bluuebunny/crossref_metadata_2025 huggingface dataset:
Paramagnetic anisotropy of Co-doped ZnO single crystal
Authors: Li Wei , Kang Qingqing , Lin Zhang , Chu Wangsheng , Chen Dongliang , Wu Ziyu , Yan Yu , Chen Dagui , Huang Feng
Published: September 2006

Zn 0.95 Co 0.05 O single crystal was obtained through hydrothermal crystal growth method. Extended x-ray absorption fine structure and x-ray absorption near-edge structure spectra as well as UV absorption measurements reveal that Co2+ ions have substituted Zn2+ ions and incorporated into ZnO lattice. The single crystal shows typical paramagnetic property from 2to300K. A paramagnetic anisotropy property in the crystal is found. The single ion anisotropy origin from tetrahedral coordination Co in the ZnO lattice was introduced to explain the phenomena. This work verified the paramagnetic anisotropy phenomena in ZnO–Co.
Backward Tamm states in left-handed metamaterials
Authors: Namdar Abdolrahman , Shadrivov Ilya V. , Kivshar Yuri S.
Published: September 2006

The authors study the electromagnetic surface waves localized at an interface separating a one-dimensional photonic crystal and left-handed metamaterial, the so-called surface Tamm states. They demonstrate that the metamaterial allows for a flexible control of the dispersion properties of surface states and can support the Tamm states with a backward energy flow and a vortexlike structure.
Charge retention enhancement in stack nanocrystalline-Si based metal-insulator-semiconductor memory structure
Authors: Wu L. C. , Chen K. J. , Wang J. M. , Huang X. F. , Song Z. T. , Liu W. L.
Published: September 2006

Stack nanocrystalline-Si (nc-Si) based metal-insulator-semiconductor memory structure was put forward and fabricated by plasma-enhanced chemical vapor deposition. The capacitance hysteresis, and asymmetric current peaks were observed at room temperature, which confirm the memory effects and results from the nc-Si. The sharper upward current peak and the broader upward current peak for the annealed sample are explained by resonant tunneling of electrons into stack nc-Si and single nc-Si, respectively. The stack nc-Si has better charge-storage ability than single nc-Si, and a model was put forward to explain the retention mechanism of this stack nc-Si based memory structure.
Enhanced dipole-dipole interaction of CdSe∕CdS nanocrystal quantum dots inside a planar microcavity
Authors: Wang Xiaoyong , Shih Chih-Kang , Xu Jianfeng , Xiao Min
Published: September 2006

The energy transfer (ET) dynamics of closely packed CdSe∕CdS nanocrystal quantum dots (NQDs) embedded in a planar microcavity were studied by using time-resolved photoluminescence measurements. An increase of ∼20% was observed in the rates of ET from smaller to larger NQDs in the microcavity as compared with those measured in free space. This behavior was attributed to the enhanced dipole-dipole interactions between donor and acceptor NQDs at the spectral positions of the cavity modes.
Optical coatings by ion-beam sputtering deposition for long-wave infrared quantum cascade lasers
Authors: Nguyen J. , Yu J. S. , Evans A. , Slivken S. , Razeghi M.
Published: September 2006

The authors report on the development of high-reflection and multilayer antireflection coatings using ion-beam sputtering deposition for long-wave infrared (λ∼9.4μm) quantum cascade lasers. A metallic high-reflection coating structure using Y2O3 and Au is demonstrated to achieve a high reflectance of 96.70%, and the use of a multilayer anti-reflection coating structure using PbTe and ZnO is demonstrated to achieve a very low reflectance of 1.64%. A 170% improvement of peak laser output power and a 169% increase in wall-plug efficiency are reported without any beam steering effects.
Self-assembly of laterally aligned GaAs quantum dot pairs
Authors: Yamagiwa M. , Mano T. , Kuroda T. , Tateno T. , Sakoda K. , Kido G. , Koguchi N. , Minami F.
Published: September 2006

The authors report the fabrication of self-assembled, strain-free GaAs∕Al0.27Ga0.73As quantum dot pairs which are laterally aligned in the growth plane, utilizing the droplet epitaxy technique and the anisotropic surface potentials of the GaAs (100) surface for the migration of Ga adatoms. Photoluminescence spectra from a single quantum dot pair, consisting of a doublet, have been observed. Finite element energy level calculations of a model quantum dot pair are also presented.
Optical properties of colloidal InGaP∕ZnS core/shell nanocrystals
Authors: Joshi Abhishek , Manasreh M. O. , Davis E. A. , Weaver B. D.
Published: September 2006

The energy band gap (Eg) of colloidal InGaP∕ZnS core/shell nanocrystals is investigated by using the optical absorption and the photoluminescence techniques. While the photoluminescence spectra exhibit a strong emission, the optical absorption spectra show a very weak excitonic absorption. From Eg values estimated from the optical absorption spectra, the In composition is calculated to be on the order of 45%–48%. The estimated In mole fraction suggests that InGaP is still a direct band gap semiconductor. The energy band gap is recorded as a function of temperature from which the Debye temperature and the average phonon energy were extracted.
Photoinduced reflectivity oscillation in LiNbO3 crystals irradiated by a KrF laser
Authors: Bentini G. G. , Bianconi M. , Cerutti A. , Chiarini M. , Pennestrì G. , Argiolas N. , Bazzan M. , Mazzoldi P. , Sada C.
Published: September 2006

A study on LiNbO3 crystal irradiation by pulsed KrF excimer laser beam is presented. The interaction with the 248nm laser light modifies the material properties so that, when the irradiation is switched off, a time-periodic variation in the material reflectivity, depending on the irradiation conditions, was observed. This phenomenon can be explained in terms of the electro-optic effect induced by the buildup of internal electric fields since the compositional characterization, performed by the secondary ion mass spectrometry, showed no modification in the element concentration and the high resolution x-ray diffraction did not detect any structural deformation within the crystal.
Effect of soil acidity and liming on lucerne and following crops in central-western New South Wales
Authors: Mullen C. L. , Scott B. J. , Evans C. M. , Conyers M. K.
Published: September 2006

On some of the lighter textured soils in the wheatbelt of central-western New South Wales near Dubbo, soil acidity is a major problem, and lucerne (Medicago sativa) often establishes and grows poorly. We selected a site with a surface soil pHCa of 4.4 and an exchangeable aluminium of 0.4 cmol(+)/kg, which was also acidic down the soil profile. Experimental plots of 4 application rates of lime (nil, 1, 2 and 3 t/ha) in 4 replications were established. The site was limed in 1990 and lucerne sown in May 1991. Over the next 6 years the trial was periodically grazed with sheep, and lucerne regrowth and stand density were monitored. In October 1997, the lucerne was removed and 3 crops of varying acid tolerance (wheat, barley and canola) were sown as split plots in both 1998 and 1999. Lucerne density was higher in the limed plots compared with the unlimed treatment, and this difference persisted for 6 years. Dry matter production of lucerne was increased by lime applied at rates up to 2 t/ha. All 3 crops sown after the lucerne phase responded to lime applied 8 and/or 9 years earlier. The responses were attributed to the strong residual effect of the lime in the 0–10 cm soil layer, to smaller improvements in the 10–20 cm zone (possibly due to the movement of lime down the soil profile over the 7 years before the date of measurement) and to carry over effects of nitrogen fixation by the lucerne into the cropping phase. The protein content of the wheat grain was increased concurrently with grain yield due to the previous liming and resultant legume nitrogen effects. The results support the application of lime to improve the productivity of lucerne and subsequent crops, even when the soil is acidic to depths below the cultivation layer.
Narbon bean (Vicia narbonensis) agronomy in south-western Australia
Authors: Seymour M.
Published: September 2006

Narbon bean (Vicia narbonensis L.) shows promise as a fodder, green manure and grain crop in south-western Australia. This study examines the effect of time of sowing (2 experiments), plant density (3 experiments) and reaction to herbicides (4 experiments on tolerance to herbicides and 1 experiment on removing narbon bean from a wheat crop) in 10 separate field experiments sown at 4 locations in the mallee region of Western Australia from 1998 to 2001. Narbon bean was found to be unresponsive to changes in sowing date with yield maintained until the first week of June. The optimum plant density (90% of fitted maximum) for seed yield was found to be 31 plants/m2, equivalent to sowing rates in the range of 75–100 kg/ha. A wide range of herbicides applied either before sowing or immediately after sowing and before emergence had no significant effect on grain yield. These included simazine (750 g a.i./ha), cyanazine (1.25 kg a.i./ha) and diuron (500 g a.i./ha), which were applied immediately before sowing, and imazethapyr (29 g a.i./ha), which was applied after sowing, before emergence. Diflufenican (75 g a.i./ha) was found to be the only available option for post-emergence control of broadleaf weeds. The use of the non-selective herbicides glyphosate (450 g a.i./L) and Sprayseed 250 (paraquat 135 g a.i./L and diquat 115 g a.i./L) as post-emergence herbicides was found to be unpredictable at a range of application rates. Results ranged from a yield loss of 47% to a yield increase of 23%. In an experiment to test a range of herbicides for the selective control of narbon bean within a wheat crop, numerous herbicides were found to effectively remove volunteer narbon bean indicating that narbon bean is unlikely to become a weed in most cereal cropping systems.
Spatial variability of regolith leaching and salinity in relation to Whole Farm Planning
Authors: Williams B. , Walker J. , Anderson J.
Published: September 2006

An electromagnetic induction (EM31) survey was carried out on a 700-ha property in the western basalt plains of Victoria. The apparent electrical conductivity (ECa) was interpreted in terms of the inferred salt content and, hence, the degree of leaching or recharge through the upper 5 m of the regolith. The focus of the survey was to determine the spatial variability of ECa across a landscape of low relief which included salt lakes. The area mapped is subject to regional groundwater discharge. All parts of the property exhibited hydrological ‘sinks’ and ‘trenches’ of relatively low ECa values, interpreted as areas of preferential recharge or leaching through the regolith. They ranged in size from 200 to 500 m in diameter and/or length and were not related to relief. This apparent hydrological ‘holeyness’ of the upper regolith suggests local recharge into the regional groundwater system. This finding has important implications for Whole Farm Planning and Environmental Management Strategies as local recharge can be reduced by manipulating ground cover and land-use practices. Both the mean and standard deviation of ECa values across the property provide a rational basis for planning land management practices. The location of hydrological ‘holes’ can be built in as significant layers in Whole Farm Plans to minimise water entering the water table and/or salt lakes.
Variation in soil properties on two partially revegetated saline scalds in south-eastern Australia
Authors: Semple W. S. , Koen T. B. , Eldridge D. J. , Düttmer K. M. , Parker B.
Published: September 2006

During 1999 and 2000, topsoil properties were sampled on a 3 by 3 m grid at 2 saline scalds on the inland slopes of New South Wales (NSW): Bocobra (0.11 ha) and Rugby (0.12 ha). Variability was examined in terms of range, standard deviation and coefficient of variation, maps with interpolated ‘contours’, and variograms. High variability was evident in all soil properties. pH1:5 water ranged from 4.8 to 8.0 at Bocobra and 5.9 to 9.0 at Rugby. Spatial ‘highs’ were evident at both sites but Rugby, which was mostly neutral, had both highs (alkalinity) and lows (acidity). Electrical conductivity (EC1:5 water) ranged from 0.5 to 6.6 dS/m at Bocobra and 0.1 to 2.6 dS/m at Rugby and was expressed spatially as highs across the sites. Concentrations of soluble ions were highly variable with both highs and lows evident. Concentrations of sodium and magnesium at Bocobra were highly correlated with EC1:5 water. Variability in EC and pH were high in comparison with published data from much larger areas of non-saline soils. An indication of temporal variability was obtained by carrying out an electromagnetic induction survey on 2 occasions. Despite changes in spatial patterns over time, EMh and EMv values were highly correlated at 1 site but not at the other. Variogram analysis suggested that changes in some variables, e.g. soluble potassium, changed markedly over distances less than 3 m. For most variables, the full range of variability occurred over distances of 8–10 m, though for some, e.g. soluble calcium, a distance of around 19 m was indicated. Variability cannot be ignored when planning revegetation projects or experiments. Partly because of their temporal variability, electromagnetic induction survey results (which were not calibrated with soil profile ECs in this study) may not provide useful guidelines for strategic soil sampling nor for locating experimental plots on scalded saline sites. Consideration should also be given to testing variables other than EC, e.g. pH and calcium, which may also limit plant growth on saline scalds.
Crop damage caused by residual acetolactate synthase herbicides in the soils of south-eastern Australia
Authors: Hollaway K. L. , Kookana R. S. , Noy D. M. , Smith J. G. , Wilhelm N.
Published: September 2006

Grain growers in south-eastern Australia have reported unexpected crop failures with theoretically safe recropping periods for acetolactate synthase herbicides in alkaline soils. This experience has led to the concern that these herbicides may degrade very slowly in alkaline soils, and herbicide residues have at times been blamed for unexplained crop losses. To address this issue, we established 5 recropping trials across Victoria and South Australia with 5 acetolactate synthase herbicides (chlorsulfuron, triasulfuron, metsulfuron-methyl, imazethapyr, and flumetsulam). The herbicides were applied to separate plots in years 1, 2 or 3, and sensitive crop species were sown in year 4 to measure the impact of herbicide residues. We observed that the persistence of the sulfonylureas (chlorsulfuron, triasulfuron, metsulfuron-methyl) varied between herbicides, but all persisted longer in alkaline soils than in acid soils, and were, therefore, more likely to damage crops in alkaline soil. Imazethapyr persisted longer in clay soils than in sandy soils and was, therefore, more likely to damage crops in clay soils. All herbicides persisted longer when rainfall was below average. Canola was more sensitive to imazethapyr than either pea, lentil or medic, but was less sensitive to the sulfonylureas. In contrast, lentil and medic were the most sensitive to sulfonylureas. Despite some damage, we found that safe recropping periods could be predicted from the product labels in all but one situation. The sole exception was that metsulfuron-methyl reduced dry matter and yield of lentil and medic sown 10 months after application in a soil with pH 8.5. We hypothesise that the real cause of crop failure in many situations is not unusual herbicide persistence, but failure to take full account of soil type (pH and clay content including variation in the paddock) and rainfall when deciding to recrop after using acetolactate synthase herbicides.
Shelterbelts in agricultural landscapes suppress invertebrate pests
Authors: Tsitsilas A. , Stuckey S. , Hoffmann A. A. , Weeks A. R. , Thomson L. J.
Published: September 2006

The homogenous nature of agricultural landscapes generally reduces biodiversity of invertebrate species, but this can be partly offset by developing refuges at field margins. In Australia, shelterbelts are widely planted to provide protection for livestock and to counter salinity problems associated with rising water tables. Shelterbelts may also play a role in acting as reservoirs for organisms that are beneficial to pastures, although this has rarely been directly evaluated. We sampled invertebrates along transects running from replicated shelterbelts into pastures, and in glasshouse trials we tested the impact of the beneficial organisms from the shelterbelts on the collected pests. Contrary to popular views, numbers of pest mites and lucerne fleas were low within shelterbelts. Moreover, numbers were typically lower adjacent to shelterbelts compared with >30 m into the pasture, an effect that was much more apparent when shelterbelts carried a groundcover of high (>30 cm) grass. Numbers of predatory mites and spiders were higher in shelterbelts and in adjacent pasture when there was taller grass and higher grass cover in the shelterbelts. Samples of potential predators collected from a shelterbelt were more effective at suppressing pest mite numbers than those collected in pasture. Shelterbelts with ground cover appear to harbour a diversity of beneficial organisms that suppress pest numbers in adjacent pastures.
Influence of reduced irrigation on beneficial invertebrates in vineyards
Authors: Thomson L. J.
Published: September 2006

An important aspect of increasing the sustainability of agricultural production in dry continents such as Australia is decreasing water use. In this study full irrigation is compared with partial rootzone drying, a method that uses targeted controlled watering to reduce water use while maintaining production in vineyards. The impact of the 2 irrigation methods on invertebrates with potential to influence productivity (pests, predators, parasitoids and soil macroinvertebrates) in a vineyard in south-eastern Australia is also investigated. Invertebrates were sampled at ground level and in the canopy using 3 methods: pitfall traps and 2 types of sticky trap. Earthworms were sampled by hand sorting soil. Initial sorting of the collections was to the order level. The implementation of partial rootzone drying throughout the growing season (December–March) over 2 consecutive years had little effect on the invertebrate orders analysed. Only 2 generalist predator orders (Araneae and Coleoptera) and earthworms (Haplotaxida) were significantly affected under conditions of water stress. These data suggest that reduction of irrigation of the magnitude required for partial rootzone drying has limited consequences for natural enemies of vineyard pests and soil macroinvertebrates in the short term.
Construction and operation of open-circuit methane chambers for small ruminants
Authors: Klein L. , Wright A.-D. G.
Published: September 2006

A detailed description of the construction, calibration and operation of 4 open-circuit chambers designed to measure methane emissions from sheep is given. These chambers have accommodated sheep under ad libitum feeding and have been used in short-term experiments and over extended periods of time. A real-time base data acquisition and process control system provided 24 h operation of the methane chambers. The gas volume measurement system consisted of dry test meters and sensors for differential and absolute pressure, temperature and relative humidity. This enabled correction of methane chamber exhaust air volume to standard temperature and pressure. Temperatures and relative humidity during measurements ranged from 21.0 to 23.1°C and 53.8 to 78.9%, respectively. The gas chromatograms were calibrated 3 times a day using commercially available gas standards. Recovery tests were conducted on each chamber by bleeding a methane gas standard into the chamber at a rate similar to methane production by sheep, with 94.4–107.1% of the methane gas recovered. Measurements on 32 sheep gave methane emissions within predicted levels and identified several low methane-producing sheep.
Predicting the epidemiological impact of antiretroviral allocation strategies in KwaZulu-Natal: The effect of the urban–rural divide
Authors: Wilson David P. , Kahn James , Blower Sally M.
Published: September 2006

Antiretroviral therapy (ART) is becoming available in South Africa. Demand will exceed supply; thus, difficult decisions will have to be made in allocating ART. The majority of those treated for HIV are likely to be in cities, because health infrastructure and personnel are concentrated in urban centers. We predict the epidemiological impact of drug allocation strategies (DAS) by using a spatially explicit model that links urban and rural epidemics. We parameterize our model by using data from the KwaZulu-Natal province in South Africa. We model the South African government's treatment plan from 2004–2008, and we predict the consequences of one DAS that allocates drugs only to Durban and of two DAS that allocate drugs to both urban and rural areas. All three strategies would treat 500,000 people by 2008. Not surprisingly, the Durban-only DAS would prevent the greatest number of infections (an additional 15,000 infections by 2008). However, it may have been expected that this DAS would generate the highest levels of transmitted resistance, because it concentrates ART in one location. Paradoxically, we found that this DAS would generate the lowest levels of transmitted resistance. Concentrating treatment in Durban would also avert the greatest number of AIDS-related deaths. We discuss the difference between using the principle of treatment equity versus using the principle of utilitarianism/efficiency to allocate ART. Decisions about allocating scarce drugs should consider treatment equity as well as epidemiological consequences. Notably, a Durban-only DAS would lead to new disparities in healthcare between urban and rural areas in KwaZulu-Natal.
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
Authors: Lee Su-In , Pe'er Dana , Dudley Aimée M. , Church George M. , Koller Daphne
Published: September 2006

Sequence polymorphisms affect gene expression by perturbing the complex network of regulatory interactions. We propose a probabilistic method, called Geronemo, which directly aims to identify the mechanism by which genetic changes perturb the regulatory network. Geronemo automatically constructs a set of coregulated genes (modules), whose regulation can involve both sequence variations and expression of regulators. By exploiting the modularity of genetic regulatory systems, Geronemo reveals regulatory relationships that are indiscernible when genes are considered in isolation, allowing the recovery of intricate combinatorial regulation. By incorporating both expression and genotype of regulators, Geronemo captures cases where the effect of sequence variation on its targets is indirect. We applied Geronemo to a data set from the progeny generated by a cross between laboratory BY4716 (BY) and wild RM11-1a (RM) isolates of
Saccharomyces cerevisiae
. Geronemo produced previously undescribed hypotheses regarding genetic perturbations in the yeast regulatory network, including transcriptional regulation, signal transduction, and chromatin modification. In particular, we find a large number of modules that have both chromosomal characteristics and are regulated by chromatin modification proteins. Indeed, a large fraction of the variance in the expression can be explained by a small number of markers associated with chromatin modifiers. Additional analysis reveals positive selection for sequence evolution of elements in the Swi/Snf chromatin remodeling complex. Overall, our results suggest that a significant part of individual expression variation in yeast arises from evolution of a small number of chromatin structure modifiers.
Mechanisms of uropathogenic
Escherichia coli
persistence and eradication from the urinary tract
Authors: Mysorekar Indira U. , Hultgren Scott J.
Published: September 2006

Recurrent urinary tract infections (rUTIs) are a source of considerable morbidity in women. The infecting bacteria in both rUTIs and a
de novo
acute infection have been thought to originate from an extraurinary location. Here, we show in a murine model of UTI that uropathogenic
Escherichia coli
(UPEC) established quiescent intracellular reservoirs (QIRs) in Lamp1
+
endosomes within the urinary bladder epithelium. Depending on the integrity of the urothelial barriers at the time of initial infection, these QIRs were established within terminally differentiated superficial facet cells and/or underlying transitional epithelial cells. Treatment of infected bladders harboring exclusively superficial facet cell QIRs with the cationic protein, protamine sulfate, led to epithelial exfoliation and eradication of bacteria in 100% of treated animals. However, when the bacterial QIRs were harbored in underlying transitional cells, stimulation of epithelial turnover triggered reemergence of viable organisms and recurrence of infection. Thus, our results suggest (
i
) that bacterial QIRs within the bladder may be a previously unappreciated source of recurrent UTIs and (
ii
) that inducing epithelial exfoliation may be a therapeutic avenue for treating this heretofore recalcitrant disease.
Pathogenesis and treatment of autosomal-dominant nephrogenic diabetes insipidus caused by an aquaporin 2 mutation
Authors: Sohara Eisei , Rai Tatemitsu , Yang Sung-Sen , Uchida Keiko , Nitta Kosaku , Horita Shigeru , Ohno Mayuko , Harada Akihiro , Sasaki Sei , Uchida Shinichi
Published: September 2006

Frame-shift mutations within the C terminus of aquaporin 2 (AQP2) cause autosomal-dominant nephrogenic diabetes insipidus (AD-NDI). To identify the molecular mechanism(s) of this disease
in vivo
and to test possible therapeutic strategies, we generated a mutant AQP2 (763–772 del) knockin mouse. Heterozygous knockin mice showed a severely impaired urine-concentrating ability. However, they were able to slightly increase urine osmolality after dehydration. This milder phenotype, when compared with autosomal-recessive NDI, is a feature of AD-NDI in humans, thus suggesting successful establishment of an AD-NDI mouse model. Immunofluorescence of collecting duct cells in the AD-NDI mouse revealed that the mutant AQP2 was missorted to the basolateral instead of apical plasma membrane. Furthermore, the mutant AQP2 formed a heterooligomer with wild-type AQP2 and showed a dominant-negative effect on the normal apical sorting of wild-type AQP2 even under dehydration. Using this knockin mouse, we tested several drugs for treatment of AD-NDI and found that rolipram, a phosphodiesterase 4 inhibitor, was able to increase urine osmolality. Phosphodiesterase inhibitors may thus be useful drugs for the treatment of AD-NDI. This animal model demonstrates that a mutant monomer gains a dominant-negative effect that reverses the normal polarized sorting of multimers.
β-Arrestin2 mediates nephrin endocytosis and impairs slit diaphragm integrity
Authors: Quack Ivo , Rump L. Christian , Gerke Peter , Walther Inga , Vinke Tobias , Vonend Oliver , Grunwald Thomas , Sellin Lorenz
Published: September 2006

β-Arrestins mediate internalization of plasma membrane receptors. Nephrin, a structural component of the glomerular slit diaphragm, is a single transmembrane spanning receptor and belongs to the family of adhesion molecules. Its mutation causes a hereditary nephrotic syndrome. We report the previously undescribed interaction of β-arrestin2 with the nephrin C terminus. The phosphorylation status of nephrin Y1193 regulates inversely the binding of β-arrestin2 and podocin. The Src-family member Yes, known to enhance podocin–nephrin interaction by nephrin phosphorylation, diminishes β-arrestin2–nephrin interaction. β-Arrestin2 induces nephrin endocytosis and attenuates nephrin signaling. This finding suggests that nephrin Y1193 serves as a molecular switch that determines the integrity of the slit diaphragm by functional competition between β-arrestin2 and podocin. This concept offers a molecular pathomechanism of slit diaphragm distortion and opens therapeutic avenues for glomerular diseases.
Self-assembled single-crystal silicon circuits on plastic
Authors: Stauth Sean A. , Parviz Babak A.
Published: September 2006

We demonstrate the use of self-assembly for the integration of freestanding micrometer-scale components, including single-crystal, silicon field-effect transistors (FETs) and diffusion resistors, onto flexible plastic substrates. Preferential self-assembly of multiple microcomponent types onto a common platform is achieved through complementary shape recognition and aided by capillary, fluidic, and gravitational forces. We outline a microfabrication process that yields single-crystal, silicon FETs in a freestanding, powder-like collection for use with self-assembly. Demonstrations of self-assembled FETs on plastic include logic inverters and measured electron mobility of 592 cm
2
/V-s. Finally, we extend the self-assembly process to substrates each containing 10,000 binding sites and realize 97% self-assembly yield within 25 min for 100-μm-sized elements. High-yield self-assembly of micrometer-scale functional devices as outlined here provides a powerful approach for production of macroelectronic systems.
The transcriptome of human oocytes
Authors: Kocabas Arif Murat , Crosby Javier , Ross Pablo J. , Otu Hasan H. , Beyhan Zeki , Can Handan , Tam Wai-Leong , Rosa Guilherme J. M. , Halgren Robert G. , Lim Bing , Fernandez Emilio , Cibelli Jose Bernardo
Published: September 2006

The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the oocyte. Of the oocyte up-regulated probe sets, 1,430 have unknown function. A core group of 66 transcripts was identified by intersecting significantly up-regulated genes of the human oocyte with those from the mouse oocyte and from human and mouse embryonic stem cells. GeneChip array results were validated using RT-PCR in a selected set of oocyte-specific genes. Within the up-regulated probe sets, the top overrepresented categories were related to RNA and protein metabolism, followed by DNA metabolism and chromatin modification. This report provides a comprehensive expression baseline of genes expressed in
in vivo
matured human oocytes. Further understanding of the biological role of these genes may expand our knowledge on meiotic cell cycle, fertilization, chromatin remodeling, lineage commitment, pluripotency, tissue regeneration, and morphogenesis.
A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein
Authors: Kötting Carsten , Blessenohl Marco , Suveyzdis Yan , Goody Roger S. , Wittinghofer Alfred , Gerwert Klaus
Published: September 2006

The hydrolysis of nucleoside triphosphates by enzymes is used as a regulation mechanism in key biological processes. Here, the GTP hydrolysis of the protein complex of Ras with its GTPase-activating protein is monitored at atomic resolution in a noncrystalline state by time-resolved FTIR spectroscopy. At 900 ms, after the attack of water at the γ-phosphate, there appears a H2PO4−intermediate that is shown to be hydrogen-bonded in an eclipsed conformation to the β-phosphate of GDP. The H2PO4−intermediate is in a position where it can either reform GTP or be released from the protein in 7 s in the rate-limiting step of the GTPase reaction. We propose that such an intermediate also occurs in other GTPases and ATPases.
Hedgehog modulates cell cycle regulators in stem cells to control hematopoietic regeneration
Authors: Trowbridge Jennifer J. , Scott Matthew P. , Bhatia Mickie
Published: September 2006

The signals that control the regenerative ability of hematopoietic stem cells (HSCs) in response to damage are unknown. Here, we demonstrate that downstream activation of the Hedgehog (Hh) signaling pathway induces cycling and expansion of primitive bone marrow hematopoietic cells under homeostatic conditions and during acute regeneration. However, this effect is at the expense of HSC function, because continued Hh activation during regeneration represses expression of specific cell cycle regulators, leading to HSC exhaustion.
In vivo
treatment with an inhibitor of the Hh pathway rescues these transcriptional and functional defects in HSCs. Our study establishes Hh signaling as a regulator of the HSC cell cycle machinery that balances hematopoietic homeostasis and regeneration
in vivo
.
A molecular mechanism for osmolyte-induced protein stability
Authors: Street Timothy O. , Bolen D. Wayne , Rose George D.
Published: September 2006

Osmolytes are small organic compounds that affect protein stability and are ubiquitous in living systems. In the equilibrium protein folding reaction, unfolded (U) ⇌ native (N), protecting osmolytes push the equilibrium toward N, whereas denaturing osmolytes push the equilibrium toward U. As yet, there is no universal molecular theory that can explain the mechanism by which osmolytes interact with the protein to affect protein stability. Here, we lay the groundwork for such a theory, starting with a key observation: the transfer free energy of protein backbone from water to a water/osmolyte solution, Δgtr, is negatively correlated with an osmolyte’s fractional polar surface area. Δgtrmeasures the degree to which an osmolyte stabilizes a protein. Consequently, a straightforward interpretation of this correlation implies that the interaction between the protein backbone and osmolyte polar groups is more favorable than the corresponding interaction with nonpolar groups. Such an interpretation immediately suggests the existence of a universal mechanism involving osmolyte, backbone, and water. We test this idea by using it to construct a quantitative solvation model in which backbone/solvent interaction energy is a function of interactant polarity, and the number of energetically equivalent ways of realizing a given interaction is a function of interactant surface area. Using this model, calculated Δgtrvalues show a strong correlation with measured values (R= 0.99). In addition, the model correctly predicts that protecting/denaturing osmolytes will be preferentially excluded/accumulated around the protein backbone. Taken together, these model-based results rationalize the dominant interactions observed in experimental studies of osmolyte-induced protein stabilization and denaturation.
The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor
Authors: Milon Pohl , Tischenko Eugene , Tomšic Jerneja , Caserta Enrico , Folkers Gert , La Teana Anna , Rodnina Marina V. , Pon Cynthia L. , Boelens Rolf , Gualerzi Claudio O.
Published: September 2006

Translational initiation factor 2 (IF2) is a guanine nucleotide-binding protein that can bind guanosine 3′,5′-(bis) diphosphate (ppGpp), an alarmone involved in stringent response in bacteria. In cells growing under optimal conditions, the GTP concentration is very high, and that of ppGpp very low. However, under stress conditions, the GTP concentration may decline by as much as 50%, and that of ppGpp can attain levels comparable to those of GTP. Here we show that IF2 binds ppGpp at the same nucleotide-binding site and with similar affinity as GTP. Thus, GTP and the alarmone ppGpp can be considered two alternative physiologically relevant IF2 ligands. ppGpp interferes with IF2-dependent initiation complex formation, severely inhibits initiation dipeptide formation, and blocks the initiation step of translation. Our data suggest that IF2 has the properties of a cellular metabolic sensor and regulator that oscillates between an active GTP-bound form under conditions allowing active protein syntheses and an inactive ppGpp-bound form when shortage of nutrients would be detrimental, if not accompanied by slackening of this synthesis.
Critical Role of PICT-1, a Tumor Suppressor Candidate, in Phosphatidylinositol 3,4,5-Trisphosphate Signals and Tumorigenic Transformation
Authors: Okahara Fumiaki , Itoh Kouichi , Nakagawara Akira , Murakami Makoto , Kanaho Yasunori , Maehama Tomohiko
Published: September 2006

The tumor suppressor phosphatase and tensin homolog deleted on chromosome 10 (PTEN) regulates diverse cellular functions by dephosphorylating the lipid second messenger, phosphatidylinositol 3,4,5-trisphosphate (PIP3). Recent study revealed that PICT-1/GLTSCR2 bound to and stabilized PTEN protein in cells, implicating its roles in PTEN-governed PIP3 signals. In this study, we demonstrate that RNA interference-mediated knockdown of PICT-1 in HeLa cells down-regulated endogenous PTEN and resulted in the activation of PIP3 downstream effectors, such as protein kinase B/Akt. Furthermore, the PICT-1 knockdown promoted HeLa cell proliferation; however the proliferation of PTEN-null cells was not altered by the PICT-1 knockdown, suggesting its dependency on PTEN status. In addition, apoptosis of HeLa cells induced by staurosporine or serum-depletion was alleviated by the PICT-1 knockdown in the similar PTEN-dependent manner. Most strikingly, the PICT-1 knockdown in HeLa and NIH3T3 cells promoted anchorage-independent growth, a hallmark of tumorigenic transformation. Furthermore, PICT-1 was aberrantly expressed in 18 (41%) of 44 human neuroblastoma specimens, and the PICT-1 loss was associated with reduced PTEN protein expression in spite of the existence of PTEN mRNA. Collectively, these results suggest that PICT-1 plays a role in PIP3 signals through controlling PTEN protein stability and the impairment in the PICT-1–PTEN regulatory unit may become a causative factor in human tumor(s).
Loss of T-Cell Protein Tyrosine Phosphatase Induces Recycling of the Platelet-derived Growth Factor (PDGF) β-Receptor but Not the PDGF α-Receptor
Authors: Karlsson Susann , Kowanetz Katarzyna , Sandin Åsa , Persson Camilla , Östman Arne , Heldin Carl-Henrik , Hellberg Carina
Published: September 2006

We have previously shown that the T-cell protein tyrosine phosphatase (TC-PTP) dephosphorylates the platelet-derived growth factor (PDGF) β-receptor. Here, we show that the increased PDGF β-receptor phosphorylation in TC-PTP knockout (ko) mouse embryonic fibroblasts (MEFs) occurs primarily on the cell surface. The increased phosphorylation is accompanied by a TC-PTP–dependent, monensin-sensitive delay in clearance of cell surface PDGF β-receptors and delayed receptor degradation, suggesting PDGF β-receptor recycling. Recycled receptors could also be directly detected on the cell surface of TC-PTP ko MEFs. The effect of TC-PTP depletion was specific for the PDGF β-receptor, because PDGF α-receptor homodimers were cleared from the cell surface at the same rate in TC-PTP ko MEFs as in wild-type MEFs. Interestingly, PDGF αβ-receptor heterodimers were recycling. Analysis by confocal microscopy revealed that, in TC-PTP ko MEFs, activated PDGF β-receptors colocalized with Rab4a, a marker for rapid recycling. In accordance with this, transient expression of a dominant-negative Rab4a construct increased the rate of clearance of cell surface receptors on TC-PTP ko MEFs. Thus, loss of TC-PTP specifically redirects the PDGF β-receptor toward rapid recycling, which is the first evidence of differential trafficking of PDGF receptor family members.
Delayed Cell Cycle Progression and Apoptosis Induced by Hemicellulase‐Treated Agaricus blazei
Authors: Kawamura Masaki , Kasai Hirotake
Published: September 2006

We examined the effects of hemicellulase‐treated Agaricus blazei (AB fraction H, ABH) on growth of several tumor cell lines. ABH inhibited the proliferation of some cell lines without cytotoxic effects. It markedly prolonged the S phase of the cell cycle. ABH also induced mitochondria‐mediated apoptosis in different cell lines. However, it had no impact on the growth of other cell lines. ABH induced strong activation of p38 mitogen‐activated protein kinase (MAPK) in the cells in which it evoked apoptosis. On the other hand, ABH showed only a weak p38 activation effect in those cell lines in which it delayed cell cycle progression with little induction of apoptosis. However, p38 MAPK‐specific inhibitor inhibited both ABH‐induced effects, and ABH also caused apoptosis in the latter cells under conditions of high p38 MAPK activity induced by combined treatment with TNF‐α. These results indicate that the responsiveness of p38 MAPK to ABH, which differs between cell lines, determines subsequent cellular responses on cell growth.
Development of the Client‐Centred Care Questionnaire
Authors: De Witte Luc , Schoot Tineke , Proot Ireen
Published: September 2006

Aim.  This paper reports the development and testing of the Client‐Centred Care Questionnaire, aimed at evaluating the client‐centredness of professional home nursing care from a client perspective.

Background.  Client‐centred care has become an important theme in health care. To evaluate the client‐centredness of care and services from a client's perspective, there is a need for measurement instruments.

Method.  The questionnaire was developed on the basis of a qualitative study into client perspectives on home nursing care. Items were formulated that closely followed the aspects clients mentioned as central to client‐centred home care. A pilot study was conducted with a sample of 107 clients in three home care organizations in 2003 and 2004. These clients had chronic diseases and were expected to receive care for at least another 6 months. The questionnaire comprises 15 items.

Findings.  Principal components analysis and internal consistency analysis show strong internal consistency of the items. All items had strong factor loadings on one dimension, and Cronbach's alpha was 0·94. Clients tended to be most critical about their say in the practical arrangements and organization of care: which person came, how often and when? Clients of the three organizations differed in their perceptions of client‐centredness, which may indicate that the questionnaire is capable of differentiating between respondents.

Conclusion.  The results of this pilot study are promising. The validity of the questionnaire needs further testing.
Human biogeography: evidence of our place in nature
Authors: Terrell John Edward
Published: September 2006

Focusing on human biogeography as a research endeavour may make sense to biogeographers, but in the academic world generally this particular scholarly niche has long been filled by other rival disciplines such as sociology, human ecology, geography, anthropology and archaeology. It may be true that having so many ways of looking at ourselves as a species is a good thing, but it can also be argued that this academic fragmentation of effort has often nurtured the commonplace view that we as a species are ‘above’ or ‘not part of’ what plain folks call the ‘natural world’. Here I review the historical and basic intellectual ingredients of what might be (but often isn't) called human biogeography. I offer a case study drawn from my research work on the Sepik coast of Papua New Guinea. This research illustrates how adopting an explicitly biogeographical approach to human diversity can lead to unexpected insights into the character and history of human settlement in this part of the world. One benefit of having a field with this explicit orientation might be that the conservation of biodiversity would make more sense to more people.
Successful renal transplantation despite low levels of donor‐specific HLA class I antibody without IVIg or plasmapheresis
Authors: Bryan Christopher F. , McDonald Scott B. , Luger Alan M. , Shield Charles F. , Winklhofer Franz T. , Michael Borkon A. , Warady Bradley A. , Aeder Mark I. , Murillo Daniel
Published: September 2006

Abstract:  We prospectively transplanted 10 primary kidney recipients with deceased donor organs (nine kidney and one pancreas/kidney) when their flow cytometric T‐cell IgG, HLA class I donor‐specific crossmatch was positive but the AHG T‐cell crossmatch was negative, with a median follow‐up of 1.8 yr. No pre‐ or peri‐operative IVIg or plasmapheresis was administered to any patient. All but one of the 11 organs transplanted into patients with a flow T+/AHG− crossmatch is currently functioning despite the continued presence of circulating low levels of HLA class I antibody. Flow HLA class I antigen‐coated beads showed the presence of at least one donor‐specific HLA class I antibody at transplantation in each of the 10 cases. No rejections were observed in seven of the 10 cases (70%). Six rejection episodes, four cellular and two humoral, occurred in three patients. Each rejection was successfully treated. The only graft loss occurred in a kidney recipient on day 667 secondary to ischemia to the kidney because of cardiac surgery. Thus, short‐term (one to two years) graft survival in primary transplants was not influenced by low levels of donor‐specific HLA class I antibody present at transplantation and no prophylactic treatment such as IVIg, plasmapheresis, anti‐CD20 or splenectomy was needed peri‐operatively.
Steroid‐free immunosuppression regime reduces both long‐term cardiovascular morbidity and patient mortality in renal transplant recipients
Authors: Sandrini Silvio , Maffeis Roberto , Setti Gisella , Bossini Nicola , Maiorca Paolo , Maffei Camilla , Guerini Simona , Zubani Roberto , Portolani Nazario , Bonardelli Stefano , Nodari Franco , Giulini Stefano Maria , Cancarini Giovanni
Published: September 2006

Abstract:  The aim of this retrospective study was to assess the impact of steroid therapy on cardiovascular disease (CVD) and patient mortality, in 486 on‐CsA renal transplant recipients, with a follow‐up of 9.5 ± 4.3 yr. Two hundred and one patients had their steroids permanently withdrawn at sixth month after transplantation (G1); 285 patients did not (G2) as they were unable (acute rejection after suspension) or unsuitable (because of clinical criteria or immunosuppressive protocols). The CVD considered were coronary artery disease diagnosed by angiography and myocardial infarction. G1 and G2 patients were well‐matched regarding CVD risk factors, except for age (G1: 44 ± 14 yr; G2: 40 ± 12 yr; p < 0.003), incidence of male (G1: 62%; G2: 72%, p < 0.02) incidence of acute rejection (G1: 39%; G2: 83%, p < 0.0001). Both CVD and deaths occurring during the first year of transplantation were excluded from the analysis. At 20 yr, the cumulative probability of developing a CVD, was 3.8% in G1; 23.8% in G2 (p < 0.0005). Patient survival rate was 95% in G1; 62% in G2 (p < 0.003). Mortality caused by CVD was higher in G2 (4.2% vs. 0.5%; p < 0.03). The Cox analysis identified in steroid therapy the main independent risk factors for both CVD (hazard ratio 9.56 p < 0.0001) and patient mortality (hazard ratio 5.99, p < 0.0001). At 10th and 15th year after transplantation, the mean‐daily dose of steroids was 4.2 mg.

In the long‐term, steroid therapy, even in low‐doses, increases significantly both the rate of CVD and patient mortality. This retrospective study suggests that steroid‐free regime should always be recommended for the prevention of post‐transplant CVD. This relevant statement should be followed by a long‐term prospective study.