , Rumbold Alice , Silver Bronwyn , Donovan Basil , Kaldor John M.
Published: November 2011

Objective To systematically review evaluations of the impact of sexually transmissible infection (STI) programs delivered by primary health care services in remote Aboriginal communities. Methods: PubMed, Google Scholar, InfoNet, Cochrane Controlled Trials Register, Australian New Zealand Clinical Trial Registry, conference proceedings and bulletins were searched to April 2011 using variations of the terms ‘Aboriginal’, ‘programs’ and ‘STI’. The primary outcome of interest in the review was the change in bacterial STI infection prevalence in the target age group assessed through cross-sectional screening studies over a 5-year period or more. The characteristics of the primary health care service, STI programs and other clinical service outcomes were also described. Results: Twelve reports described four distinct STI programs in remote communities and their impact on STI prevalence. In the Anangu Pitjantjatjara Yankunytjatjara (APY) lands of northern South Australia, there was a reduction in the age-adjusted chlamydia and gonorrhoea prevalence by 58% and 67%, respectively (1996–2003). In the Tiwi Islands of Northern Territory (NT), chlamydia and gonorrhoea positivity decreased by 94% and 34%, respectively (2002–2005). In the Ngaanyatjarra Lands of Western Australia, crude chlamydia and gonorrhoea prevalence decreased by 36% and 48%, respectively (2001–2005), and in the central Australian region of NT, there was no sustained decline in crude prevalence (2001–2005). Conclusion: In three of the four programs, there was some evidence that clinical best practice and well coordinated sexual health programs can reduce STI prevalence in remote Aboriginal communities.
Challenges to teacher resilience: conditions count
Authors: Gu Qing , Day Christopher
Published: November 2011

Drawing upon findings of a four‐year national research project on variations in the work and lives of teachers in England, this paper provides empirical evidence which contributes to understandings about the importance of resilience in teachers' work. The experience of resilience as perceived by teachers in this research was that it was neither innate nor stable and was much more than a capacity to survive and thrive in extremely adverse circumstances. Rather, it was perceived as being closely allied to their everyday capacity to sustain their educational purposes and successfully manage the unavoidable uncertainties which are inherent in the practice of being a teacher. Their capacity to be resilient fluctuated as a result of the influences of the personal, relational and organisational settings in which they worked. The findings have implications for initial and in‐service professional development programmes, school leadership and the quality retention of teachers.
Laser-assisted surface patterning of magnesium with silver nanoparticles: synthesis, characterization and modelling
Authors: Foroozmehr Ehsan , Alemohammad Hamidreza , Wang Xiang , Toyserkani Ehsan , Esmaeili Shahrzad
Published: November 2011

Surface patterning of biocompatible materials may improve cell adhesion, infiltration and proliferation. Magnesium is a biocompatible metal which has bioresorption capability, as well as a low elastic modulus. This unique combination of properties has attracted researchers to develop biodegradable magnesium devices. In this work, the patterning of magnesium with silver nanoparticles printed by the laser-assisted maskless microdeposition (LAMM) process was studied. The geometry and microstructure of the printed silver patterns and the diffusion zone at the Mg/Ag interface were studied using profilometry, scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDS) and transmission electron microscopy (TEM). The TEM analysis suggested that some intermetallic particles may form at the interface during laser sintering. The penetration curve of the Ag–Mg diffusion couple was obtained using EDS analysis. A finite element model is developed to simulate the LAMM process of silver nanoparticles on magnesium substrates. The model included a thermal analysis for determining the temperature history throughout the process, coupled with a diffusion model for evaluating compositional profiles across the interface. A comparison of the predicted profiles with the EDS results showed that the modelling and the experimental results qualitatively match. The analysis of SEM micrographs of the sintered nanoparticles, in light of the thermal modelling results, suggested that a minimum laser heat input was required for effective sintering of the nanoparticles.
Physiological type I collagen organization induces the formation of a novel class of linear invadosomes
Authors: Juin Amélie , Billottet Clotilde , Moreau Violaine , Destaing Olivier , Albiges-Rizo Corinne , Rosenbaum Jean , Génot Elisabeth , Saltel Frédéric
Published: November 2011

Invadosomes are F-actin structures capable of degrading the matrix through the activation of matrix metalloproteases. As fibrillar type I collagen promotes pro-matrix metalloproteinase 2 activation by membrane type 1 matrix metalloproteinase, we aimed at investigating the functional relationships between collagen I organization and invadosome induction. We found that fibrillar collagen I induced linear F-actin structures, distributed along the fibrils, on endothelial cells, macrophages, fibroblasts, and tumor cells. These structures share features with conventional invadosomes, as they express cortactin and N-WASP and accumulate the scaffold protein Tks5, which proved essential for their formation. On the basis of their ability to degrade extracellular matrix elements and their original architecture, we named these structures “linear invadosomes.” Interestingly, podosomes or invadopodia were replaced by linear invadosomes upon contact of the cells with fibrillar collagen I. However, linear invadosomes clearly differ from classical invadosomes, as they do not contain paxillin, vinculin, and β1/β3 integrins. Using knockout mouse embryonic fibroblasts and RGD peptide, we demonstrate that linear invadosome formation and activity are independent of β1 and β3 integrins. Finally, linear invadosomes also formed in a three-dimensional collagen matrix. This study demonstrates that fibrillar collagen I is the physiological inducer of a novel class of invadosomes.
Regulation of exocytosis by the exocyst subunit Sec6 and the SM protein Sec1
Authors: Morgera Francesca , Sallah Margaret R. , Dubuke Michelle L. , Gandhi Pallavi , Brewer Daniel N. , Carr Chavela M. , Munson Mary
Published: November 2011

Trafficking of protein and lipid cargo through the secretory pathway in eukaryotic cells is mediated by membrane-bound vesicles. Secretory vesicle targeting and fusion require a conserved multisubunit protein complex termed the exocyst, which has been implicated in specific tethering of vesicles to sites of polarized exocytosis. The exocyst is directly involved in regulating soluble N-ethylmaleimide–sensitive factor (NSF) attachment protein receptor (SNARE) complexes and membrane fusion through interactions between the Sec6 subunit and the plasma membrane SNARE protein Sec9. Here we show another facet of Sec6 function—it directly binds Sec1, another SNARE regulator, but of the Sec1/Munc18 family. The Sec6–Sec1 interaction is exclusive of Sec6–Sec9 but compatible with Sec6–exocyst assembly. In contrast, the Sec6–exocyst interaction is incompatible with Sec6–Sec9. Therefore, upon vesicle arrival, Sec6 is proposed to release Sec9 in favor of Sec6–exocyst assembly and to simultaneously recruit Sec1 to sites of secretion for coordinated SNARE complex formation and membrane fusion.
AMPK directly inhibits NDPK through a phosphoserine switch to maintain cellular homeostasis
Authors: Onyenwoke Rob U. , Forsberg Lawrence J. , Liu Lucy , Williams Tyisha , Alzate Oscar , Brenman Jay E.
Published: November 2011

AMP-activated protein kinase (AMPK) is a key energy sensor that regulates metabolism to maintain cellular energy balance. AMPK activation has also been proposed to mimic benefits of caloric restriction and exercise. Therefore, identifying downstream AMPK targets could elucidate new mechanisms for maintaining cellular energy homeostasis. We identified the phosphotransferase nucleoside diphosphate kinase (NDPK), which maintains pools of nucleotides, as a direct AMPK target through the use of two-dimensional differential in-gel electrophoresis. Furthermore, we mapped the AMPK/NDPK phosphorylation site (serine 120) as a functionally potent enzymatic “off switch” both in vivo and in vitro. Because ATP is usually the most abundant cellular nucleotide, NDPK would normally consume ATP, whereas AMPK would inhibit NDPK to conserve energy. It is intriguing that serine 120 is mutated in advanced neuroblastoma, which suggests a mechanism by which NDPK in neuroblastoma can no longer be inhibited by AMPK-mediated phosphorylation. This novel placement of AMPK upstream and directly regulating NDPK activity has widespread implications for cellular energy/nucleotide balance, and we demonstrate in vivo that increased NDPK activity leads to susceptibility to energy deprivation–induced death.
A new role for the architecture of microvillar actin bundles in apical retention of membrane proteins
Authors: Revenu Céline , Ubelmann Florent , Hurbain Ilse , El-Marjou Fatima , Dingli Florent , Loew Damarys , Delacour Delphine , Gilet Jules , Brot-Laroche Edith , Rivero Francisco , Louvard Daniel , Robine Sylvie
Published: November 2011

Actin-bundling proteins are identified as key players in the morphogenesis of thin membrane protrusions. Until now, functional redundancy among the actin-bundling proteins villin, espin, and plastin-1 has prevented definitive conclusions regarding their role in intestinal microvilli. We report that triple knockout mice lacking these microvillar actin-bundling proteins suffer from growth delay but surprisingly still develop microvilli. However, the microvillar actin filaments are sparse and lack the characteristic organization of bundles. This correlates with a highly inefficient apical retention of enzymes and transporters that accumulate in subapical endocytic compartments. Myosin-1a, a motor involved in the anchorage of membrane proteins in microvilli, is also mislocalized. These findings illustrate, in vivo, a precise role for local actin filament architecture in the stabilization of apical cargoes into microvilli. Hence, the function of actin-bundling proteins is not to enable microvillar protrusion, as has been assumed, but to confer the appropriate actin organization for the apical retention of proteins essential for normal intestinal physiology.
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation
Authors: Gatto Laurent , Lilley Kathryn S.
Published: November 2011

Summary:  MSnbase is an R/Bioconductor package for the analysis of quantitative proteomics experiments that use isobaric tagging. It provides an exploratory data analysis framework for reproducible research, allowing raw data import, quality control, visualization, data processing and quantitation. MSnbase allows direct integration of quantitative proteomics data with additional facilities for statistical analysis provided by the Bioconductor project.

Availability:  MSnbase is implemented in R (version ≥2.13.0) and available at the Bioconductor web site (http://www.bioconductor.org/). Vignettes outlining typical workflows, input/output capabilities and detailing underlying infrastructure are included in the package.

Contact:  lg390@cam.ac.uk

Supplementary information:  Supplementary data are available from Bioinformatics online.
Cell cycle commitment in budding yeast emerges from the cooperation of multiple bistable switches
Authors: Zhang Tongli , Schmierer Bernhard , Novák Béla
Published: November 2011

The start-transition (START) in the G1 phase marks the point in the cell cycle at which a yeast cell initiates a new round of cell division. Once made, this decision is irreversible and the cell is committed to progressing through the entire cell cycle, irrespective of arrest signals such as pheromone. How commitment emerges from the underlying molecular interaction network is poorly understood. Here, we perform a dynamical systems analysis of an established cell cycle model, which has never been analysed from a commitment perspective. We show that the irreversibility of the START transition and subsequent commitment can be consistently explained in terms of the interplay of multiple bistable molecular switches. By applying an existing mathematical model to a novel problem and by expanding the model in a self-consistent manner, we achieve several goals: we bring together a large number of experimental findings into a coherent theoretical framework; we increase the scope and the applicability of the original model; we give a systems level explanation of how the START transition and the cell cycle commitment arise from the dynamical features of the underlying molecular interaction network; and we make clear, experimentally testable predictions.
Labile disulfide bonds are common at the leucocyte cell surface
Authors: Metcalfe Clive , Cresswell Peter , Ciaccia Laura , Thomas Benjamin , Barclay A. Neil
Published: November 2011

Redox conditions change in events such as immune and platelet activation, and during viral infection, but the biochemical consequences are not well characterized. There is evidence that some disulfide bonds in membrane proteins are labile while others that are probably structurally important are not exposed at the protein surface. We have developed a proteomic/mass spectrometry method to screen for and identify non-structural, redox-labile disulfide bonds in leucocyte cell-surface proteins. These labile disulfide bonds are common, with several classes of proteins being identified and around 30 membrane proteins regularly identified under different reducing conditions including using enzymes such as thioredoxin. The proteins identified include integrins, receptors, transporters and cell–cell recognition proteins. In many cases, at least one cysteine residue was identified by mass spectrometry as being modified by the reduction process. In some cases, functional changes are predicted (e.g. in integrins and cytokine receptors) but the scale of molecular changes in membrane proteins observed suggests that widespread effects are likely on many different types of proteins including enzymes, adhesion proteins and transporters. The results imply that membrane protein activity is being modulated by a ‘redox regulator’ mechanism.