bluuebunny/crossref_metadata_2025 huggingface dataset:
Particle separation and collection using an optical chromatographic filter
Authors: Hart Sean J. , Terray Alex V. , Arnold Jonathan
Published: October 2007

An optofluidic design has been used to completely separate and collect fractions of an injected mixture of colloidal particles. A three-dimensional glass microfluidic device was constructed such that the fluid was directed though a 50-μm-diameter channel. A laser was introduced opposite the flow and its spot size adjusted to completely fill the channel. Thus, for a given laser power and flow rate, certain particles are completely retained while others pass through unhindered. Separation efficiencies in excess of 99% have been attained for a mixture of polymer and silica beads.
Channel-length and gate-bias dependence of contact resistance and mobility for In2O3 nanowire field effect transistors
Authors: Jo Gunho , Maeng Jongsun , Kim Tae-Wook , Hong Woong-Ki , Choi Byung-Sang , Lee Takhee
Published: October 2007

We demonstrate the scaling properties of the gate-bias-dependent transfer characteristics of In2O3 nanowire field effect transistors (FETs) studied using a conducting atomic force microscope. The contact resistance was extracted from the scaling of the resistance of an In2O3 nanowire FET with respect to its channel length. This contact resistance was found to be significant for short channel devices and decreased as the gate bias increased. We also investigated the apparent and intrinsic mobilities of the nanowire FET as a function of channel length and gate bias. It was determined that the intrinsic mobility could be corrected by considering the non-negligible contact resistance.
On the origin of Si nanocrystal formation in a Si suboxide matrix
Authors: Yu Decai , Lee Sangheon , Hwang Gyeong S.
Published: October 2007

We examined mechanisms underlying Si nanocrystal formation in Si-rich SiO2 using a combination of quantum mechanical and Monte Carlo (MC) simulations. We find that this process is mainly driven by suboxide penalty arising from incomplete O coordination, with a minor contribution of strain, and it is primarily controlled by O diffusion rather than excess Si diffusion and agglomeration. The overall behavior of Si cluster growth from our MC simulations based on these fundamental findings agrees well with experiments.
Loss current minimization during ion extraction from an inductively coupled plasma
Authors: Vozniy Oleksiy , Polozhiy Kostyantyn , Yeom Geun Young
Published: October 2007

In ion sources with a grid-type acceleration system, the output current often decreases with increasing power at a constant extraction voltage despite the fact that the carrier density inside the source increases linearly. At this point, the loss and output currents have the same magnitude. This paper proposes a mechanism for loss current minimization when restrictions are placed on the beam focusing efficiency with increasing rf power. The influence of the plasma potential on the magnitude of the loss current was examined. The beam intensity was found to increase considerably when the plasma potential was sufficiently high to suppress sheath curvature growth.
Fabrication and properties of coherent-structure In-polarity InN∕In0.7Ga0.3N multiquantum wells emitting at around 1.55μm
Authors: Che Song-Bek , Mizuno Tomoyasu , Wang Xinqiang , Ishitani Yoshihiro , Yoshikawa Akihiko
Published: October 2007

In-polarity InN∕In0.7Ga0.3N multiquantum wells (MQWs) were fabricated on a thick In0.7Ga0.3N interlayer/Ga-polarity GaN template by radio-frequency plasma-assisted molecular beam epitaxy. We then investigated how the lattice relaxation and piezoelectric field in InN wells affect their structural and photoluminescence (PL) properties, respectively. It was found that the critical thickness of InN well on In0.7Ga0.3N barrier was about 1nm. A clear PL peak shift from 1.40to1.95μm was observed depending on the InN well thickness from 0.7to2.0nm. Correspondingly, PL-intensity reduction was also observed with increasing well thickness. No PL was observed for the sample with 4.1nm thick InN wells. On the basis of theoretical estimation of transition energies in InN∕In0.7Ga0.3N MQWs, it was confirmed that the quantum-confined Stark effect (QCSE) played an important role for both the observed PL peak shift and the decrease in intensity. The piezoelectric field in coherently grown InN wells was about 3MV∕cm but it was reduced to about 1–2MV∕cm for the samples with relaxed InN wells. It was confirmed that the InN wells must be thinner than the critical thickness (1nm) in following two points: to reduce defects arising from lattice relaxation and to reduce QCSE leading to emission-peak redshift and a decrease in intensity.
In-plane thermal conductivity of disordered layered WSe2 and (W)x(WSe2)y superlattice films
Authors: Mavrokefalos Anastassios , Nguyen Ngoc T. , Pettes Michael T. , Johnson David C. , Shi Li
Published: October 2007

It was recently reported that misoriented layered WSe2 and (W)x(WSe2)y films possess extremely low cross-plane thermal conductivity. Here, we report that the in-plane thermal conductivity results for WSe2 and W4(WSe2)10 films measured by using a suspended device are about 30 times higher than the cross-plane values because of the in-plane ordered and cross-plane disordered structures and about six times lower than that of compacted single-crystal WSe2 platelets. The additional W layers in the W4(WSe2)10 films were found to greatly increase the in-plane electrical conductivity relative to the WSe2 films, but reduce the in-plane lattice thermal conductivity assuming the Wiedemann-Franz law.
Discrete-dopant-induced characteristic fluctuations in 16nm multiple-gate silicon-on-insulator devices
Authors: Li Yiming , Hwang Chih-Hong
Published: October 2007

The impact of the number and position of discrete dopants on device characteristics is crucial in determining the behavior of nanoscale semiconductor devices. This study explores discrete-dopant-induced characteristic fluctuations in 16nm single-, double-, triple-, and (square shape) surrounding-gate silicon-on-insulator (SOI) devices. Discrete dopants are statistically positioned in the three-dimensional channel region to examine associated carrier transportation characteristics, concurrently capturing “dopant concentration variation” and “dopant position fluctuation.” An experimentally validated simulation was conducted to investigate the threshold voltage (Vth) fluctuation and the variation of the on- and off-state currents of the four explored structures. The fluctuations of Vth of the double-, triple- and surrounding-gate devices are 2.2, 3.3 and 4 times smaller, respectively, than that of planar SOI. Results of this study provide further insight into the problem of fluctuation and the mechanism of immunity against fluctuation in ultrasmall field effect transistors (FETs) with vertical channel structures, such as fin-typed FETs.
Wake potential in a nonuniform self-gravitating dusty magnetoplasma in the presence of ion streaming
Authors: Salimullah M. , Ehsan Z. , Zubia K. , Shah H. A. , Murtaza G.
Published: October 2007

A detailed investigation of the electrostatic asymmetric shielding potential and consequent generation of the dynamical oscillatory wake potential has been examined analytically in an inhomogeneous self-gravitating dusty magnetoplasma in the presence of uniform ion streaming. It is found that the wake potential depends significantly on the test particle speed, ambient magnetic field, ion streaming velocity, and the plasma inhomogeneity. The periodic oscillatory potential might lead to an alternative approach to the Jeans instability for the formation of dust agglomeration leading to gravitational collapse of the self-gravitating systems.
X
- and Y-line equilibria
Authors: Yoon P. H. , Lui A. T. Y.
Published: October 2007

In this Brief Communication, it is shown that an analytical solution for an exact two-dimensional X- or Y-line equilibrium may be constructed quite easily on the basis of the fundamental theoretical equation. The equilibria discussed in the present report show the potential for a rich variety of current sheet structures that satellites may encounter in space.
Surface relief gratings on poly(3-hexylthiophene) and fullerene blends for efficient organic solar cells
Authors: Na Seok-In , Kim Seok-Soon , Kwon Soon-Shin , Jo Jang , Kim Juhwan , Lee Takhee , Kim Dong-Yu
Published: October 2007

The use of periodic submicrometer structures as an efficient light-trapping scheme was investigated for high performance organic solar cells (OSCs) based on poly(3-hexylthiophene) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61. The gratings on an active layer are achieved by a soft lithographic approach using photoinduced surface-relief gratings (SRGs) on azo polymer films and poly(dimethylsiloxane) as a master and stamp, respectively. Incident photon to current conversion efficiency and the power conversion efficiency of OSC with gratings increased primarily due to enhanced short circuit current density, indicating that SRGs induce further photon absorption in active layers by increasing the optical path length and light trapping.
The temperature dependence of the electron mobility degradation mechanisms in n-channel metal-oxide-semiconductor field effect transistors with ZrO2 and Sm2O3 gate dielectrics
Authors: Ho Hsiao-shuo , Chang Ingram Yin-ku , Lee Joseph Ya-min
Published: October 2007

The mobility degradation mechanisms of n-channel metal-oxide-semiconductor field effect transistors with ZrO2 and Sm2O3 gate dielectrics were studied. The temperature dependence of device characteristics was studied in the temperature range from 11to300K. n-channel metal-oxide-semiconductor field effect transistors (MOSFETs) with SiO2 gate dielectric are used as reference. The electron mobility of ZrO2-gated n-MOSFETs is limited by Coulomb scattering. The extra source of Coulomb scattering is attributed to additional oxide trapped charges. The electron mobility in Sm2O3-gated n-MOSFETs is limited by phonon scattering. The extra source for phonon scattering is attributed to soft optical phonons in Sm2O3.
Scanning optical homodyne detection of high-frequency picoscale resonances in cantilever and tuning fork sensors
Authors: Zeltzer G. , Randel J. C. , Gupta A. K. , Bashir R. , Song S.-H. , Manoharan H. C.
Published: October 2007

Higher harmonic modes in nanoscale silicon cantilevers and microscale quartz tuning forks are detected and characterized using a custom scanning optical homodyne interferometer. Capable of both mass and force sensing, these resonators exhibit high-frequency harmonic motion content with picometer-scale amplitudes detected in a 2.5MHz bandwidth, driven by ambient thermal radiation. Quartz tuning forks additionally display both in-plane and out-of-plane harmonics. The first six electronically detected resonances are matched to optically detected and mapped fork eigenmodes. Mass sensing experiments utilizing higher tuning fork modes indicate greater than six times sensitivity enhancement over fundamental mode operation.
On the structure of the Si(103) surface
Authors: Ciobanu Cristian V. , Chuang Feng-Chuan , Lytle Damon E.
Published: October 2007

Although (103) is a stable nominal orientation for both silicon and germanium, experimental observations revealed that in the case of silicon, this surface remains disordered at the atomic scale even after careful annealing. We report here a set of low-energy reconstruction models corresponding to 1×2, 2×2, and 1×4 periodicities, and propose that the observed disorder stems from the presence of several coexisting reconstructions with different morphologies and nearly equal surface energies. The reconstructions found also suggest that the models previously reported in the literature for the (103) orientation have very high surface energies and are thus unlikely to be experimentally observed.
A numerical study of flame geometry and potential for crown fire initiation for a wildfire propagating through shrub fuel
Authors: Morvan Dominique
Published: October 2007

The efficiency of fuel breaks installed in wildland–urban interfaces to reduce fire hazard depends strongly on the conditions of spread (rate of spread, flame height) of a surface fire through the shrub on the ground and also on the possibility of a transition for this fire from the understorey vegetation to the canopy. The aim of the present paper was to study (using numerical simulation with a physics-based model) the behaviour of surface fires propagating through Mediterranean shrub and to evaluate, from the characteristic dimensions of the flame, the onset of transition from a surface fire to a crown fire. The geometry of the flame was defined from the energy loss in the gas resulting from the radiation emission of soot particles, the flame contour was reconstructed from a threshold level fixed at 60 kW m–3. The numerical results were compared with experimental correlations of the geometry of the flame obtained for static and spreading fires. Extensive calculations were performed through a shrubland (Quercus coccifera and Brachypodium ramosum) for various fuel depths Hfuel ranging from 0.25 to 1.5 m and for wind speeds UH ranging from 1 to 10 m s–1. Then this study was extended to situations including a supplementary fuel layer representing the canopy of small trees (Pinus halepensis). The numerical results were analysed, introducing a dimensionless physical parameter, the Froude number, defined as the ratio between the inertial force due to the wind flow and the buoyancy. The results obtained with an upper fuel layer highlighted the role played by radiation heat transfer for the transition of surface fire to the crown. Some calculations were also carried out to study how a reduction of surface fuel on the ground can affect the vertical transition of the fire.
The role of extinction on the re-ignition potential of wood-based embers in bushfires
Authors: Moghtaderi Behdad , Poespowati Tri , Kennedy Eric M. , Dlugogorski Bogdan Z.
Published: October 2007

The re-ignition potential of partially burnt wood-based embers was investigated theoretically by studying their extinction characteristics. An adaptation of Semenov’s thermal explosion theory was used in conjunction with a linear stability analysis to determine the critical particle size at which extinction occurs. Particles of various shapes were studied and the analysis was carried out for both thermally thin and thermally thick particles. The results of our analysis indicate that thermally thick embers are less susceptible to extinction than thermally thin ones and, as such, are more prone to re-ignition. The results also show that the extinction of wood embers is strongly affected by the particle temperature, particle shape, and reaction kinetics. The effects of ambient conditions were found to be less pronounced than particle properties.
Evaluation of FARSITE simulator in Mediterranean maquis
Authors: Arca Bachisio , Duce P. , Laconi M. , Pellizzaro G. , Salis M. , Spano D.
Published: October 2007

In the last two decades, several models were developed to provide temporal and spatial variations of fire spread and behaviour. The most common models (i.e. BEHAVE and FARSITE) are based on Rothermel's original fire spread equation and describe fire spread and behaviour taking into account the influences of fuels, terrain and weather conditions. The use of FARSITE on areas different from those where the simulator was originally developed requires a local calibration to produce reliable results. This is particularly true for Mediterranean ecosystems, where plant communities are characterised by high specific and structural heterogeneity and complexity. To perform FARSITE calibration, an appropriate fuel model or the development of a specific custom fuel model is needed. In this study, FARSITE was employed to simulate three fire events in Mediterranean areas using different fuel models and meteorological input data, and the accuracy of results was analysed. A custom fuel model designed and developed for shrubland vegetation (maquis) provided realistic values of rate of spread, when compared with estimated values obtained using standard fuel models. Our results confirm that the use of both wind field data and appropriate custom fuel models are crucial to obtain reasonable simulations of wildfire events occurring on Mediterranean vegetation during the drought season.
The contribution of fire research to fire management: a critical review of a long-term experiment in the Kruger National Park, South Africa
Authors: van Wilgen Brian W. , Govender Navashni , Biggs Harry C.
Published: October 2007

The present paper reviews a long-term fire experiment in the Kruger National Park, South Africa, established in 1954 to support fire management. The paper’s goals are: (1) to assess learning, with a focus on relevance for fire management; (2) to examine how findings influenced changes in fire management; and (3) to reflect on the experiment’s future. Results show that fire treatments affected vegetation structure and biomass more than species composition. Effects on vegetation were most marked in extreme treatments (annual burning, burning in the summer wet season, or long periods of fire exclusion), and were greater in areas of higher rainfall. Faunal communities and soil physiology were largely unaffected by fire. Since the inception of the experiment, paradigms in savanna ecology have changed to encompass heterogeneity and variability. The design of the experiment, reflecting the understanding of the 1950s, does not cater for variability, and as a result, the experiment had little direct influence on changes in management policy. Notwithstanding this, managers accept that basic research influences the understanding of fundamental ecosystem function, and they recognise that it promotes appropriate adaptive management by contributing to predictive understanding. This has been a major reason for maintaining the experiment for over 50 years.
Historical fire regime shifts related to climate teleconnections in the Waswanipi area, central Quebec, Canada
Authors: Le Goff Héloïse , Flannigan Mike D. , Bergeron Yves , Girardin Martin P.
Published: October 2007

The synchrony of regional fire regime shifts across the Quebec boreal forest, eastern Canada, suggests that regional fire regimes are influenced by large-scale climate variability. The present study investigated the relationship of the forest-age distribution, reflecting the regional fire activity, to large-scale climate variations. The interdecadal variation in forest fire activity in the Waswanipi area, north-eastern Canada, was reconstructed over 1720–2000. Next, the 1880–2000 reconstructed fire activity was analysed using different proxies of the Pacific Decadal Oscillation (PDO) and the North Atlantic Oscillation (NAO) and the Atlantic Multidecadal Oscillation (AMO). We estimated the global fire cycle around 132–153 years, with a major lengthening of the fire cycle from 99 years before 1940, to 282 years after 1940. Correlations between decadal fire activity and climate indices indicated a positive influence of the PDO. The positive influence of PDO on regional fire activity was also validated using t-tests between fire years and non-fire years between 1899 and 1996. Our results confirmed recent findings on the positive influence of the PDO on the fire activity over northern Quebec and the reinforcing role of the NAO in this relationship.
Impairment of actions chains in autism and its possible role in intention understanding
Authors: Cattaneo Luigi , Fabbri-Destro Maddalena , Boria Sonia , Pieraccini Cinzia , Monti Annalisa , Cossu Giuseppe , Rizzolatti Giacomo
Published: October 2007

Experiments in monkeys demonstrated that many parietal and premotor neurons coding a specific motor act (e.g., grasping) show a markedly different activation when this act is part of actions that have different goals (e.g., grasping for eating vs. grasping for placing). Many of these “action-constrained” neurons have mirror properties firing selectively to the observation of the initial motor act of the actions to which they belong motorically. By activating a specific action chain from its very outset, this mechanism allows the observers to have an internal copy of the whole action before its execution, thus enabling them to understand directly the agent's intention. Using electromyographic recordings, we show that a similar chained organization exists in typically developing children, whereas it is impaired in children with autism. We propose that, as a consequence of this functional impairment, high-functioning autistic children may understand the intentions of others cognitively but lack the mechanism for understanding them experientially.
Bone marrow cells adopt the cardiomyogenic fate
in vivo
Authors: Rota Marcello , Kajstura Jan , Hosoda Toru , Bearzi Claudia , Vitale Serena , Esposito Grazia , Iaffaldano Grazia , Padin-Iruegas M. Elena , Gonzalez Arantxa , Rizzi Roberto , Small Narissa , Muraski John , Alvarez Roberto , Chen Xiongwen , Urbanek Konrad , Bolli Roberto , Houser Steven R. , Leri Annarosa , Sussman Mark A. , Anversa Piero
Published: October 2007

The possibility that adult bone marrow cells (BMCs) retain a remarkable degree of developmental plasticity and acquire the cardiomyocyte lineage after infarction has been challenged, and the notion of BMC transdifferentiation has been questioned. The center of the controversy is the lack of unequivocal evidence in favor of myocardial regeneration by the injection of BMCs in the infarcted heart. Because of the interest in cell-based therapy for heart failure, several approaches including gene reporter assay, genetic tagging, cell genotyping, PCR-based detection of donor genes, and direct immunofluorescence with quantum dots were used to prove or disprove BMC transdifferentiation. Our results indicate that BMCs engraft, survive, and grow within the spared myocardium after infarction by forming junctional complexes with resident myocytes. BMCs and myocytes express at their interface connexin 43 and N-cadherin, and this interaction may be critical for BMCs to adopt the cardiomyogenic fate. With time, a large number of myocytes and coronary vessels are generated. Myocytes show a diploid DNA content and carry, at most, two sex chromosomes. Old and new myocytes show synchronicity in calcium transients, providing strong evidence in favor of the functional coupling of these two cell populations. Thus, BMCs transdifferentiate and acquire the cardiomyogenic and vascular phenotypes restoring the infarcted heart. Together, our studies reveal that locally delivered BMCs generate
de novo
myocardium composed of integrated cardiomyocytes and coronary vessels. This process occurs independently of cell fusion and ameliorates structurally and functionally the outcome of the heart after infarction.
Pelvic floor sex steroid hormone receptors, distribution and expression in pre‐ and postmenopausal stress urinary incontinent women
Authors: SÖDERBERG MARIE WESTERGREN , JOHANSSON BENGT , MASIRONI BRITT , BYSTRÖM BIRGITTA , FALCONER CHRISTIAN , SAHLIN LENA , EKMAN ORDEBERG GUNVOR
Published: October 2007

Background. Hormonal influence on stress urinary incontinence (SUI) is under debate. Sex steroid hormonal activity is mediated by nuclear receptor proteins. The aim of this study is to identify receptor isoforms and their genetic expression in the pelvic floor extra cellular matrix (ECM), and to compare women with and without SUI before and after menopause. Methods. Sub‐mucosal para‐urethral biopsies from 4 pre‐menopausal and 8 postmenopausal patients with SUI were analysed immunohistochemically regarding estrogen receptors (ER) α and β, the progesterone receptor (PR) (A+B) and B, and the androgen receptor (AR). Six pre‐menopausal and 5 postmenopausal women served as controls. All receptors were scored manually. Additionally, ER‐α and ER‐β were quantified by image analysis. Biopsies from 7 pre‐menopausal and 7 postmenopausal women suffering from SUI were studied by real‐time RT‐PCR for expression of ER‐α, ER‐β, PR and AR. The control group consisted of 5 pre‐menopausal and 5 postmenopausal women. Results. Immunohistochemistry revealed receptor‐positive cells for all isoforms in all groups. Higher ER‐β scores were seen in the pre‐menopausal SUI group compared to controls. Lower PR‐B scores were found after menopause in both groups. The image analysis confirmed that ER‐β was significantly increased in the pre‐menopausal SUI group compared to controls (p = 0.02). By real‐time RT‐PCR, no difference of mRNA expression regarding any receptor was detected between any SUI and control group. ER‐β mRNA levels were low or undetectable. There was a significant down‐regulation of PR among postmenopausal women (p = 0.001). Conclusions. The para‐urethral ECM is a target for sex steroid hormones mediated by the respective receptor. The significant higher expression of ER‐β protein in the pre‐menopausal SUI‐group was not reflected by a corresponding up‐regulation of mRNA which was poorly expressed in all groups.
Individual variation in agrammatism: a single case study of the influence of interaction
Authors: Beeke Suzanne , Wilkinson Ray , Maxim Jane
Published: October 2007

Background: Agrammatic speech can manifest in different ways in the same speaker if task demands change. Individual variation is considered to reflect adaptation, driven by psycholinguistic factors such as underlying deficit. Recently, qualitative investigations have begun to show ways in which conversational interaction can influence the form of an agrammatic speaker's output.

Aims: To explore qualitative patterns of individual variation in the output of a single case, in order to address the following questions: (1) in what ways do grammatical structure, verbs and argument structure differ qualitatively between data samples?; and (2) what is the influence of interaction on the structure of utterances?

Methods & Procedures: A man with severe and chronic agrammatism is videotaped completing tests of spoken sentence construction, composite, and cartoon strip picture descriptions and a story telling task. In addition, he independently videotapes a sample of conversation with a family member at home. Analyses of these data draw on cognitive neuropsychological, linguistic and psycholinguistic methodologies as well as the data‐driven procedures of conversation analysis.

Outcomes & Results: The qualitative analysis uncovers considerable variation between data sets with respect to grammatical structure, verbs and argument structure. The agrammatic speaker appears more skilled at imposing order on his spontaneous speech than the results of sentence construction tests might predict. Interaction influences his output style. Adaptation is found to be a collaborative process that occurs between two speakers in the quest for mutual understanding, not something that takes place within an individual.

Conclusions: It is concluded that an interactional approach to agrammatism has the potential to yield important insights into the characteristics of telegraphic speech and individual variation. The failure of sentence‐level tests to capture this individual's skill in producing systematically structured utterances in conversation implies that the assessment of agrammatism could benefit from the additional sampling and analysis of conversational grammar.
Railroads and Time Consciousness in the Antebellum South
Authors: Marrs Aaron W.
Published: October 2007

Historians have often looked to industrial capitalism to further our understanding of “time consciousness.” This article explores time consciousness through the experience of a railroad in pre-Civil War South Carolina. Examining the South Carolina Railroad allows us to examine how time consciousness operated in a region not associated with industrial capitalism, and also see how multiple times could function simultaneously. While clocks were important to railroad operations, companies also had to address an array of non-clock times. Moreover, companies were never fully in control of their own time, but were in constant conflict and negotiation with various groups in the community. While industrialization and factory labor remain important ways to understand time consciousness, looking beyond the factory walls can help historians make better use of the analytical power of time.
Diet studies of seabirds: a review and recommendations
Authors: Barrett Robert T. , Camphuysen Kees (C. J.) , Anker-Nilssen Tycho , Chardine John W. , Furness Robert W. , Garthe Stefan , Hüppop Ommo , Leopold Mardik F. , Montevecchi William A. , Veit Richard R.
Published: October 2007

Barrett, R. T., Camphuysen, C. J., Anker-Nilssen, T., Chardine, J. W., Furness, R. W., Garthe, S., Hüppop, O., Leopold, M. F., Montevecchi, W. A., and Veit, R. R. 2007. Diet studies of seabirds: a review and recommendations. – ICES Journal of Marine Science, 64. We review the different methods that are used to collect dietary data from marine birds. We consider their limitations and practicalities and emphasize critical data gaps in our knowledge of the feeding ecology of seabirds (na mely diets outside breeding seasons). To enhance comparability of findings among studies, species, and oceanographic regions, we make recommendations on standards for the reporting of results in the literature.
FTIR detection of water reactions in the oxygen-evolving centre of photosystem II
Authors: Noguchi Takumi
Published: October 2007

Flash-induced Fourier transform infrared (FTIR) difference spectroscopy has been used to study the water-oxidizing reactions in the oxygen-evolving centre of photosystem II. Reactions of water molecules were directly monitored by detecting the OH stretching bands of weakly H-bonded OH of water in the 3700–3500 cm−1region in FTIR difference spectra during S-state cycling. In the S1→S2transition, a band shift from 3588 to 3617 cm−1was observed, indicative of a weakened H-bond. Decoupling experiments using D2O : H2O (1 : 1) showed that this OH arose from a water molecule with an asymmetric H-bonding structure and this asymmetry became more significant upon S2formation. In the S2→S3, S3→S0and S0→S1transitions, negative bands were observed at 3634, 3621 and 3612 cm−1, respectively, representing formation of a strong H-bond or a proton release reaction. In addition, using complex spectral features in the carboxylate stretching region (1600–1300 cm−1) as ‘fingerprints’ of individual S-state transitions, pH dependency of the transition efficiencies and the effect of dehydration were examined to obtain the information of proton release and water insertion steps in the S-state cycle. Low-pH inhibition of the S2→S3, S3→S0and S0→S1transitions was consistent with a view that protons are released in the three transitions other than S1→S2, while relatively high susceptibility to dehydration in the S2→S3and S3→S0transitions suggested the insertion of substrate water into the system during these transitions. Thus, a possible mechanism of water oxidation to explain the FTIR data is proposed.
Site-directed mutations at D1-His198 and D1-Thr179 of photosystem II in
Synechocystis
sp. PCC 6803: deciphering the spectral properties of the PSII reaction centre
Authors: Schlodder Eberhard , Coleman William J , Nixon Peter J , Cohen Rachel O , Renger Thomas , Diner Bruce A
Published: October 2007

Site-directed mutations were constructed in photosystem II of
Synechocystis
sp. PCC6803 in which the axial ligand, D1-His198, of special pair chlorophyll P
D1
was replaced with Gln and where D1-Thr179, which overlies monomeric chlorophyll Chl
D1
, was replaced with His. The D1-His198Gln mutation produces a 3 nm displacement to the blue of the bleaching minimum in the Soret and in the Qy region of the

–

absorbance difference spectrum. To a first approximation, the bleaching can be assigned to the low-energy exciton transition of the special pair chlorophylls P
D1
/P
D2
. The D1-Thr179His mutation produces a 2 nm displacement to the red of the bleaching minimum in the Qy region of the (
3
P–
1
P) absorbance difference spectrum. Analysis of the flash-induced

–

and (
3
P–
1
P) absorbance difference spectra of both mutants compared with wild-type at 80 K indicate that the cation of the oxidized donor P
+
is predominantly localized on the chlorophyll P
D1
of the special pair and that the reaction centre triplet state, produced upon charge recombination from
3
[P
+
Pheo
−
], when the primary quinone electron acceptor Q
A
is doubly reduced, is primarily localized on Chl
D1
.
Principia ætiologica: taking causality beyond Koch's postulates
Authors: Inglis Timothy J. J.
Published: October 2007

There is no single accepted method to establish a causal relationship between an infective agent and its corresponding infectious disease. Different biomedical disciplines use a patchwork of distinct but overlapping approaches. To a greater or lesser extent these are based on criteria known as the Koch–Henle postulates, or ‘Koch's postulates' for short. Deficiencies in Koch's postulates were recognized by their principal author shortly after their formulation. Now, over a century later, a more rigorous method to test causality has still to be finalized. One contender is a method that uses molecular methods to establish a causal relationship (‘molecular Koch's postulates'). Recognizing the wider range of contemporary approaches used to build an argument for a causal relationship, the use of a more inclusive approach to establish proof of causality is proposed. This method uses an argument built from a series of assertions. Assertion 1: congruence or reproducible correlation of a taxonomically defined life form with the clinico-pathological and epidemiological features of infection. Assertion 2: consistency of the demonstrable biological response in the subject to an encounter with the prospective infective agent. Assertion 3: progressive or cumulative dissonance as an explanation for pathophysiological processes at every known level of biological organization in the subject. Assertion 4: curtailment of that pathophysiological process on the deliberate introduction of a specified biomedical intervention. Evidence to implicate the candidate biological entity as an initiator of or primer for cumulative dissonance places it in a subcategory of micro-organisms to be known as ‘priobes’. A priobe is the sufficient and necessary antecedent cause of a pathophysiological process evident as an infectious disease.
Characterization of RagA and RagB in Porphyromonas gingivalis: study using gene-deletion mutants
Authors: Nagano Keiji , Murakami Yukitaka , Nishikawa Kiyoshi , Sakakibara Junpei , Shimozato Kazuo , Yoshimura Fuminobu
Published: October 2007

The major outer-membrane proteins RagA and RagB ofPorphyromonas gingivalisare considered to form a receptor complex functionally linked to TonB. In this study,P.gingivalismutants withragA,ragBor both deleted were constructed from strain W83 as the parent to examine the physiological and pathological functions of RagA and RagB. The double-deletion mutant completely lacked both RagA and RagB, whereas the ΔragAmutant reduced RagB expression considerably and the ΔragBmutant produced degraded RagA. Growth of the three mutants in a nutrient-rich medium and synthetic media containing digested protein as a unique nutrient source was similar to that of the parental strain; however, both the ΔragAand ΔragABmutants exhibited very slow growth in a synthetic medium containing undigested, native protein, and the two mutants tended to lose their viability during experiments, although gingipain (protease) activities were unchanged in the mutants. A mouse model showed that the ΔragBmutant had reduced virulence. Cell-surface labelling with biotin and dextran revealed that both RagA and RagB localized on the outermost cell surface. A cross-linking experiment using wild-typeP. gingivalisshowed that RagA and RagB were closely associated with each other. Furthermore, co-immunoprecipitation confirmed that RagA and RagB formed a protein–protein complex. These results suggest that physically associated RagA and RagB may stabilize themselves on the cell surface and function as active transporters of large degradation products of protein and in part as a virulence factor.
Chemical structure and immunobiological activity of lipid A from Serratia marcescens LPS
Authors: Makimura Yutaka , Asai Yasuyuki , Sugiyama Akiko , Ogawa Tomohiko
Published: October 2007

The chemical structure and immunobiological activities ofSerratia marcescenslipid A, an active centre of LPS, were investigated. LPS preparations ofS. marcescenswere extracted using a hot phenol/water method, after which purified lipid A specimens were prepared by weak acid hydrolysis, followed by normal phase and gel filtration chromatographic separation. The lipid A structure was determined by MS to be a diglucosamine backbone with diphosphates and five C14normal chain acyl groups, including two acyloxyacyl groups at the 2 and 3 positions of the non-reducing side.S. marcescenslipid A andEscherichia coli-type synthetic lipid A (compound 506) exhibited definite reactivity inLimulusamoebocyte lysate assays. The lethal toxicity ofS. marcescenslipid A was nearly comparable to that of compound 506, and both induced nuclear factor-κB activation in murine cells via Toll-like receptor (TLR)4/MD-2 but not TLR2, as well as various inflammatory cytokines in peritoneal macrophages of C3H/HeN mice but not C3H/HeJ mice. Furthermore,S. marcescenslipid A induced nearly the same amounts of tumour necrosis factor alpha, interleukin-6, and nitric oxide production by the murine alveolar macrophage cell line MH-S as compared with compound 506. These results indicate thatS. marcescenspossesses a penta-acylated lipid A, which is nearly identical toE. colilipid A in regard to biological activities, while it also may be a crucial virulence factor of the bacterium.
In vitro activity of azithromycin, newer quinolones and cephalosporins in ciprofloxacin-resistant Salmonella causing enteric fever
Authors: Capoor Malini R. , Rawat Deepti , Nair Deepthi , Hasan Azra S. , Deb Monorama , Aggarwal Pushpa , Pillai Parukutty
Published: October 2007

The therapeutic alternatives available for use against ciprofloxacin-resistant enteric fever isolates in an endemic area are limited. The antibiotics currently available are the quinolones, third-generation cephalosporins and conventional first-line drugs. In this study, the MICs of various newer drugs were determined for 31 ciprofloxacin-resistant enteric fever isolates (26 Salmonella enterica serovar Typhi and 5 S. enterica serovar Paratyphi A). MICs for ciprofloxacin, ofloxacin, gatifloxacin, levofloxacin, cefotaxime, cefixime, cefepime and azithromycin were determined using Etest strips and the agar dilution method. By Etest, all of the ciprofloxacin-resistant isolates had ciprofloxacin MICs ≥32 μg ml−1. S. Typhi showed MIC90 values of 0.50, 0.25 and 0.38 μg ml−1 for cefixime, cefotaxime and cefepime, respectively. For the cephalosporins, a negligible difference in MIC90 and MIC50 values for S. Typhi and S. Paratyphi A was observed. A single isolate of S. Typhi showed a high azithromycin MIC of 64 μg ml−1. The MIC90 value for azithromycin in S. Typhi and S. Paratyphi was 24 μg ml−1. Gatifloxacin demonstrated lower resistance (80.8 %) compared with the other quinolones (92–100 %) in S. Typhi. The rise in MIC levels of these antimicrobials is a matter for serious concern.
Development of a multiplex PCR assay for identification of Campylobacter coli, Campylobacter fetus, Campylobacter hyointestinalis subsp. hyointestinalis, Campylobacter jejuni, Campylobacter lari and Campylobacter upsaliensis
Authors: Yamazaki-Matsune Wataru , Taguchi Masumi , Seto Kazuko , Kawahara Ryuji , Kawatsu Kentaro , Kumeda Yuko , Kitazato Miyoshi , Nukina Masafumi , Misawa Naoaki , Tsukamoto Teizo
Published: October 2007

A multiplex PCR assay has been developed for the identification of the six commonCampylobactertaxa associated with human gastroenteritis and/or septicaemia, namelyCampylobacter coli,Campylobacter fetus,Campylobacter hyointestinalissubsp.hyointestinalis,Campylobacter jejuni,Campylobacter lariandCampylobacter upsaliensis. The assay was developed using a combination of newly designed and published primers. It provided a specific PCR product for each of the fiveCampylobacterspecies and the one subspecies, and each of the PCR products was sufficiently distinguished by a difference in size by agarose gel electrophoresis. On evaluation of efficacy with 142Campylobacterstrains, the assay correctly identified all strains as 1 of the 6Campylobactertaxa. This multiplex PCR assay is a rapid, simple and practical tool for identification of the sixCampylobactertaxa commonly associated with gastroenteritis and/or septicaemia in humans, and offers an effective alternative to conventional biochemical-based assays.
Marker-Free Transgenic Plants through Genetically Programmed Auto-Excision
Authors: Verweire Dimitri , Verleyen Kristof , De Buck Sylvie , Claeys Martine , Angenon Geert
Published: October 2007

We present here a vector system to obtain homozygous marker-free transgenic plants without the need of extra handling and within the same time frame as compared to transformation methods in which the marker is not removed. By introducing a germline-specific auto-excision vector containing a cre recombinase gene under the control of a germline-specific promoter, transgenic plants become genetically programmed to lose the marker when its presence is no longer required (i.e. after the initial selection of primary transformants). Using promoters with different germline functionality, two modules of this genetic program were developed. In the first module, the promoter, placed upstream of the cre gene, confers CRE functionality in both the male and the female germline or in the common germline (e.g. floral meristem cells). In the second module, a promoter conferring single germline-specific CRE functionality was introduced upstream of the cre gene. Promoter sequences used in this work are derived from the APETALA1 and SOLO DANCERS genes from Arabidopsis (Arabidopsis thaliana) Columbia-0 conferring common germline and single germline functionality, respectively. Introduction of the genetic program did not reduce transformation efficiency. Marker-free homozygous progeny plants were efficiently obtained, regardless of which promoter was used. In addition, simplification of complex transgene loci was observed.
Newly Formed Vacuoles in Root Meristems of Barley and Pea Seedlings Have Characteristics of Both Protein Storage and Lytic Vacuoles
Authors: Olbrich Andrea , Hillmer Stefan , Hinz Giselbert , Oliviusson Peter , Robinson David G.
Published: October 2007

Plant cells are considered to possess functionally different types of vacuoles in the same cell. One of the papers cited in support of this concept reported that protein storage and lytic vacuoles in root tips of barley (Hordeum vulgare) and pea (Pisum sativum) seedlings were initially separate compartments that later fused to form a central vacuole during cell elongation. We have reinvestigated the situation in these two roots using immunogold electron microscopy as well as immunofluorescence microscopy of histological sections. Using antisera generated against the whole protein of α-tonoplast intrinsic protein (TIP) as well as specific C-terminal TIP peptide antisera against α-, γ-, and δ-TIP, together with antisera against the storage proteins barley lectin and pea legumin and vicilin, we were unable to obtain evidence for separate vacuole populations. Instead, our observations point to the formation of a single type of vacuole in cells differentiating both proximally and distally from the root meristem. This is a hybrid-type vacuole containing storage proteins and having both α- and γ-TIPs, but not δ-TIP, in its tonoplast. As cells differentiate toward the zone of elongation, their vacuoles are characterized by increasing amounts of γ-TIP and decreasing amounts of α-TIP.
Building Blocks for Plant Gene Assembly
Authors: Karimi Mansour , Bleys Annick , Vanderhaeghen Rudy , Hilson Pierre
Published: October 2007

The MultiSite Gateway cloning system, based on site-specific recombination, enables the assembly of multiple DNA fragments in predefined order, orientation, and frame register. To streamline the construction of recombinant genes for functional analysis in plants, we have built a collection of 36 reference Gateway entry clones carrying promoters, terminators, and reporter genes, as well as elements of the LhG4/LhGR two-component system. This collection obeys simple engineering rules. The genetic elements (parts) are designed in a standard format. They are interchangeable, fully documented, and can be combined at will according to the desired output. We also took advantage of the MultiSite Gateway recombination sites to create vectors in which two or three genes can be cloned simultaneously in separate expression cassettes. To illustrate the flexibility of these core resources for the construction of a wide variety of plant transformation vectors, we generated various transgenes encoding fluorescent proteins and tested their activity in plant cells. The structure and sequence of all described plasmids are accessible online at http://www.psb.ugent.be/gateway/. All accessions can be requested via the same Web site.
MPB2C, a Microtubule-Associated Protein, Regulates Non-Cell-Autonomy of the Homeodomain Protein KNOTTED1
Authors: Winter Nikola , Kollwig Gregor , Zhang Shoudong , Kragler Friedrich
Published: October 2007

Plasmodesmata establish a pathway for the intercellular trafficking of viral movement proteins and endogenous non-cell-autonomous proteins, such as the two closely related meristem-maintaining KNOTTED1-like homeobox (KNOX) proteins Zea mays KNOTTED1 (KN1) and Arabidopsis thaliana SHOOTMERISTEMLESS (STM). KNOX family members are DNA binding proteins that regulate the transcriptional activity of target genes in conjunction with BEL1-like homeodomain proteins. It has been shown previously, using in vivo transport assays, that the C-terminal domain of KN1, including the homeodomain, is necessary and sufficient for cell-to-cell transport through plasmodesmata. Here, using interaction and coexpression assays, we demonstrate that the microtubule-associated and viral movement protein binding protein MPB2C from Nicotiana tabacum, and its homolog in Arabidopsis, At MPB2C, are KN1/STM binding factors. Interaction between the MPB2C proteins and KN1/STM was mapped to the KN1 homeodomain, a region not essential for heterodimerization with BEL1. Expression of MPB2C in single cells prevented KN1 cell-to-cell movement. Furthermore, in vivo trichome rescue studies established that MPB2C negatively regulates KN1 association to plasmodesmata and, consequently, cell-to-cell transport. These findings are discussed in terms of the role played by MPB2C proteins in regulating the cell-to-cell trafficking of homeodomain proteins in plants.