bluuebunny/crossref_metadata_2025 huggingface dataset:
Water‐vapor climate feedback inferred from climate fluctuations, 2003–2008
Authors: Dessler A. E. , Zhang Z. , Yang P.
Published: October 2008

Between 2003 and 2008, the global‐average surface temperature of the Earth varied by 0.6°C. We analyze here the response of tropospheric water vapor to these variations. Height‐resolved measurements of specific humidity (q) and relative humidity (RH) are obtained from NASA's satellite‐borne Atmospheric Infrared Sounder (AIRS). Over most of the troposphere, q increased with increasing global‐average surface temperature, although some regions showed the opposite response. RH increased in some regions and decreased in others, with the global average remaining nearly constant at most altitudes. The water‐vapor feedback implied by these observations is strongly positive, with an average magnitude of λq = 2.04 W/m2/K, similar to that simulated by climate models. The magnitude is similar to that obtained if the atmosphere maintained constant RH everywhere.
Downstream development and Kona low genesis
Authors: Moore R. W. , Martius O. , Davies H. C.
Published: October 2008

A composite analysis of 43 Kona lows in conjunction with a case study of a particularly damaging Kona low indicate that downstream development is dynamically important to the subtropical cyclogenesis. It takes the form of eastward propagating, statistically significant upstream potential vorticity (PV) anomalies with accompanying meridional wind anomalies at the tropopause level prior to the formation of a Kona low. The downstream development culminates in the formation of a PV streamer, a meridionally‐elongated stratospheric intrusion of high PV air into the troposphere, associated with a breaking wave on the dynamical tropopause. Subsequently, the streamer ‘cuts off’ from the stratospheric reservoir of high PV and translates equatorward, thereby providing a necessary dynamical forcing for the subtropical surface cyclogenesis.
DEMETER observations of an intense upgoing column of ELF/VLF radiation excited by the HAARP HF heater
Authors: Piddyachiy D. , Inan U. S. , Bell T. F. , Lehtinen N. G. , Parrot M.
Published: October 2008

DEMETER spacecraft observations of ELF signals generated by the recently upgraded High‐Frequency Active Auroral Research Program (HAARP) HF facility (3.6 MW) reveal three distinctive regions characterizing upgoing ELF waves. These regions are classified by signal intensity and the minimum lateral distance d between the magnetic footprint of the satellite at 75‐km altitude (D layer) and the point at 75‐km altitude immediately above HAARP where the source is located. The first large region within d ≃ 900 km contains waves which propagate in the Earth‐ionosphere waveguide and then leak upward to the spacecraft. The second region of d ≃ 200–300 km contains waves propagating to the spacecraft from the ionospheric source region without reflection from the ground. The third region contains waves of very high intensity (E ≃ 350 μV/m, B ≃ 20 pT) within a narrow cylindrical column of ∼10–20 km radius, also observed once before on the ISIS 1 spacecraft. The observed intense columnar radiation is consistent with predictions of a recent full‐wave model of ELF radiation from HF‐heater‐produced ionospheric source currents.
Reliability of dynamic cerebral autoregulation measurement using spontaneous fluctuations in blood pressure
Authors: Brodie Fiona G. , Atkins Emily R. , Robinson Thompson G. , Panerai Ronney B.
Published: October 2008

Spontaneous fluctuations in BP (blood pressure) and subsequent change in CBFV (cerebral blood flow velocity) in the MCA (middle cerebral artery) can be used to assess dynamic cerebral autoregulation using transfer function analysis; however, the reliability of this technique has not been assessed, in particular the contribution of intra-subject variability relative to inter-subject variability. Three bilateral CBFV, BP and RR interval recordings were performed in ten healthy volunteers on four separate occasions over a 2-week period. Data were analysed to provide the ARI (autoregulatory index), CBFV, RAP (resistance-area product) and CrCP (critical closing pressure). We also measured systolic and diastolic BP, and resting HR (heart rate). We calculated the SEM (standard error of measurement) and the ICC (intra-class correlation coefficient) and their 95% CIs (confidence intervals) for each parameter to assess their absolute (intra-subject) and relative (inter-subject) reliability. The CV (coefficient of variation) of SEM ranged from 1.7% (for CBFV) to 100.0% (for RAP), whereas the ICC was <0.5 for ARI, rising to >0.8 for CBFV and diastolic BP. These data demonstrate excellent absolute and relative reliability of CBFV, whereas ARI is of comparable reliability with the measurement of HR. Using these results it is possible to determine the sample size required to demonstrate a change in ARI, with a sample of 45 subjects in each group required to show a change in ARI of 1, whereas to detect a change in ARI >2 would require only 11 subjects per group. The results of the present study could be valuable to the future planning of cerebral autoregulation studies, but more work is needed to understand the determinants of intra-subject variability in autoregulatory parameters.
The internal limits to firms' nonmarket activities
Authors: Bonardi Jean‐Philippe
Published: October 2008

It is well documented that firms develop nonmarket strategies to try to shape public policy changes to their advantage. But are there no limits to this? This paper argues that there is in fact an important limitation, internal to the firm, which comes from the necessity for firms to integrate market and nonmarket activities. Because the two types of activities are not always complements but sometimes substitutes, firms end up giving up part of their nonmarket activities to avoid restricting the development of their market strategies. This argument is tested in the context of the European telecommunications industry. Results suggest that there is reasonable ground for optimism regarding the potentially negative influence that firms' nonmarket activities might play in a democracy.
Social issues in the study of management
Authors: Guthrie Doug , Durand Rodolphe
Published: October 2008

The last 30 years have seen an explosion of activity in the areas of corporate social responsibility (CSR) and social enterprise. With these emergent corporate practices has come a significant amount of attention among scholars and practitioners to how we should understand this phenomenon. What forces have driven managers and owners to re‐think their responsibilities as extending beyond profit maximization and increasing shareholder value? In this paper, we introduce some of the key issues that have guided research on the social issues of management over the last 30 years. We argue that, despite the growing strength of research in this area, there are four key ways in which we would like to see scholarship in this area develop further: (i) Scholarship in this area should incorporate a greater appreciation for the institutional history in which these practices have emerged. Research in this area tends to be ahistorical, and it is often the case that corporate social practices have emerged because of deep‐seated institutional struggles. (ii) Scholarship should rely more on comparative analysis to illuminate the importance of the contexts in which these practices emerge. (iii) Scholarship should engage more thoroughly with the legal and finance literatures on corporate governance. Many of the issues that fall under the ‘social issues of management’ rubric are fundamentally issues of corporate governance, and while some management scholars have embraced the corporate governance literature, research on the social issues of management rarely draws upon this important body of work. (iv) Methodological plurality is key to thinking through the mechanisms that drive organizational practices, and we would like to see more work in this area that employs multi‐method approaches to examine the organizational practices.
A method for measuring the nonlinear response in dielectric spectroscopy through third harmonics detection
Authors: Thibierge C. , L’Hôte D. , Ladieu F. , Tourbot R.
Published: October 2008

We present a high sensitivity method allowing the measurement of the nonlinear dielectric susceptibility of an insulating material at finite frequency. It has been developed for the study of dynamic heterogeneities in supercooled liquids using dielectric spectroscopy at frequencies 0.05 Hz≤f≤3×104 Hz. It relies on the measurement of the third harmonics component of the current flowing out of a capacitor. We first show that standard laboratory electronics (amplifiers and voltage sources) nonlinearities lead to limits on the third harmonics measurements that preclude reaching the level needed by our physical goal, a ratio of the third harmonics to the fundamental signal about 10−7. We show that reaching such a sensitivity needs a method able to get rid of the nonlinear contributions both of the measuring device (lock-in amplifier) and of the excitation voltage source. A bridge using two sources fulfills only the first of these two requirements, but allows to measure the nonlinearities of the sources. Our final method is based on a bridge with two plane capacitors characterized by different dielectric layer thicknesses. It gets rid of the source and amplifier nonlinearities because in spite of a strong frequency dependence of the capacitor impedance, it is equilibrated at any frequency. We present the first measurements of the physical nonlinear response using our method. Two extensions of the method are suggested.
Sub-Doppler spectroscopy of the Ã Σ2+−X̃ Π2 and B̃ Π2−X̃ Π2 transitions of NCO
Authors: Elliott Nicola L. , Fitzpatrick James A. J. , Western Colin M.
Published: October 2008

Sub-Doppler laser induced florescence spectra were recorded of a selection of bands within the Ã Σ2+−X̃ Π2 and B̃ Π2−X̃ Π2 transitions of NCO in a supersonic molecular beam. The light source was a diode seeded optical parametric oscillator, which gave an effective resolution of 0.01 cm−1 in the ultraviolet. Analysis of the Ã Σ2+−X̃ Π2 transition at high resolution allowed fitting of both the fine and hyperfine structures, and a set of rotational and hyperfine constants were obtained for 13 vibronic levels within the Ã Σ2+ state including levels of both Σ2+ and Π2 vibronic characters. Analysis of the 000 and 101 bands of the B̃ Π2−X̃ Π2 transition, together with a band from the Ã Σ2+ state at the same energy, was also performed. These did not reveal any hyperfine structure although the resolution was the same as the work at lower total energy, and this observation is discussed. Refined rotational constants and perturbation parameters for the interaction between the Ã and B̃ states were also obtained.
Synthesis, growth mechanism, and light-emission properties of twisted SiO2 nanobelts and nanosprings
Authors: Zhang Z. Y. , Wu X. L. , Xu L. L. , Shen J. C. , Siu G. G. , Chu Paul K.
Published: October 2008

Amorphous twisted SiO2 nanobelts have been synthesized on Si wafers using facile thermal evaporation. These nanobelts are produced together with SiO2 nanowires and a small quantity of SiO2 nanosprings. Spectral and microstructural analyses suggest that the twisted SiO2 nanobelts and nanosprings form via a polar surface driven process. Spontaneous polarization on the very thin polar crystalline SiO2 layers on the amorphous SiO2 nanobelt and nanospring surfaces makes the nuclei rearrange orderly and causes the nanobelt and nanowire to roll up at a certain twisty angle. The cathodoluminescence spectrum acquired from these SiO2 nanostructures reveals three emission bands at 4.4, 3.7, and 2.7eV originating from oxygen-related defect centers. The polar surface driven mechanism can adequately explain the growth of these novel twisty nanobelts and nanosprings which have potential applications in sensors, transducers, resonators, and photonics.
Toward a better description of the nucleation rate of crystals and crystalline monolayers
Authors: Kashchiev Dimo
Published: October 2008

The ability of the classical nucleation theory (CNT) and atomistic nucleation theory (ANT) to predict the stationary nucleation rate J of single-component crystals and crystalline monolayers is verified with the aid of numerical and computer simulation data obtained in the scope of the Kossel crystal model. It is found that in both cases CNT significantly overestimates J because it does not account for the work needed to attach an atom to the periphery of the two-dimensional nucleus or to form such a nucleus on the surface of the three-dimensional one. In contrast, ANT is successful in providing a good quantitative description of J, especially for high enough effective binding energy between nearest-neighbor atoms in the crystal and in capturing the existence of extended, nearly linear portions in the dependence of ln J on the supersaturation s when the values of both s and the binding energy are sufficiently great. However, the ANT prediction about broken linear ln J versus s dependence is not confirmed by the numerical and simulation results presented. General formulas for the nucleation work, the nucleus size, and the nucleation rate are proposed which are applicable to nucleation of single-component crystals and crystalline monolayers in vapors, solutions, or melts and which correct the respective CNT formulas. The proposed J(s) formula provides a good description of the numerical and simulation data and can justifiably be used up to the supersaturation at which the nucleus becomes monomer. When experimental data for the J(s) dependence are available and the nucleus specific edge and surface energies are unknown parameters, the proposed J(s) formula can be employed for estimation of these energies even if the nucleus is constituted of a few atoms only.
Heteroepitaxial growth and optoelectronic properties of layered iron oxyarsenide, LaFeAsO
Authors: Hiramatsu Hidenori , Katase Takayoshi , Kamiya Toshio , Hirano Masahiro , Hosono Hideo
Published: October 2008

The epitaxial thin films of LaFeAsO were fabricated on MgO(001) and mixed-perovskite (La,Sr)(Al,Ta)O3(001) single-crystal substrates by pulsed laser deposition using a Nd-doped yttrium aluminum garnet second harmonic source and a 10at.% F-doped LaFeAsO disk target. Temperature dependences of the electrical resistivities showed no superconducting transition in the temperature range of 2–300K and were similar to those of undoped polycrystalline bulk samples. The transmittance spectrum exhibited a clear peak at ∼0.2eV, which is explained by ab initio calculations.
Enthalpy difference between conformations of normal alkanes: Intramolecular basis set superposition error (BSSE) in the case of n-butane and n-hexane
Authors: Balabin Roman M.
Published: October 2008

In this paper, an extra error source for high-quality ab initio calculation of conformation equilibrium in normal alkanes—intramolecular basis set superposition error (BSSE)—is discussed. Normal butane (n-butane) and normal hexane (n-hexane) are used as representative examples. Single-point energy difference and BSSE values of trans and gauche conformations for n-butane (and trans-trans-trans and gauche-gauche-gauche conformations for n-hexane) were calculated using popular electron correlation methods: The second-order Moller–Plesset (MP2), the fourth-order Moller–Plesset (MP4), and coupled cluster with single and double substitutions with noniterative triple excitation [CCSD(T)] levels of theory. Extrapolation to the complete basis set is applied. The difference between BSSE-corrected and uncorrected relative energy values ranges from ∼100 cal/mol (in case of n-butane) to more than 1000 cal/mol (in case of n-hexane). The influence of basis set type (Pople or Dunning) and size [up to 6-311G(3df,3pd) and aug-cc-pVQZ] is discussed.
Effect of the growth temperature and the AlN mole fraction on In incorporation and properties of quaternary III-nitride layers grown by molecular beam epitaxy
Authors: Fernández-Garrido S. , Redondo-Cubero A. , Gago R. , Bertram F. , Christen J. , Luna E. , Trampert A. , Pereiro J. , Muñoz E. , Calleja E.
Published: October 2008

Indium incorporation into wurtzite (0001)-oriented InxAlyGa1−x−yN layers grown by plasma-assisted molecular beam epitaxy was studied as a function of the growth temperature (565–635 °C) and the AlN mole fraction (0.01<y<0.27). The layer stoichiometry was determined by Rutherford backscattering spectrometry (RBS). RBS shows that indium incorporation decreased continuously with increasing growth temperature due to thermally enhanced dissociation of In–N bonds and for increasing AlN mole fractions. High resolution x-ray diffraction and transmission electron microscopy (TEM) measurements did not show evidence of phase separation. The mosaicity of the quaternary layers was found to be mainly determined by the growth temperature and independent on alloy composition within the range studied. However, depending on the AlN mole fraction, nanometer-sized composition fluctuations were detected by TEM. Photoluminescence spectra showed a single broad emission at room temperature, with energy and bandwidth S- and W-shaped temperature dependences typical of exciton localization by alloy inhomogeneities. Cathodoluminescence measurements demonstrated that the alloy inhomogeneities, responsible of exciton localization, occur on a lateral length scale below 150 nm, which is corroborated by TEM.
Rapid photoreflectance spectroscopy for strained silicon metrology
Authors: Chouaib H. , Murtagh M. E. , Guènebaut V. , Ward S. , Kelly P. V. , Kennard M. , Le Vaillant Y. M. , Somekh M. G. , Pitter M. C. , Sharples S. D.
Published: October 2008

We present an improved photoreflectance (PR) spectroscopy technique upon the prior art in providing a rapid acquisition method of the PR spectrum in a simultaneous and multiplexed manner. Rapid PR (RPR) application is the on-line monitoring of strained silicon. Shrinkage in the silicon bandgap is measured and converted to strain, using theoretical models. Experimental RPR results are in good correlation with Raman spectroscopy.
Magnetic polaron for a spin memory application
Authors: Enaya H. , Semenov Y. G. , Zavada J. M. , Kim K. W.
Published: October 2008

A memory concept based on the interfacial exchange energy between itinerant holes in a quantum dot and magnetic ions in an adjacent magnetic insulator is theoretically investigated. A model based on the free energy analysis demonstrates the existence of bistable states through the mechanism of bound collective magnetic polaron, whose formation and dissolution can be controlled electrically via a gate bias pulse. The parameter window suitable for bistability is discussed along with the conditions that support maximum nonvolatility. The analysis is extended to the influence of material choices as well as different designs. The calculation results clearly indicate the possibility of room temperature operation, given the availability of insulating ferromagnetic or antiferromagnetic materials whose Curie temperature is above room temperature.
Optical bandwidth enhancement of heterojunction bipolar transistor laser operation with an auxiliary base signal
Authors: Then H. W. , Walter G. , Feng M. , Holonyak N.
Published: October 2008

We report the improvement, from 10.5to22GHz, in the optical modulation bandwidth of a quantum-well (QW) heterojunction bipolar transistor laser (TL) by the use of an ac auxiliary base signal. Because of the three-terminal form of the TL, an auxiliary signal can be used to peak the photon output, e.g., stimulated recombination which simultaneously reduces the operating current gain, β(=ICO∕IBO), and increases the laser differential gain. A shorter effective base carrier lifetime, τ, owing to the increased QW recombination rate (stimulated recombination), enhanced carrier transport to the “faster” QW collector (reduced β) and differential gain, result in a higher 3dB bandwidth (f3dB=1∕2πτ).
Calculations of electronic states in ultrasmall quantum boxes of diamond
Authors: Nishida Masahiko
Published: October 2008

The electronic structure of ultrasmall quantum boxes (QBs) of diamond with (110), (11¯0), and (001) planes saturated by hydrogen is calculated using the extended Hückel-type nonorthogonal tight-binding method. It is shown that in contrast to the QBs with the ideal surfaces, which show a clear dependence of the lowest unoccupied molecular orbital (LUMO) energy on the size variation along the [001] direction, the energy of the LUMO state in the QBs with a monohydrogenated dimer on the (001) surface depends little on the size variation in agreement with the experiment. It is found that the LUMO state in the latter is surfacelike in character and associated with backbonds of the surface dimers. It is also demonstrated that optical transitions across the energy gap exhibit significant oscillator strength.
Observation of near total polarization in the ultrafast laser ablation of Si
Authors: Liu Yaoming , Singha Sima , Witt Tana E. , Cheng Yongtao , Gordon Robert J.
Published: October 2008

We report nearly completely polarized emission from the plasma produced in the femtosecond ablation of Si(111). Pairs of ultrashort laser pulses were focused onto the target in air, and the polarization spectrum was measured as a function of energy, pulse delay, and polarization state of the laser. When the laser was focused on the surface, the fluorescence continuum was strongly polarized, whereas discrete lines appeared as minima in the polarization spectrum. Under this focusing condition, the continuum polarization increased with pulse delay and decreased with pulse energy and fluorescence wavelength, with >95% polarization in the ultraviolet.
Electro-oxidation of organic fuels catalyzed by ultrasmall silicon nanoparticles
Authors: Choi Yongki , Wang Gang , Nayfeh Munir H. , Yau Siu-Tung
Published: October 2008

Ultrasmall colloidal silicon nanoparticles behave as electrocatalysts for the oxidation of ethanol, methanol, and glucose. Electrochemical characterization of particle-immobilized electrodes shows a catalytic onset between −0.4 and 0 V versus Ag/AgCl at neutral pH. The onset potential and the catalytic strength are dependent on the particle size. A prototype hybrid biofuel cell was constructed, using the particles as the anode catalyst. The catalytic activity undergoes a 50-fold increase under alkaline condition compared to that under acidic condition. An unexpected light dependence of the catalytic current was observed. A significant increase in the catalytic current is obtained when the catalysis is performed in darkness.
A tough nanofiber hydrogel incorporating ferritin
Authors: Shin Min Kyoon , Kim Sun I. , Kim Seon Jeong , Kim Byung Joo , So Insuk , Kozlov Mikhail E. , Oh Jiyoung , Baughman Ray H.
Published: October 2008

We have developed tough nanofiber hydrogels incorporating ferritin nanoparticles with a core-shell structure that is suitable for stress concentration reduction. The swelling properties of the nanocomposite hydrogel under external forces were enhanced, leading to fast water absorption. The elastic modulus, tensile strength, and elongation at break of the nanocomposite hydrogel measured in solutions were dramatically enhanced as compared to those of the bare polymer hydrogel. During the tensile tests, the strong bonding between the nanofiller and polymer matrix played an important role in enhancing the toughness of the composite hydrogel fibers.
Label-free porous silicon membrane waveguide for DNA sensing
Authors: Rong Guoguang , Ryckman Judson D. , Mernaugh Raymond L. , Weiss Sharon M.
Published: October 2008

We report a label-free porous silicon membrane waveguide biosensor based on a 1μm thick freestanding porous silicon film with 100nm diameter pores. The sensor operates in the Kretschmann configuration. A formvar polymer film provides robust adhesion of the porous silicon membrane to a rutile prism and enables confinement of guided modes in the porous silicon membrane. Attenuated total reflectance measurements are performed, along with theoretical calculations, to fully characterize the waveguide. The sensitivity of the sensor is investigated through DNA hybridization in the porous silicon membrane. A detection limit of 42nM was demonstrated for 24-base pair DNA oligonucleotides.
Interfacial reactions between Cu alloy and GaAs
Authors: Chu J. P. , Leau W. K. , Lin C. H.
Published: October 2008

Interfacial reactions between Cu alloy and GaAs are characterized at various temperatures. The Cu alloy, as Cu(TaNx), is prepared by cosputtering of Cu, Ta, and N. While the pure Cu/GaAs is stable up to 350 °C, the Cu(TaNx)/GaAs is more stable without harmful interfacial reactions up to 450 °C for 1 h. At 500 °C, the Cu(TaNx)/GaAs suffers a relatively small extent of interfacial reactions as compared with that of Cu/GaAs that failed at 400 °C. The TaNx is found not only to retard the interactions but also to refine the grain structure. The thermally stable Cu(TaNx)/GaAs structure is thus favorable for the barrierless metallization.
Low-temperature structural and dielectric phenomena in La1/3NbO3 and La1/3TaO3: Comparative study
Authors: Salak Andrei N. , Vyshatko Nikolai P. , Khalyavin Dmitry D. , Prokhnenko Oleksandr , Ferreira Victor M.
Published: October 2008

The crystal structures of the perovskites La1/3NbO3 and La1/3TaO3 were studied between 10 and 350 K using high-resolution neutron powder diffraction and compared with their radio-frequency dielectric response over the same temperature range. The structure of La1/3NbO3 remains orthorhombic Cmmm, while La1/3TaO3 undergoes continuous transition from the high-temperature tetragonal P4/mmm to Cmmm phase at about 220 K. This transition is tricritical in nature and accompanied by no dielectric anomaly. In La1/3NbO3, the frequency-dependent peak of the dielectric permittivity is associated with an atypical increase in the lattice parameters below about 80 K.
Nuclear and plastid DNA sequences reveal complex reticulate patterns in Australian water-lilies (Nymphaea subgenus Anecphya, Nymphaeaceae)
Authors: Löhne Cornelia , Borsch Thomas , Jacobs Surrey W. L. , Hellquist C. Barre , Wiersema John H.
Published: October 2008

This study represents the first comprehensive analysis of phylogenetic relationships within the Australian water-lilies, Nymphaea subg. Anecphya. Our 51-accession dataset covers all 10 species of the subgenus, except the newly described N. alexii, and includes information from the nuclear ITS as well as from the chloroplast trnT–trnF region. The results show that molecular data are consistent with morphology, because the subdivision of subg. Anecphya into two major clades, a large-seeded and a small-seeded group, could be confirmed. Within the large-seeded group, Nymphaea atrans and N. immutabilis seem to form one clade, whereas samples of N. gigantea, N. georginae, N. macrosperma and N. carpentariae form another. Relationships within the small-seeded group, containing all samples of N. violacea, N. elleniae and N. hastifolia, are less clear, since the trees obtained from the chloroplast and the nuclear marker are incongruent. The samples of N. violacea do not form a monophyletic group in each of the trees, but—at least in the ITS tree—group with either N. elleniae or N. hastifolia/Ondinea, respectively. Polymorphisms among ITS paralogues, i.e. substitutions at single nucleotide positions and length polymorphisms, have been observed in some samples of N. violacea. This fact as well as the incongruent phylogenetic signal obtained from the chloroplast and the nuclear genomes point to recent hybridisation or introgression in this group. Remarkably, Ondinea purpurea is resolved within the small-seeded group by both markers and seems to have a close relationship to N. hastifolia. Although incomplete lineage sorting cannot be fully excluded to explain high variability in N. violacea, molecular data potentially hint to a case of still imperfect taxonomy.
Population-level effects of immunocontraception in white-tailed deer (Odocoileus virginianus)
Authors: Rutberg Allen T. , Naugle Ricky E.
Published: October 2008

In North America, dense populations of white-tailed deer (Odocoileus virginianus) in suburbs, cities and towns have stimulated a search for new population-management tools. Most research on deer contraception has focused on the safety and efficacy of immunocontraceptive vaccines, but few studies have examined population-level effects. We report here results from two long-term studies of population effects of the porcine zona pellucida (PZP) immunocontraceptive vaccine, at the National Institute of Standards and Technology (NIST), Gaithersburg, Maryland, USA, and at Fire Island National Seashore (FIIS), New York, USA. Annual population change at NIST was strongly correlated with population fertility (rP = 0.82, P = 0.001); when population fertility at NIST dropped below 0.40 fawns per female, the population declined. Contraceptive treatments at NIST were associated with a 27% decline in population between 1997 and 2002, and fluctuated thereafter with the effectiveness of contraceptive treatments. In the most intensively treated segment of FIIS, deer population density declined by ~58% between 1997 and 2006. These studies demonstrate that, in principle, contraception can significantly reduce population size. Its usefulness as a management tool will depend on vaccine effectiveness, accessibility of deer for treatment, and site-specific birth, death, immigration, and emigration rates.
The use of a GnRH vaccine to suppress mare ovarian activity in a large group of mares under field conditions
Authors: Botha A. E. , Schulman M. L. , Bertschinger H. J. , Guthrie A. J. , Annandale C. H. , Hughes S. B.
Published: October 2008

The aim of this study was to evaluate the effect of active immunisation against GnRH on ovarian activity and serum progesterone concentrations in a large group of mares (10 control and 55 experimental) under field conditions as a model for wildlife species such as zebra and African elephants. Within the experimental group, mares were subdivided into three age categories: Category 1 (4 years and younger, n = 26), Category 2 (4–10 years old, n = 18), and Category 3 (≥11 years old, n = 11). Experimental mares were vaccinated intramuscularly with 2 mL (400 μg) of the GnRH vaccine Improvac (Pfizer Animal Health, Sandton, South Africa). Control mares received the same amount of saline solution. The vaccinations were repeated 35 days later. The ovaries and reproductive tracts of each mare were examined by means of rectal palpation and ultrasonography on Days 0, 35 and 70. Blood was collected weekly for determination of serum progesterone concentration until Day 175. On Day 35 after primary vaccination all of the control mares and 14.5% of the experimental mares showed evidence of ovarian activity on the basis of clinical examination and serum progesterone concentration. On Day 70, all control mares and none of the experimental mares showed evidence of cyclic activity. No age-related effect within treatment groups was found. The serum progesterone concentration indicated that all experimental mares remained in anoestrus until Day 175. Five of the control mares fell pregnant between Days 35 and 70. The five non-pregnant control mares continued to cycle until the end of the observation period. Having achieved such promising results in this trial we now plan to test the GnRH vaccine in Burchell’s zebra mares and African elephant cows.
The use of deslorelin implants for the long-term contraception of lionesses and tigers
Authors: Bertschinger H. J. , Guimarães M. A. de Barros Vaz , Trigg T. E. , Human A.
Published: October 2008

Contraception is an essential tool for controlling reproduction in captive and free-ranging lions. This paper describes the treatment and contraception of 23 captive and 40 free-ranging lionesses (Panthera leo) and four captive tigers (Panthera tigris) in South Africa using 3 × 4.7 mg, 2 × 4.7 mg, 9.4 mg or 4.7 + 9.4 mg deslorelin implants. Thirty-one lionesses were treated more than once at 11- to 60-month intervals. In Brazil, two lionesses were treated with 9.4-mg implants and faecal progesterone and oestradiol concentrations were monitored for 920 days. All combinations of deslorelin showed the length of contraception to be around 30 months with one 3 × 4.7 mg treatment lasting 40 months in one captive lioness. The mean time taken to reconception was 30.1 months for the 3 × 4.7 mg combination. The faecal analyses of the lionesses in Brazil reflected quiescent ovarian activity for periods of 17 and 30 months, respectively, when small oestradiol peaks but no progesterone peaks started to appear. This confirmed the field observations in South Africa. No side effects occurred although several of the lionesses were treated repeatedly for up to 8 years. Deslorelin (Suprelorin) is a safe and effective means of controlling reproduction in captive or free-ranging populations of lions. Where contraception is to be maintained, the implementation of implants at 24-month intervals is recommended.
Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions
Authors: Vallur Aarthy C. , Maizels Nancy
Published: October 2008

Eukaryotic exonuclease 1 functions in replication, recombination, mismatch repair, telomere maintenance, immunoglobulin (Ig) gene class switch recombination, and somatic hypermutation. The enzyme has 5′–3′ exonuclease, flap endonuclease, and weak RNaseH activity
in vitro
, but it has been difficult to reconcile these activities with its diverse biological functions. We report robust cleavage by human exonuclease 1 of transcribed G-rich DNA sequences with potential to form G loops and G4 DNA. Predicted Ig switch recombination intermediates are substrates for both exonucleolytic and 5′ flap endonucleolytic cleavage. Excision is nick-dependent and structure-dependent. These results lead to a model for exonuclease 1 function in class switch recombination in which cleavage at activation-induced deaminase (AID)-initiated nicks produces gaps that become substrates for further attack by AID and subsequent repair.
Delayed plasticity of inhibitory neurons in developing visual cortex
Authors: Gandhi Sunil P. , Yanagawa Yuchio , Stryker Michael P.
Published: October 2008

During postnatal development, altered sensory experience triggers the rapid reorganization of neuronal responses and connections in sensory neocortex. This experience-dependent plasticity is disrupted by reductions of intracortical inhibition. Little is known about how the responses of inhibitory cells themselves change during plasticity. We investigated the time course of inhibitory cell plasticity in mouse primary visual cortex by using functional two-photon microscopy with single-cell resolution and genetic identification of cell type. Initially, local inhibitory and excitatory cells had similar binocular visual response properties, both favoring the contralateral eye. After 2 days of monocular visual deprivation, excitatory cell responses shifted to favor the open eye, whereas inhibitory cells continued to respond more strongly to the deprived eye. By 4 days of deprivation, inhibitory cell responses shifted to match the faster changes in their excitatory counterparts. These findings reveal a dramatic delay in inhibitory cell plasticity. A minimal linear model reveals that the delay in inhibitory cell plasticity potently accelerates Hebbian plasticity in neighboring excitatory neurons. These findings offer a network-level explanation as to how inhibition regulates the experience-dependent plasticity of neocortex.
Acid phosphatase 5 is responsible for removing the mannose 6-phosphate recognition marker from lysosomal proteins
Authors: Sun Pengling , Sleat David E. , Lecocq Michèle , Hayman Alison R. , Jadot Michel , Lobel Peter
Published: October 2008

Most newly synthesized proteins destined for the lysosome reach this location via a specific intracellular pathway. In the Golgi, a phosphotransferase specifically labels lysosomal proteins with mannose 6-phosphate (Man-6-P). This modification is recognized by receptors that target the lysosomal proteins to the lysosome where, in most cell types, the Man-6-P recognition marker is rapidly removed. Despite extensive characterization of this pathway, the enzyme responsible for the removal of the targeting modification has remained elusive. In this study, we have identified this activity. Preliminary investigations using a cell-based bioassay were used to follow a dephosphorylation activity that was associated with the lysosomal fraction. This activity was high in the liver, where endogenous lysosomal proteins are efficiently dephosphorylated, but present at a much lower level in the brain, where the modification persists. This observation, combined with an analysis of the expression of lysosomal proteins in different tissues, led us to identify acid phosphatase 5 (ACP5) as a candidate for the enzyme that removes Man-6-P. Expression of ACP5 in N1E-115 neuroblastoma cells, which do not efficiently dephosphorylate lysosomal proteins, significantly decreased the steady state levels of Man6-P glycoproteins. Analysis of ACP5-deficient mice revealed that levels of Man-6-P glycoproteins were highly elevated in tissues that normally express ACP5, and this resulted from a failure to dephosphorylate lysosomal proteins. These results indicate a central role for ACP5 in removal of the Man-6-P recognition marker and open up new avenues to investigate the importance of this process in cell biology and medicine.
The Role of Theoretical Modeling in Microcirculation Research
Authors: SECOMB TIMOTHY W. , BEARD DANIEL A. , FRISBEE JEFFERSON C. , SMITH NICOLAS P. , PRIES AXEL R.
Published: October 2008

Theoretical modeling approaches have made important contributions to research in the biological sciences, including the microcirculation, and their value is increasingly recognized. However, misconceptions about the nature and role of theoretical models persist, and such work is often presented in a way that does not maximize its value, especially for scientists who are not themselves using such models. In this review, a categorization of models as phenomenological, qualitative conceptual, quantitative conceptual, or predictive is proposed, and the characteristics of each type are discussed. Recommendations are made for the presentation of models and for the future development of modeling approaches. The concepts discussed are generally applicable to the theoretical modeling of biological systems and are illustrated by using examples of modeling in microcirculation research.
The Arab nation and indigenous acquisition of scientific knowledge (tawṭīn al-ilm)
Authors: Rashed Roshdi
Published: October 2008

In this article, the author deals with the factors he considers to be essential for the genuine acquisition of knowledge and, specifically, scientific knowledge – the Arabic term al- ilm being a referent to either or both. The phrase tawṭīn al- ilm used in the title and throughout could be translated literally as the ‘nationalization of science/knowledge’, however, the import is wider in scope and is intended to connote the process of making knowledge, science and scientific culture indigenous in and endemic to the Arab nation. In the view of the author, among the chief factors in such an initiative is to Arabize the language of scientific discourse in order to render original scientific thought and research innate and to facilitate its dissemination to a wider society that also must, of a necessity, become scientific and oriented towards the output of nationally-funded scientific research institutions.
The Hariri and Saddam tribunals: two expressions of tortured justice
Authors: Khairallah Daoud
Published: October 2008

This article establishes that politically motivated pursuit of criminal justice at the international level undermines trust in the international legal order and inflicts multilateral harm that goes far beyond the facts subject to judicial process. The author analyzes the pursuit of justice in relation to two major events: the murder of Rafiq Hariri, a former Lebanese prime minister, and the international crimes that Saddam Hussein, former president of Iraq, was accused of committing. In the first example, the author examines the role of the UN Security Council, including reference to the efforts of the US, relative to the investigation and establishment of a special tribunal for Lebanon; and in the second, the role of the US in the trial and execution of Saddam Hussein. Both cases demonstrate that justice is the main victim of politicizing the judicial process.
The Palestinian cause: the road to peace not travelled and the imperative of return to the basics
Authors: Kanaan Taher H.
Published: October 2008

With the end of 60 years since the termination of the British Mandate on Palestine and the first round of failure to effect a two-state solution of the conflict over Palestine, both sides to the conflict are no closer to a just, durable and peaceful solution. The peace process proved to be an end in itself, to be a fetish which commands elaborate rituals but one which tenders no genuine faith. There is a simple reason for this, namely, that the more powerful side to the conflict, blinded by the supremacy of its military might, has been pursuing a solution that reflects the imbalance of power, pure and simple. Like individuals who are immune to learning, there are also peoples who never learn. History teaches us that there are only two alternative bases for conflict resolution, each with entirely different prospects for stability and durability: (1) a basis which reflects the balance of brute force and weight of conquest; and, this is doomed to be unstable and short-lived; (2) a basis which reflects fidelity to moral norms and international rules of law; and, this is the basis which assures long-term stability and durability.
The Arab Organization for Human Rights
Authors: Awad Mohsen
Published: October 2008

The Arab Organization for Human Rights was founded in 1983, at a time when the legal, political and cultural environment in the Arab world was not at all amenable to human rights. On the legal level and when present, societies’ laws ranged between banning outright and imposing restrictions, and the very concept of human rights was deeply misunderstood. This was due to the many relevant interpretations and reference points and to its use by the West to contain communist ideology and apply pressure on the Soviet Union. In the meantime, all across the Arab region, public freedoms were experiencing crises of varying degrees of severity. It is in this legally restricted, culturally dubious and politically stifled environment that efforts to establish the Organization first saw the light of day in what amounted to an effort to swim against the current.
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Authors: Busch Anke , Richter Andreas S. , Backofen Rolf
Published: October 2008

Motivation: During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.

Results: We introduce INTARNA, a new general and fast approach to the prediction of RNA–RNA interactions incorporating accessibility of target sites as well as the existence of a user-definable seed. We successfully applied INTARNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.

Availability:  http://www.bioinf.uni-freiburg.de/Software/

Contact:  IntaRNA@informatik.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Prediction of kinase-specific phosphorylation sites using conditional random fields
Authors: Dang Thanh Hai , Van Leemput Koenraad , Verschoren Alain , Laukens Kris
Published: October 2008

Motivation: Phosphorylation is a crucial post-translational protein modification mechanism with important regulatory functions in biological systems. It is catalyzed by a group of enzymes called kinases, each of which recognizes certain target sites in its substrate proteins. Several authors have built computational models trained from sets of experimentally validated phosphorylation sites to predict these target sites for each given kinase. All of these models suffer from certain limitations, such as the fact that they do not take into account the dependencies between amino acid motifs within protein sequences in a global fashion.

Results: We propose a novel approach to predict phosphorylation sites from the protein sequence. The method uses a positive dataset to train a conditional random field (CRF) model. The negative training dataset is used to specify the decision threshold corresponding to a desired false positive rate. Application of the method on experimentally verified benchmark phosphorylation data (Phospho.ELM) shows that it performs well compared to existing methods for most kinases. This is to our knowledge that the first report of the use of CRFs to predict post-translational modification sites in protein sequences.

Availability: The source code of the implementation, called CRPhos, is available from http://www.ptools.ua.ac.be/CRPhos/

Contact:  kris.laukens@ua.ac.be

Suplementary Information: Supplementary data are available at http://www.ptools.ua.ac.be/CRPhos/
Effective cluster-based seed design for cross-species sequence comparisons
Authors: Zhou Leming , Mihai Ingrid , Florea Liliana
Published: October 2008

Summary: To annotate newly sequenced organisms, cross-species sequence comparison algorithms can be applied to align gene sequences to the genome of a related species. To improve the accuracy of alignment, spaced seeds must be optimized for each comparison. As the number and diversity of genomes increase, an efficient alternative is to cluster pairwise comparisons into groups and identify seeds for groups instead of individual comparisons. Here we investigate a measure of comparison closeness and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed.

Availability: Source code is freely available at http://dna.cs.gwu.edu and from Bioinformatics online.

Contact:  lmzhou@gwmail.gwu.edu, florea@gwu.edu

Supplementary information: Supplementary data are available at http://dna.cs.gwu.edu and Bioinformatics online.
Dynamics of closed areas in Norway lobster fisheries
Authors: Smith I. Philip , Jensen Antony C.
Published: October 2008

Smith, I. P., and Jensen, A. C. 2008. Dynamics of closed areas in Norway lobster fisheries. – ICES Journal of Marine Science, 65: 1600–1609. A dynamic, age-structured population model was developed to investigate the potential effects of introducing a closed area to a fishery for a species with limited adult mobility and planktonic dispersal of larvae, using biological and fishery information from a Norway lobster fishery in eastern Scotland. Simulated closure of part of the fishing grounds led to a long-term increase in total biomass and recruitment to the fished zone, but the larval subsidy did not compensate for the loss of fishing ground, and fishery yield was reduced under all modelled combinations of closed-area size and prior fishing effort. Concentration of effort in the fished zone and increased recruitment there led to reduced average size, and therefore value, of animals in the catch, as well as increased destruction of biomass by discarding undersized lobsters. Implementation of a closed area also led to oscillations in stock biomass, recruitment, and yield over several years after the closure, particularly with large closed areas and high fishing effort.