bluuebunny/crossref_metadata_2025 huggingface dataset:
X-ray photoelectron spectroscopy study of ZrO2∕TiO2∕Si stack
Authors: Zhu L. Q. , Zhang L. D. , Fang Q.
Published: October 2007

A ZrO2∕TiO2∕Si gate stack has been prepared by using solid phase reaction between sputtered ZrO2∕Ti stack and underlying SiO2∕Si substrate through in situ vacuum annealing. X-ray photoelectron spectroscopy was used to analyze interfacial properties of the ZrO2∕TiO2∕Si stack after annealing at high temperatures. The interfacial silicate is composed of Ti silicate and ZrO2 layer does not take part in the interfacial reaction to form Zr silicate. Such a stack has the advantage of combining high dielectric constant of ZrO2 and excellent interfacial property of Ti silicate/Si interface, and will have potential applications in the advanced metal-oxide-semiconductor devices.
Metal-oxide-semiconductor capacitors on GaAs with germanium nitride passivation layer
Authors: Zhao Han , Kim Hyoung-Sub , Zhu Feng , Zhang Manhong , OK Injo , Park Sung Il , Yum Jung Hwan , Lee Jack C.
Published: October 2007

We present gallium arsenide (GaAs) metal-oxide-semiconductor capacitors (MOSCAPs) with a thin HfO2 gate dielectric and a thin germanium nitride (GexNy) interfacial passivation layer (IPL). TaN∕HfO2∕GexNy∕GaAs MOSCAPs show a low interface state density and a thin equivalent oxide thickness (1.6nm). Compared to GaAs MOSCAPs with germanium (Ge) IPL, the GexNy IPL has a smaller slow trap density, which is confirmed by improved C-V characteristics without humps near the flatband voltage. The lower rate of flatband voltage shift and gate leakage decreasing under constant gate voltage stress were also demonstrated in GaAs MOSCAPs with GexNy IPL than the Ge IPL.
Conduction mechanism and dielectric relaxation in high dielectric KxTiyNi1−x−yO
Authors: Jana Pradip Kumar , Sarkar Sudipta , Karmakar Shilpi , Chaudhuri B. K.
Published: October 2007

Complex impedance spectroscopic study has been made to elucidate the conductivity mechanism and dielectric relaxations in a low loss giant dielectric (ε′∼104) KxTiyNi1−x−yO (KTNO) system with x=0.05–0.30 and y=0.02 over a wide temperature range (200–400K). Below ambient temperature (300K), dc conductivity follows variable range hopping mechanism. The estimated activation energy for dielectric relaxation is found to be higher than the corresponding polaron hopping energy, which is attributed to the combined effect of K-doped grains and highly disordered grain boundary (GB) contributions in KTNO. Observed sharp fall of ε′ below ∼270K is ascribed to the freezing of charge carriers. Comparatively lower value of relaxation time distribution parameter β of KTNO than that of the CaCu3Ti4O12 (CCTO) system reveals more disorder in KTNO. It is also found that KTNO is structurally more stable compared to the CCTO system, both having giant ε′ value.
Spectral function and responsivity of resonant tunneling and superlattice quantum dot infrared photodetectors using Green’s function
Authors: Naser M. A. , Deen M. J. , Thompson D. A.
Published: October 2007

Theoretical modeling of resonant tunneling (RT) and superlattice (SL) quantum dot infrared photodetectors (QDIPs) using Green’s function is reported. The RT QDIP gives very low dark current which improves the detectivity of the device and allows for high temperature operation. The SL QDIP gives high responsivity and is suitable for low-level signal detection. The theoretical model is based on Green’s function method which is used to calculate the spectral function and the density of states of the two detectors. The kinetic equation that governs Green’s functions is solved numerically using the method of finite differences. From the information obtained from the density of states, the possible energy transitions are obtained. The bound states are calculated by solving the eigenvalue problem using the method of finite differences, while the continuum states localized in the quantum dot region are calculated using Green’s functions. Using the first order dipole approximation and Fermi golden rule, the eigenstates are used to calculate the responsivity of the detectors which is compared with available experimental results. The theoretical model is then used for studying the effect of changing the quantum dot height-to-diameter ratio on the normal incidence responsivity of the SL structure.
Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement
Authors: Arnold Axel , Bozorgui Behnaz , Frenkel Daan , Ha Bae-Yeun , Jun Suckjoon
Published: October 2007

We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation time of the chain, τ, with the chain length N and pore diameter D. An earlier scaling analysis based on the de Gennes blob picture led to τ∼N2D1∕3. Our numerical effort that combines molecular dynamics and Monte Carlo simulations, however, consistently produces different τ results for N up to 2000. We argue that the previous scaling prediction is only asymptotically valid in the limit N⪢D5∕3⪢1, which is currently inaccessible to computer simulations and, more interestingly, is also difficult to reach in experiments. Our results are thus relevant for the interpretation of recent experiments with DNA in nano- and microchannels.
Nonlinear capacitance variations in amorphous oxide metal-insulator-metal structures
Authors: Blonkowski S.
Published: October 2007

An analytical model for the electric field and temperature dependence of the nonlinear dielectric susceptibility of amorphous oxides is developed and compared with experimental measurements on metal-insulator-metal capacitors. Using the model, experimental capacitance variations with applied field, as well as temperature, are tied to an increase in system entropy due to thermal expansion of the lattice. In addition, our model explains the CV-curve sign reversal (slope of the capacitance versus voltage curve) that is frequently seen for metal oxide versus SiO2 capacitors.
Magnetic nanowires as permanent magnet materials
Authors: Maurer T. , Ott F. , Chaboussant G. , Soumare Y. , Piquemal J.-Y. , Viau G.
Published: October 2007

We present the fabrication of metallic magnetic nanowires using a low temperature chemical process. We show that pressed powders and magnetically oriented samples exhibit a very high coercivity (6.5kOe at 140K and 4.8kOe at 300K). We discuss the magnetic properties of these metamaterials and show that they have the suitable properties to realize “high temperature magnets” competitive with AlNiCo or SmCo permanent magnets. They could also be used as recording media for high density magnetic recording.
Lattice dynamical, dielectric, and thermodynamic properties of β-Ga2O3 from first principles
Authors: Liu Bo , Gu Mu , Liu Xiaolin
Published: October 2007

Lattice dynamical, dielectric, and thermodynamic properties of β-Ga2O3 are investigated by first principles. The calculated phonon frequencies for the Raman-active and the infrared-active modes are assigned. The phonon dispersion curves along high symmetry lines in the Brillouin zone and the phonon density of states are also calculated. The electronic and static dielectric tensors are calculated. The calculated static dielectric constants are much larger than the electronic constants, showing the rather strong ionic contributions to static dielectric constants. These calculated results are in a good agreement with available experimental values. The thermodynamic functions are calculated by using the phonon density of states.
Solid phase epitaxy in uniaxially stressed (001) Si
Authors: Rudawski N. G. , Jones K. S. , Gwilliam R.
Published: October 2007

The effect of [110] uniaxial stresses up to 1.5GPa on defect nucleation during solid phase epitaxy of amorphous (001) Si created via ion implantation was examined. The solid phase epitaxial regrowth velocity was slowed in compression. However, in tension, the velocity was unaffected. Both compression and tension resulted in an increase in regrowth defects compared to the stress-free case. The defects in compression appear to arise from roughening of the crystallizing interface whereas in tension it is proposed that reorientation of crystallites near the initial amorphous/crystalline interface is responsible for defect formation.
Evidence of short-range magnetic ordering above TC in the double perovskite La2NiMnO6
Authors: Zhou Shiming , Shi Lei , Yang Haipeng , Zhao Jiyin
Published: October 2007

The magnetic properties of the double perovskite La2NiMnO6 polycrystalline sample have been investigated by magnetometry and electron spin resonance. The magnetization curve shows a paramagnetic-ferromagnetic transition at TC∼280K. However, the electron spin resonance spectra reveal that a pure paramagnetic regime only exists above T*∼390K in which the behaviors of the spectra can be well described by the small polaron hopping model. Between TC and T*, a short-range magnetic ordering appears which maybe derives from the correlation of those magnetic polarons. The possible relationship between those polarons and the observed multifunctions in La2NiMnO6 is briefly discussed.
Reducing dark-cutting in pasture-fed beef steers by high-energy supplementation
Authors: Knee B. W. , Cummins L. J. , Walker P. J. , Kearney G. A. , Warner R. D.
Published: October 2007

Dark-cutting in muscles of the beef carcass is due to low muscle glycogen levels at slaughter and occurs particularly in autumn and winter in grass-fed cattle in southern Australia. The aim of these experiments was to investigate the effect of supplementary feeding of cattle grazing pasture during winter on muscle glycogen levels. The first experiment involved 70 cattle allocated to two stocking rates grazing improved perennial ryegrass and subterranean clover pastures [high stocking rate (HSR) v. low stocking rate (LSR)] by two pasture feeding regimes (control, pasture only v. pasture supplemented with a high-energy ration for 4 weeks) plus a feedlot treatment (fed high-energy ration in pens with no pasture for 11 weeks). Muscle biopsies were collected from the M. semitendinosus (ST) and M. semimembranosus (SM) muscles and analysed for muscle glycogen. The ST muscle glycogen content for supplemented animals increased (P < 0.05) over the feeding period but there was no effect (P > 0.05) of supplementation on the muscle glycogen content of the SM or on the muscle glycogen content of the ST or SM of cattle in the feedlot treatment, relative to control cattle. HSR cattle tended to have lower muscle glycogen in the ST compared to LSR cattle across both feeding regimes. The second experiment used 60 cattle allocated to two treatments (control, pasture only v. pasture supplemented with a high-energy ration for 3 weeks). The treatments were applied to cattle grazing improved perennial ryegrass and subterranean clover pastures and muscle biopsies were collected weekly from the SM and ST. Supplementation resulted in a linear increase (P < 0.05) in muscle glycogen levels over the 3 weeks in both the SM and ST muscles. These results indicate that feed quality has a major impact on muscle glycogen levels in the SM and ST of cattle destined for slaughter. At times of the year when pasture quality is poor or quantity is lacking, supplementation with a high-energy supplement has the potential to dramatically increase muscle glycogen and reduce the incidence of dark-cutting beef.
Determining the agronomic value of composts produced from garden organics from metropolitan areas of New South Wales, Australia
Authors: Chan K. Y. , Dorahy C. , Tyler S.
Published: October 2007

About 0.3 million t/year of composted garden organics (CGO) including mulches and soil conditioners are produced annually in New South Wales, Australia, although only a small proportion of this material (<4%) is used in agriculture. A lack of information on product characteristics and agronomic performance has limited the development of agricultural markets for CGO products. These CGO products are the coarse and fine fractions separated by screening after composting. This paper presents the results of a survey of CGO mulches and soil conditioners (unblended or blended with a mixture of other organic materials including biosolids, animal manures and paper), which are commercially produced in the metropolitan areas of New South Wales and assesses their agronomic and soil amendment values in terms of chemical and biological properties. It also evaluates the short-term effects of applying increasing rates (0, 25, 50 and 100 t/ha) of selected composted soil conditioners on radish growth in a pot experiment. The mulch products had low nutrient concentrations but had high carbon (C) contents (mean C = 45%) and C/Nitrogen (N) ratios (mean C/N = 72) and are most suitable for use as surface mulch. The unblended soil conditioners were low in nutrients, particularly N (average total N = 1.0%, range 0.9–12%), and had lower and variable C contents. The pot trial results indicated lack of growth response of radish at application rates up to 100 t/ha of unblended soil conditioners from garden organics. The blended soil conditioners were more variable in quality and as confirmed by pot trial results produced highly variable plant responses. The high variability in product quality and performance of the soil conditioners, particularly the blended products might be related to the source and type of blending material as well as the composting conditions used in the manufacturing process. These results highlight the need to improve compost quality and consistency and the need for further research to advance understanding of the benefits using CGO in terms of improving soil quality, crop productivity and net economic returns to growers.
Alternative replenishment regimens to maintain diazinon concentration during shower, plunge and immersion cage dipping of Merino sheep
Authors: Levot G. W. , Lund R. D.
Published: October 2007

Constant replenishment of a 1000-L Buzzacott shower dip sump with diazinon solution at concentrations 100, 200, 300 or 500 mg/L failed to maintain the initial charge rate of 100 mg/L when short-wool Merino sheep were showered for 12 min. According to these regimens, by the completion of dipping the third pen of sheep working concentrations had dropped to 11, 29, 35 and 51 mg/L for sheep treated with replenishment solutions of 100, 200, 300 and 500 mg/L, respectively. These results suggest that the working concentration of diazinon sheep dips may be increased and maintained by raising the concentration of the replenishment solution. On average, wool samples taken from these sheep immediately after dipping contained 207, 453, 473 and 730 mg/kg, respectively. Comparison of dip concentration and wool residues indicated a linear relationship. This suggests that the capacity for Merino wool to absorb diazinon had not yet reached saturation. Compounding the difficulties with the reliability of constant replenishment shower dipping, current label directions for reinforcement and topping-up of diazinon sheep dips are unclear and often misinterpreted. A simpler and far more reliable strategy that ensured that each pen of sheep was treated similarly was tested. In this scheme, sufficient fresh dip wash (540 mg/L) from the replenishment tank was transferred to the dip sump to restore the initial sump volume after showering of each pen of sheep. This scheme reliably restored the sump concentration to the current nominal initial charge rate (100 mg/L) and was by far the easiest and most practical replenishment scheme tested. This should be the preferred strategy for shower dipping. Working concentrations of diazinon in a 5000-L mobile plunge dip charged at 100 mg/L and constantly replenished with 200 mg/L solution were maintained close to the nominal application rate of 100 mg/L. Current product label directions for reinforcement and topping-up of plunge dips were shown to be suitable for immersion cage dips operated according to these principles.
Concentrates based on sorghum grain provide a basis for a finishing system for crossbred lambs
Authors: Bowen M. K. , Pepper P. M. , Winkleman J. , McConnel I.
Published: October 2007

In parts of Australia, sorghum grain is a cheaper alternative to other cereal grains but its use and nutritive value in sheep feeding systems is not well understood. The aim of this work was to compare growth and carcass characteristics for crossbred lambs consuming several simple, sorghum-based diets. The treatments were: (1) whole sorghum grain, (2) whole sorghum grain + urea and ammonium sulfate, (3) cracked sorghum grain + urea and ammonium sulfate, (4) expanded sorghum grain + urea and ammonium sulfate, (5) whole sorghum grain + cottonseed meal, and (6) whole sorghum grain + whole cottonseed. Nine lambs were slaughtered initially to provide baseline carcass data and the remaining 339 lambs were gradually introduced to the concentrate diets over 14 days before being fed concentrates and wheaten hay ad libitum for 41, 56 or 76 days.
Neither cracking nor expanding whole sorghum grain with added non-protein nitrogen (N) resulted in significantly (P > 0.05) increased final liveweight, growth rates or carcass weights for lambs, or in decreased days on feed to reach 18-kg carcass weight, although carcass fat depth was significantly (P < 0.05) increased compared with the whole sorghum plus non-protein N diet. However, expanding sorghum grain significantly (P < 0.05) reduced faecal starch concentrations compared with whole or cracked sorghum diets with added non-protein N (79 v. 189 g/kg DM after 59 days on feed). Lambs fed whole sorghum grain without an additional N source had significantly (P < 0.05) lower concentrate intake and required significantly (P < 0.05) more days on feed to reach a carcass weight of 18 kg than for all diets containing added N. These lambs also had significantly (P < 0.05) lower carcass weight and fat depth than for lambs consuming whole sorghum plus true protein diets. Substituting sources of true protein (cottonseed meal and whole cottonseed) for non-protein N (urea and ammonium sulfate) did not significantly (P > 0.05) affect concentrate intakes or carcass weights of lambs although carcass fat depth was significantly (P < 0.05) increased and the days to reach 18-kg carcass weight were significantly (P < 0.05) decreased for the whole sorghum plus cottonseed meal diet.
In conclusion, processing sorghum grain by cracking or expanding did not significantly improve lamb performance. While providing an additional N source with sorghum grain significantly increased lamb performance, there was no benefit in final carcass weight of lambs from substituting sources of true protein for non-protein N.
Subsoil constraints to crop production on neutral and alkaline soils in south-eastern Australia: a review of current knowledge and management strategies
Authors: Adcock D. , McNeill A. M. , McDonald G. K. , Armstrong R. D.
Published: October 2007

Crop yield variability and productivity below potential yield on neutral and alkaline soils in the semiarid Mediterranean-type environments of south-eastern Australia have been attributed, in part, to variable rooting depth and incomplete soil water extraction caused by physical and chemical characteristics of soil horizons below the surface. In this review these characteristics are referred to as subsoil constraints. This document reviews current information concerning subsoil constraints typical of neutral and alkaline soils in south-eastern Australia, principally salinity, sodicity, dense soils with high penetration resistance, waterlogging, nutrient deficiencies and ion toxicities. The review focuses on information from Australia (published and unpublished), using overseas data only where no suitable Australian data is available. An assessment of the effectiveness of current management options to address subsoil constraints is provided. These options are broadly grouped into three categories: (i) amelioration strategies, such as deep ripping, gypsum application or the use of polyacrylamides to reduce sodicity and/or bulk density, deep placement of nutrients or organic matter to overcome subsoil nutrient deficiencies or the growing of ‘primer’ crops to naturally ameliorate the soil; (ii) breeding initiatives for increased crop tolerance to toxicities such as salt and boron; and (iii) avoidance through appropriate agronomic or agro-engineering solutions. The review highlights difficulties associated with identifying the impact of any single subsoil constraint to crop production on neutral and alkaline soils in south-eastern Australia, given that multiple constraints may be present. Difficulty in clearly ranking the relative effect of particular subsoil constraints on crop production (either between constraints or in relation to other edaphic and biological factors) limits current ability to develop targeted solutions designed to overcome these constraints. Furthermore, it is recognised that the task is complicated by spatial and temporal variability of soil physicochemical properties and nutrient availability, as well as other factors such as disease and drought stress. Nevertheless, knowledge of the relative importance of particular subsoil constraints to crop production, and an assessment of impact on crop productivity, are deemed critical to the development of potential management solutions for these neutral to alkaline soils.
Response of beef calves to different levels of postweaning ingestion of gastrointestinal parasite larvae
Authors: Burggraaf V. T. , Brooky A. R. , Boom C. J.
Published: October 2007

The postweaning response of beef calves to different levels of gastrointestinal parasite larvae (L3) ingestion was investigated. Newly weaned calves (n = 77, 6 months old) were trickle-dosed with 0, 1000, 2000, 4000, 7000 or 10 000 L3 (75% Cooperia oncophora, 10% Ostertagia ostertagi, 15% Trichostrongylus axei) per day for 10 weeks or drenched with anthelmintic at 3-weekly intervals. Liveweight, faecal egg count and blood serum pepsinogen were monitored regularly. Three calves per treatment were slaughtered following infection to determine adult worm burdens. For the following 11 weeks, liveweight, faecal egg count and serum pepsinogen were monitored for the remaining calves. During the dosing period, calves that were drenched had similar liveweight gain to those receiving up to 2000 parasites per day but grew 0.13–0.20 kg per day more than calves receiving between 4000 and 10 000 L3 per day. Faecal egg counts did not reflect liveweight gains or dose rate for calves receiving more than 2000 L3 per day and pepsinogen concentration did not reflect liveweight performance. Abomasal worm burdens at the end of dosing were highest in treatments receiving 4000 or more L3 per day but intestinal (Cooperia species) burdens were highest in those receiving low infection rates. Liveweight gain during the carryover period for the 4000 L3 treatment was significantly lower than in other treatments. Calves receiving anthelmintic showed a 14–40 kg liveweight advantage by the end of the experiment. This study indicates that to avoid production losses from parasites in beef calves in the absence of anthelmintic the ingestion of parasite larvae should be below 4000 per day.
Elevated level of SUMOylated IRF-1 in tumor cells interferes with IRF-1-mediated apoptosis
Authors: Park Junsoo , Kim Kwangsoo , Lee Eun-Ju , Seo Yun-Jee , Lim Si-Nae , Park Kyoungsook , Rho Seung Bae , Lee Seung-Hoon , Lee Je-Ho
Published: October 2007

SUMOylation of transcription factors often attenuates transcription activity. This regulation of protein activity allows more diversity in the control of gene expression. Interferon regulatory factor-1 (IRF-1) was originally identified as a regulator of IFN-α/β, and its expression is induced by viral infection or IFN stimulation. Accumulating evidence supports the theory that IRF-1 functions as a tumor suppressor and represses the transformed phenotype. Here we report that the level of SUMOylated IRF-1 is elevated in tumors. Site-directed mutagenesis experiments disclose that the SUMOylation sites of IRF-1 are identical to the major ubiquitination sites. Consequently, SUMOylated IRF-1 displays enhanced resistance to degradation. SUMOylation of IRF-1 attenuates its transcription activity, and SUMOylated IRF-1 inhibits apoptosis by repression of its transcriptional activity. These data support a mechanism whereby SUMOylation of IRF-1 inactivates its tumor suppressor function, which facilitates resistance to the immune response.
Poverty reduction in Africa
Authors: Collier Paul
Published: October 2007

Poverty in Africa has been rising for the last quarter-century, while it has been falling in the rest of the developing world. Africa's distinctive problem is that its economies have not been growing. This article attempts to synthesize a range of recent research to account for this failure of the growth process. I argue that the reasons lie not in African peculiarities but rather in geographic features that globally cause problems but that are disproportionately pronounced in Africa. These features interact to create three distinct challenges that are likely to require international interventions beyond the conventional reliance on aid.
The African Millennium Villages
Authors: Sanchez Pedro , Palm Cheryl , Sachs Jeffrey , Denning Glenn , Flor Rafael , Harawa Rebbie , Jama Bashir , Kiflemariam Tsegazeab , Konecky Bronwen , Kozar Raffaela , Lelerai Eliud , Malik Alia , Modi Vijay , Mutuo Patrick , Niang Amadou , Okoth Herine , Place Frank , Sachs Sonia Ehrlich , Said Amir , Siriri David , Teklehaimanot Awash , Wang Karen , Wangila Justine , Zamba Colleen
Published: October 2007

We describe the concept, strategy, and initial results of the Millennium Villages Project and implications regarding sustainability and scalability. Our underlying hypothesis is that the interacting crises of agriculture, health, and infrastructure in rural Africa can be overcome through targeted public-sector investments to raise rural productivity and, thereby, to increased private-sector saving and investments. This is carried out by empowering impoverished communities with science-based interventions. Seventy-eight Millennium Villages have been initiated in 12 sites in 10 African countries, each representing a major agroecological zone. In early results, the research villages in Kenya, Ethiopia, and Malawi have reduced malaria prevalence, met caloric requirements, generated crop surpluses, enabled school feeding programs, and provided cash earnings for farm families.
Governance and poverty reduction in Africa
Authors: Hyden Goran
Published: October 2007

A careful review of the literature in political science and neighboring social science disciplines shows that prevailing assumptions in the international development policy community about improved governance as a principal mechanism to reduce poverty in Africa rests more on faith than science. Conventional policy models for tackling poverty fail to take into account the peculiar socioeconomic and political conditions in Africa, where the vast majority of those living on one dollar a day or less are only marginally captured by market and state institutions and instead rely on solving their problems “outside the system.” Poverty reduction through formal institutions therefore becomes ineffective. Although political science and other neighboring social science disciplines offer insights into these peculiarities, these contributions have been largely ignored to date. One reason is that economists continue to dominate the international development policy agenda. Another is that political scientists have typically looked at how economic variables shape political ones, rather than the other way around, as implied in the current governance agenda. Governance remains an undertheorized area of research held back by two chasms, one between economists and other social scientists and another between the scientific and the policy communities, to the detriment of gaining a better understanding of how it may help reduce poverty in Africa.
Nitric oxide regulates matrix metalloproteinase-9 activity by guanylyl-cyclase-dependent and -independent pathways
Authors: Ridnour Lisa A. , Windhausen Alisha N. , Isenberg Jeffrey S. , Yeung Nolan , Thomas Douglas D. , Vitek Michael P. , Roberts David D. , Wink David A.
Published: October 2007

Matrix metalloproteinases (MMPs) are of central importance in the proteolytic remodeling of matrix and the generation of biologically active molecules. MMPs are distinguished by a conserved catalytic domain containing a zinc ion, as well as a prodomain that regulates enzyme activation by modulation of a cysteine residue within that domain. Because nitric oxide (NO) and derived reactive nitrogen species target zinc ions and cysteine thiols, we assessed the ability of NO to regulate MMPs. A dose-dependent, biphasic regulatory effect of NO on the activity of MMPs (MMP-9, -1, and -13) secreted from murine macrophages was observed. Low exogenous NO perturbed MMP/tissue inhibitor of metalloproteinase (TIMP)-1 levels by enhancing MMP activity and suppressing the endogenous inhibitor TIMP-1. This was cGMP-dependent, as confirmed by the cGMP analog 8-bromo-cGMP, as well as by the NO–soluble guanylyl cyclase–cGMP signaling inhibitor thrombospondin-1. Exposure of purified latent MMP-9 to exogenous NO demonstrated a concentration-dependent activation and inactivation of the enzyme, which occurred at higher NO flux. These chemical reactions occurred at concentrations similar to that of activated macrophages. Importantly, these results suggest that NO regulation of MMP-9 secreted from macrophages may occur chemically by reactive nitrogen species-mediated protein modification, biologically through soluble guanylyl-cyclase-dependent modulation of the MMP-9/TIMP-1 balance, or proteolytically through regulation of MMP-1 and -13, which can cleave the prodomain of MMP-9. Furthermore, when applied in a wound model, conditioned media exhibiting peak MMP activity increased vascular cell migration that was MMP-9-dependent, suggesting that MMP-9 is a key physiologic mediator of the effects of NO in this model.
Absolute poverty measures for the developing world, 1981–2004
Authors: Chen Shaohua , Ravallion Martin
Published: October 2007

We report new estimates of measures of absolute poverty for the developing world for the period 1981–2004. A clear trend decline in the percentage of people who are absolutely poor is evident, although with uneven progress across regions. We find more mixed success in reducing the total number of poor. Indeed, the developing world outside China has seen little or no sustained progress in reducing the number of poor, with rising poverty counts in some regions, notably sub-Saharan Africa. There are encouraging signs of progress in all regions after 2000, although it is too early to say whether this is a new trend. We also summarize results from estimating a new series incorporating an allowance for the higher cost of living facing poor people in urban areas. This reveals a marked urbanization of poverty in the developing world, which is stronger in some regions than others, although it remains that three-quarters of the poor live in rural areas.
Linking folding with aggregation in Alzheimer's β-amyloid peptides
Authors: Khandogin Jana , Brooks Charles L.
Published: October 2007

Growing evidence suggests that the β-amyloid (Aβ) peptides of Alzheimer's disease are generated in early endosomes and that small oligomers are the principal toxic species. We sought to understand whether and how the solution pH, which is more acidic in endosomes than the extracellular environment, affects the conformational processes of Aβ. Using constant pH molecular dynamics simulations of two model peptides, Aβ(1–28) and Aβ(10–42), we found that the folding landscape of Aβ is strongly modulated by pH and is most favorable for hydrophobically driven aggregation at pH 6. Thus, our theoretical findings substantiate the possibility that Aβ oligomers develop intracellularly before secretion into the extracellular milieu, where they may disrupt synaptic activity or act as seeds for plaque formation.
Isolates of Zaire ebolavirus from wild apes reveal genetic lineage and recombinants
Authors: Wittmann Tatiana J. , Biek Roman , Hassanin Alexandre , Rouquet Pierre , Reed Patricia , Yaba Philippe , Pourrut Xavier , Real Leslie A. , Gonzalez Jean-Paul , Leroy Eric M.
Published: October 2007

Over the last 30 years, Zaire ebolavirus (ZEBOV), a virus highly pathogenic for humans and wild apes, has emerged repeatedly in Central Africa. Thus far, only a few virus isolates have been characterized genetically, all belonging to a single genetic lineage and originating exclusively from infected human patients. Here, we describe the first ZEBOV sequences isolated from great ape carcasses in the Gabon/Congo region that belong to a previously unrecognized genetic lineage. According to our estimates, this lineage, which we also encountered in the two most recent human outbreaks in the Republic of the Congo in 2003 and 2005, diverged from the previously known viruses around the time of the first documented human outbreak in 1976. These results suggest that virus spillover from the reservoir has occurred more than once, as predicted by the multiple emergence hypothesis. However, the young age of both ZEBOV lineages and the spatial and temporal sequence of outbreaks remain at odds with the idea that the virus simply emerged from a long-established and widespread reservoir population. Based on data from two ZEBOV genes, we also demonstrate, within the family
Filoviridae
, recombination between the two lineages. According to our estimates, this event took place between 1996 and 2001 and gave rise to a group of recombinant viruses that were responsible for a series of outbreaks in 2001–2003. The potential for recombination adds an additional level of complexity to unraveling and potentially controlling the emergence of ZEBOV in humans and wildlife species.
Drought mediates the importance of stochastic community assembly
Authors: Chase Jonathan M.
Published: October 2007

Historically, the biodiversity and composition of species in a locality was thought to be influenced primarily by deterministic factors. In such cases, species' niches create differential responses to environmental conditions and interspecific interactions, which combine to determine that locality's biodiversity and species composition. More recently, proponents of the neutral theory have placed a premium on how stochastic factors, such as birth, death, colonization, and extinction (termed “ecological drift”) influence diversity and species composition in a locality independent of their niches. Here, I develop the hypothesis that the relative importance of stochastic ecological drift and/or priority effects depend on the harshness of the ecological filter in those habitats. I established long-term experimental ponds to explore the relative importance of community assembly history and drought on patterns of community compositional similarity among ponds that were otherwise similar in their environmental conditions. I show considerable site-to-site variation in pond community composition in the absence of drought that likely resulted from a combination of stochastic ecological drift and priority effects. However, in ponds that experienced drought, I found much higher similarity among communities that likely resulted from niche-selection filtering out species from the regional pool that could not tolerate such environmental harshness. These results implicate the critical role for understanding the processes of community assembly when examining patterns of biodiversity at different spatial scales.
Enantioselective hydrogenation of α-aminomethylacrylates containing a free NH group for the synthesis of β-amino acid derivatives
Authors: Qiu Liqin , Prashad Mahavir , Hu Bin , Prasad Kapa , Repič Oljan , Blacklock Thomas J. , Kwong Fuk Yee , Kok Stanton H. L. , Lee Hang Wai , Chan Albert S. C.
Published: October 2007

We describe highly enantioselective synthesis of β-amino acid derivatives (1a-c) using asymmetric hydrogenation of α-aminomethylacrylates (2a-c), which contain a free basic N

H group, as the key step. The α-aminomethylacrylates (2a-c) were prepared using the Baylis–Hillman reaction of an appropriate aldehyde with methyl acrylate followed by acetylation of the resulting allylic alcohols (4a-b) and S
N
2′-type amination of the allylic acetates (3a-b).
Tackling the African “poverty trap”: The Ijebu-Ode experiment
Authors: Mabogunje Akin L.
Published: October 2007

An experiment in poverty reduction began in 1998 in the city of Ijebu-Ode, Nigeria (estimated 1999 population 163,000), where, without the remittances from relatives abroad, an estimated 90% of the population lived below the poverty line of $1.00 (U.S.) per person per day. Central to the experiment was whether poverty can be dramatically reduced through a city consultation process that seeks to mobilize the entire community along with its diaspora. With 7 years of experience, the Ijebu-Ode experiment has been successful in many ways. There is increasing evidence that poverty in the city has been reduced significantly through the microfinancing of existing and new productive activities and the estimated >8,000 jobs these activities have created. Training based on both sustainability science and technology and indigenous practitioner knowledge has been a critical factor in the establishment of cooperatives and the development of new enterprises in specialty crops, small animal, and fish production. Much of this success has been possible as a result of harnessing social capital, especially through the dynamic leadership of the traditional authorities of the city and by the provision of ample loanable funds through the National Poverty Eradication Program of the federal government. The city consultation process itself engendered a participatory focus to the experiment from the beginning and has encouraged sustainabaility. Yet long-term sustainability is still in question as the initial leadership needs replacement, and credit, the heart of the experiment, lacks sufficient collateral.
Molecular imaging of membrane interfaces reveals mode of β-glucosidase activation by saposin C
Authors: Alattia Jean-René , Shaw James E. , Yip Christopher M. , Privé Gilbert G.
Published: October 2007

Acid β-glucosidase (GCase) is a soluble lysosomal enzyme responsible for the hydrolysis of glucose from glucosylceramide and requires activation by the small nonenzymatic protein saposin C (sapC) to gain access to the membrane-embedded glycosphingolipid substrate. We have used
in situ
atomic force microscopy (AFM) with simultaneous confocal and epifluorescence microscopies to investigate the interactions of GCase and sapC with lipid bilayers. GCase binds to sites on membranes transformed by sapC, and enzyme activity occurs at loci containing both GCase and sapC. Using FRET, we establish the presence of GCase/sapC and GCase/product contacts in the bilayer. These data support a mechanism in which sapC locally alters regions of bilayer for subsequent attack by the enzyme in stably bound protein complexes.
A unique Extradenticle recruitment mode in the
Drosophila
Hox protein Ultrabithorax
Authors: Merabet Samir , Saadaoui Mehdi , Sambrani Nagraj , Hudry Bruno , Pradel Jacques , Affolter Markus , Graba Yacine
Published: October 2007

Hox transcription factors are essential for shaping body morphology in development and evolution. The control of Hox protein activity in part arises from interaction with the PBC class of partners, pre-B cell transcription factor (Pbx) proteins in vertebrates and Extradenticle (Exd) in
Drosophila
. Characterized interactions occur through a single mode, involving a short hexapeptide motif in the Hox protein. This apparent uniqueness in Hox–PBC interaction provides little mechanistic insight in how the same cofactors endow Hox proteins with specific and diverse activities. Here, we identify in the
Drosophila
Ultrabithorax (Ubx) protein a short motif responsible for an alternative mode of Exd recruitment. Together with previous reports, this finding highlights that the Hox protein Ubx has multiple ways to interact with the Exd cofactor and suggests that flexibility in Hox–PBC contacts contributes to specify and diversify Hox protein function.
The cation efflux transporter ZnT8 (Slc30A8) is a major autoantigen in human type 1 diabetes
Authors: Wenzlau Janet M. , Juhl Kirstine , Yu Liping , Moua Ong , Sarkar Suparna A. , Gottlieb Peter , Rewers Marian , Eisenbarth George S. , Jensen Jan , Davidson Howard W. , Hutton John C.
Published: October 2007

Type 1 diabetes (T1D) results from progressive loss of pancreatic islet mass through autoimmunity targeted at a diverse, yet limited, series of molecules that are expressed in the pancreatic β cell. Identification of these molecular targets provides insight into the pathogenic process, diagnostic assays, and potential therapeutic agents. Autoantigen candidates were identified from microarray expression profiling of human and rodent pancreas and islet cells and screened with radioimmunoprecipitation assays using new-onset T1D and prediabetic sera. A high-ranking candidate, the zinc transporter ZnT8 (Slc30A8), was targeted by autoantibodies in 60–80% of new-onset T1D compared with <2% of controls and <3% type 2 diabetic and in up to 30% of patients with other autoimmune disorders with a T1D association. ZnT8 antibodies (ZnTA) were found in 26% of T1D subjects classified as autoantibody-negative on the basis of existing markers [glutamate decarboxylase (GADA), protein tyrosine phosphatase IA2 (IA2A), antibodies to insulin (IAA), and islet cytoplasmic autoantibodies (ICA)]. Individuals followed from birth to T1D showed ZnT8A as early as 2 years of age and increasing levels and prevalence persisting to disease onset. ZnT8A generally emerged later than GADA and IAA in prediabetes, although not in a strict order. The combined measurement of ZnT8A, GADA, IA2A, and IAA raised autoimmunity detection rates to 98% at disease onset, a level that approaches that needed to detect prediabetes in a general pediatric population. The combination of bioinformatics and molecular engineering used here will potentially generate other diabetes autoimmunity markers and is also broadly applicable to other autoimmune disorders.
Copper-free click chemistry for dynamic
in vivo
imaging
Authors: Baskin Jeremy M. , Prescher Jennifer A. , Laughlin Scott T. , Agard Nicholas J. , Chang Pamela V. , Miller Isaac A. , Lo Anderson , Codelli Julian A. , Bertozzi Carolyn R.
Published: October 2007

Dynamic imaging of proteins in live cells is routinely performed by using genetically encoded reporters, an approach that cannot be extended to other classes of biomolecules such as glycans and lipids. Here, we report a Cu-free variant of click chemistry that can label these biomolecules rapidly and selectively in living systems, overcoming the intrinsic toxicity of the canonical Cu-catalyzed reaction. The critical reagent, a substituted cyclooctyne, possesses ring strain and electron-withdrawing fluorine substituents that together promote the [3 + 2] dipolar cycloaddition with azides installed metabolically into biomolecules. This Cu-free click reaction possesses comparable kinetics to the Cu-catalyzed reaction and proceeds within minutes on live cells with no apparent toxicity. With this technique, we studied the dynamics of glycan trafficking and identified a population of sialoglycoconjugates with unexpectedly rapid internalization kinetics.
Distinctive patterns of microRNA expression in primary muscular disorders
Authors: Eisenberg Iris , Eran Alal , Nishino Ichizo , Moggio Maurizio , Lamperti Costanza , Amato Anthony A. , Lidov Hart G. , Kang Peter B. , North Kathryn N. , Mitrani-Rosenbaum Stella , Flanigan Kevin M. , Neely Lori A. , Whitney Duncan , Beggs Alan H. , Kohane Isaac S. , Kunkel Louis M.
Published: October 2007

The primary muscle disorders are a diverse group of diseases caused by various defective structural proteins, abnormal signaling molecules, enzymes and proteins involved in posttranslational modifications, and other mechanisms. Although there is increasing clarification of the primary aberrant cellular processes responsible for these conditions, the decisive factors involved in the secondary pathogenic cascades are still mainly obscure. Given the emerging roles of microRNAs (miRNAs) in modulation of cellular phenotypes, we searched for miRNAs regulated during the degenerative process of muscle to gain insight into the specific regulation of genes that are disrupted in pathological muscle conditions. We describe 185 miRNAs that are up- or down-regulated in 10 major muscular disorders in humans [Duchenne muscular dystrophy (DMD), Becker muscular dystrophy, facioscapulohumeral muscular dystrophy, limb-girdle muscular dystrophies types 2A and 2B, Miyoshi myopathy, nemaline myopathy, polymyositis, dermatomyositis, and inclusion body myositis]. Although five miRNAs were found to be consistently regulated in almost all samples analyzed, pointing to possible involvement of a common regulatory mechanism, others were dysregulated only in one disease and not at all in the other disorders. Functional correlation between the predicted targets of these miRNAs and mRNA expression demonstrated tight posttranscriptional regulation at the mRNA level in DMD and Miyoshi myopathy. Together with direct mRNA–miRNA predicted interactions demonstrated in DMD, some of which are involved in known secondary response functions and others that are involved in muscle regeneration, these findings suggest an important role of miRNAs in specific physiological pathways underlying the disease pathology.
Structural basis for receptor specificity of influenza B virus hemagglutinin
Authors: Wang Qinghua , Tian Xia , Chen Xiaorui , Ma Jianpeng
Published: October 2007

Receptor-binding specificity of HA, the major surface glycoprotein of influenza virus, primarily determines the host ranges that the virus can infect. Influenza type B virus almost exclusively infects humans and contributes to the annual “flu” sickness. Here we report the structures of influenza B virus HA in complex with human and avian receptor analogs, respectively. These structures provide a structural basis for the different receptor-binding properties of influenza A and B virus HA molecules and for the ability of influenza B virus HA to distinguish human and avian receptors. The structure of influenza B virus HA with avian receptor analog also reveals how mutations in the region of residues 194 to 196, which are frequently observed in egg-adapted and naturally occurring variants, directly affect the receptor binding of the resultant virus strains. Furthermore, these structures of influenza B virus HA are compared with known structures of influenza A virus HAs, which suggests the role of the residue at 222 as a key and likely a universal determinant for the different binding modes of human receptor analogs by different HA molecules.