bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxygen radical and plasma damage of low-k organosilicate glass materials: Diffusion-controlled mechanism for carbon depletion
Authors: Goldman M. A. , Graves D. B. , Antonelli G. A. , Behera S. P. , Kelber J. A.
Published: July 2009

Fourier transform infrared (FTIR) analyses of low-k materials exposed to either oxygen radicals or to capacitively coupled O2 plasma indicate that carbon depletion from these materials is dominated by O radical diffusion. FTIR measurements of changes in absorbance related to silanol formation (3500 cm−1) and carbon depletion (2980 cm−1, 900–700 cm−1) exhibit a linear dependence on the square root of the exposure time. Diffusion is faster for a sample of higher porosity and interconnectedness (k=2.54) than for a sample with lower porosity (k=3.0). However, a sample with high porosity (k=2.57) but low interconnectedness (as measured by liquid diffusion) exhibits a high initial rate of carbon loss, followed by no further carbon loss at longer times. Further, pretreatment of k=3.0 material by 500 eV noble gas ions results in a sharp decrease in the rate of carbon loss upon subsequent exposure to oxygen radicals. The data indicate that the main mechanism of carbon depletion in organosilicate glass (OSG) materials during oxygen plasma exposure is loss due to a reaction front created by oxygen radicals diffusing through interconnected pores. Further, carbon depletion can be minimized for low-k OSG materials either by formation of high porosity/low interconnectedness samples, or by pretreatment by noble gas ion bombardment, which seals surface pores.
Stimulated Raman up conversion of a helicon by band-gap energy plasmons in a semiconductor
Authors: Kumar Pawan , Tripathi V. K.
Published: July 2009

Stimulated Raman up conversion of a helicon wave in a semiconductor, where free carrier plasma frequency equals band-gap energy divided by Planck’s constant, is investigated. The stimulated electron hole recombination drives a Langmuir wave. The free carrier density oscillations associated with the Langmuir wave couple with the free carrier oscillatory velocities due to the helicon and derive a sum frequency radiation. The radiation and helicon exert a ponderomotive force on free carriers that influences the Langmuir wave.
Native vacancy defects in Zn1−x(Mn,Co)xGeAs2 studied with positron annihilation spectroscopy
Authors: Kilanski L. , Zubiaga A. , Tuomisto F. , Dobrowolski W. , Domukhovski V. , Varnavskiy S. A. , Marenkin S. F.
Published: July 2009

We have studied vacancy defects in chalcopyrite semimagnetic semiconducting mixed Zn1−x(Mn,Co)xGeAs2 bulk crystals with alloy composition x varying between 0.052 to 0.182 using positron annihilation spectroscopy. We identified As vacancies, potentially complexed with the transition metal alloying elements, in all the studied samples, while no cation vacancy related defects were detected. The positron lifetimes for the bulk ZnGeAs2 lattice and neutral As vacancy were determined to be τB=220–230 ps and τAs=300±10 ps, respectively. Our results also show that the p-type conductivity in the samples is not due to cation vacancy related acceptor centers. The As vacancies were found to be present at such low concentrations that they cannot be responsible for the compensation of the p-type conductivity or the reduction of mobility in the Zn1−x(Mn,Co)xGeAs2 samples.
Arbitrary amplitude dust acoustic solitary waves and double layers in nonthermal plasma including the effect of dust temperature
Authors: Das Animesh , Bandyopadhyay Anup , Das K. P.
Published: July 2009

A computational scheme has been developed to study the arbitrary amplitude dust acoustic solitary waves and double layers in nonthermal plasma consisting of negatively charged dust grains, nonthermal ions, and isothermal electrons including the effect of dust temperature. The Sagdeev potential approach, which is valid to study the arbitrary amplitude solitary waves and double layers, has been employed. The computation has been carried out over the entire interval of β1:0≤β1<βM. This β1 is a parameter associated with the nonthermal distribution of ions and βM is the upper bound of β1. Depending on the nature of existence of solitary waves and double layers, the interval for β1 can be broken up into four disjoint subintervals holding the other parameters fixed. By nature of existence of solitary waves and double layers, it is meant that in some subinterval only negative potential solitary waves can exist, whereas in another both negative and positive potential solitary waves can coexist along with a double layer, etc. Corresponding to every β1 lying within a subinterval of β1, there is a definite interval for the Mach number (definite value of the Mach number) for which there exists solitary waves (double layer) specific for that subinterval of β1. The role of dust temperature on the subintervals of β1 and on amplitude of solitary waves and double layers has been explored.
Schottky contact surface-plasmon detector integrated with an asymmetric metal stripe waveguide
Authors: Akbari Ali , Berini Pierre
Published: July 2009

A silicon-based Schottky contact photodetector integrated into a finite width asymmetric metal stripe supporting short-range surface plasmon polaritons is presented. Input optical energy is coupled into a bound mode supported by the stripe, leading to total absorption of in-coupled energy. The absorbed energy excites carriers in the metal stripe, some of which cross the Schottky barrier (internal photoemission) leading to a photocurrent under reverse bias. Significant enhancement in the quantum efficiency is observed for a thin metal stripe due to multiple internal reflections of excited carriers. The device holds promise for short-reach high-speed optical interconnects and silicon-based photonic circuitry.
Germanium oxynitride gate dielectrics formed by plasma nitridation of ultrathin thermal oxides on Ge(100)
Authors: Kutsuki Katsuhiro , Okamoto Gaku , Hosoi Takuji , Shimura Takayoshi , Watanabe Heiji
Published: July 2009

Germanium oxynitride (GeON) gate dielectrics with surface nitrogen-rich layers were fabricated by plasma nitridation of thermally grown oxides (GeO2) on Ge(100). Insulating features of ultrathin GeO2 layers of around 2-nm-thick were found to improve with plasma treatment, in which leakage current was drastically reduced to over four orders of magnitude. Consequently, Au/GeON/Ge capacitors of an equivalent oxide thickness down to 1.7 nm were achieved while keeping sufficient leakage reduction merit. The minimum interface state density values of GeON/Ge structures as low as 3×1011 cm−2 eV−1 were obtained for both the lower and upper halves of the bandgap without any postnitridation treatments. These results were discussed based on the effects of plasma nitridation on a degraded GeO2 surface for recovering its electrical properties by creating stable nitride layers.
Fluorine microimaging and quantification using nuclear reaction analysis: A tool for validating tissue distribution of positron emission tomography tracers
Authors: Devès G. , Roudeau S. , Carmona A. , Lavielle S. , Gionnet K. , Déléris G. , Ortega R.
Published: July 2009

An application of ion beam microprobe analysis has been developed for the quantitative imaging of fluorine compounds in biological samples on a micrometer scale. The difficulty of imaging fluorine at trace level concentration in biological tissues has been addressed by using a combination of nuclear reaction analysis and proton resonant backscattering spectrometry. With this method, the limit of detection of fluorine in thin biological samples can be as low as 3 μg/g. Quantitative imaging of fluorodeoxyglucose distribution, the most widely used tracer for detection of solid tumors by positron emission tomography, is shown as an example of this application.
A nonvolatile memory capacitor based on Au nanocrystals with HfO2 tunneling and blocking layers
Authors: Mikhelashvili V. , Meyler B. , Yoffis S. , Salzman J. , Garbrecht M. , Cohen-Hyams T. , Kaplan W. D. , Eisenstein G.
Published: July 2009

We report on a nonvolatile memory capacitor based on gold nanocrystals serving as charge storage elements located between two HfO2 films acting as the tunneling and control layers. The capacitor has an equivalent oxide thicknesses of 7 nm and exhibits a large hysteresis in the C-V characteristics of 1 and 9 V for gate voltage sweeps of ±1 and ±7 V, respectively, with no frequency dependence in the range of 10 kHz to 1 MHz. The storage charge density is ∼1.2×1013 cm−2 and the flat band voltage shift is stable for write/erases operations with a voltage swing of ±5 V for over 18 h.
Experimental study on a plane shock wave accelerating a gas bubble
Authors: Layes Guillaume , Jourdan Georges , Houas Lazhar
Published: July 2009

A detailed experimental study of the interaction between a planar shock wave and an isolated spherical gas inhomogeneity is presented here. Different configurations have been considered: a shock wave moving from one gas into another, of similar density, lower density and one of higher density. Sequences of shadowgraph pictures obtained during the same run provided useful insights into several mechanisms such as shock wave reflection, refraction and focusing, distortion of the bubble interface, and vortex formation. Based on these sequences, the changes with time in the characteristic bubble sizes were plotted and the results showed that the influence of the shock wave Mach number is significantly greater in the case of light gas bubbles. The displacement of the inhomogeneity relative to the surrounding gas was determined and compared to Rudinger and Somers’ model. In all the cases studied, although the measurements were found to agree well with the theoretical predictions, in the initial acceleration phase, the final translational motions of the vortex ring were not accurately predicted by the model. The database obtained was used to estimate the resulting pattern of circulation, which was compared to other existing models. The circulation was found to increase with both the Mach number and the density ratio across the interface and was always overestimated by the models. These differences are probably caused by the presence of pulverized soap film trapped in the vortices, which reduces the motion and the strength of the resulting flow. A large number of tests are performed over a significant range of shock wave Mach numbers and density differences, with the use of high-speed imaging methods to track the vortex evolution during a single test shot. The database obtained should provide a useful tool for checking the validity of many codes and models describing the dynamics of shock/bubble interactions.
Singular waves in a magnetized pair-ion plasma
Authors: Samanta Sukanta , Misra Amar P.
Published: July 2009

The existence of singular waves along the boundary of a magnetized pair-ion plasma is proved for both plasma-metal and plasma-vacuum interfaces. Such waves are shown to propagate at the points of intersection of the complex-zone boundary and the surface wave dispersion curve in a weakly magnetized plasma. The results could be relevant for negative ion plasmas in the laboratory and space as well as for the modeling of a plasma sustained by a traveling surface wave.
Measurement of nonlinear frequency shift coefficient in spin-torque oscillators based on MgO tunnel junctions
Authors: Kudo Kiwamu , Nagasawa Tazumi , Sato Rie , Mizushima Koichi
Published: July 2009

The nonlinear frequency shift coefficient, which represents the strength of the transformation of amplitude fluctuations into phase fluctuations of an oscillator, is measured for MgO-based spin-torque oscillators by analyzing the current dependence of the power spectrum. We have observed that linewidth against inverse normalized power plots show linear behavior below and above the oscillation threshold as predicted by the analytical theories for spin-torque oscillators. The magnitude of the coefficient is determined from the ratio of the linear slopes. Small magnitude of the coefficient (∼3) has been obtained for the device exhibiting narrow linewidth (∼10 MHz) at high bias current.
Formation of multiple conductive filaments in the Cu/ZrO2:Cu/Pt device
Authors: Liu Qi , Dou Chunmeng , Wang Yan , Long Shibing , Wang Wei , Liu Ming , Zhang Manhong , Chen Junning
Published: July 2009

We report the direct electrical measurement of multiple resistance steps in the ZrO2-based solid electrolyte nonvolatile memory device using the refined dc I-V method with a very small voltage increasing rate. The results demonstrate that multiple conductive filaments are formed successively between the bottom and top metal electrodes through the insulating layer while increasing the bias voltage, which are consistent with the electrical field simulation results based on the solid electrolyte theory. The inverse relationship between resistance steps and the filament formation sequence are obtained, which helps understand the switching mechanism of the multiple conductive filaments.
A bias voltage dependent positive magnetoresistance in Cox–C1−x/Si heterostructure
Authors: Zhang Xin , Zhang Xiaozhong , Wan Caihua , Wu Lihua
Published: July 2009

Co x – C 1 − x granular films were deposited on n-type Si substrates by pulsed laser deposition method. The heterostructure, investigated in current-perpendicular-to-plane geometry, has a bias voltage dependent positive magnetoresistance (MR), and at room temperature, the MR value reaches 16% at magnetic field H=2.5 kOe and bias voltage of 6 V. All MRs have saturated behavior when H>2.5 kOe. The mechanism of this MR is attributed to that the applied magnetic field and local random magnetic field modulate the ratio of singlet and triplet spin states leading to the MR.
Conformational Analysis of 2-Formylselenophene by Means of 13C - 1H, 13C - 13C, and 77Se - 1H Spin - Spin Coupling Constants
Authors: Rusakov Yury Yu. , Krivdin Leonid B. , Istomina Natalia V. , Levanova Ekaterina P. , Levkovskaya Galina G.
Published: July 2009

Theoretical energy-based conformational analysis of 2-formylselenophene performed at the MP2/6–311G** level together with experimental measurements and SOPPA/aug-cc-pVTZ-J calculations of its 13C–1H, 13C–13C, and 77Se–1H spin–spin coupling constants showed that this compound predominantly adopts the s-cis conformation. Most of the spin–spin coupling constants under study, especially vicinal 77Se–1H couplings, demonstrate remarkable stereochemical behaviour with respect to the internal rotation of the formyl group, which is of major importance in stereochemical studies of the related selenium-containing compounds.
Solid-State and Solution-Phase Conformations of Pseudoproline-Containing Dipeptides
Authors: Clegg Jack K. , Cochrane James R. , Sayyadi Nima , Skropeta Danielle , Turner Peter , Jolliffe Katrina A.
Published: July 2009

The conformations of 14 threonine-derived pseudoproline-containing dipeptides (including four d-allo-Thr derivatives) have been investigated by NMR. In solution, the major conformer observed for all dipeptides is that in which the amide bond between the pseudoproline and the preceding amino acid is cis. For dipeptides in which the N-terminus is protected, the ratio of cis- to trans-conformers does not depend significantly on the side chain of the N-terminal amino acid, or the stereochemistry of the Thr residue. However, for dipeptides bearing a free N-terminus, there are significant differences in the ratios of cis- to trans-conformers depending on the side chain present. Three dipeptides were crystallized and their X-ray structures determined. In two cases, (benzyloxycarbonyl (Cbz)-Val-Thr(ΨMe,Mepro)-OMe and Cbz-Val-Thr(ΨMe,Mepro)-OH), the dipeptides adopt a trans-conformation in the solid state, in contrast to the structures observed in solution. In the third case, (9-fluorenylmethoxycarbonyl (Fmoc)-Val-d-allo-Thr(ΨMe,Mepro)-OH), a cis-amide geometry is observed. These structural differences are attributed to crystal-packing interactions.
Synthesis and Properties of Fullerene-Rich Dendrimers
Authors: Holler Michel , Nierengarten Jean-François
Published: July 2009

Owing to their peculiar electronic properties, fullerene derivatives are attractive building blocks for dendrimer chemistry. Whereas, for the main part, the fullerene-containing dendrimers reported so far have been prepared with a C60 core, dendritic structures with fullerene units at their surface or with C60 spheres in the dendritic branches have been more scarcely considered. This is mainly associated with the difficulties related to the synthesis of fullerene-rich molecules. In this review, the most recent developments on the molecular engineering of fullerene-rich dendrons and dendrimers are presented to illustrate the current state-of-the-art of fullerene chemistry for the preparation of new dendritic materials.
Ab Initio Studies of Carbonyl Radical Additions to Hydrazone Systems
Authors: Kyne Sara H. , Schiesser Carl H.
Published: July 2009

Ab initio and DFT calculations reveal that intermolecular radical additions of both acyl and oxyacyl radials to hydrazones occur through SOMO → π*hydrazone, πhydrazone → SOMO and LPN → SOMO interactions between the radical and the hydrazone π-system. Both acetyl and methoxycarbonyl radicals show preference for addition to the carbon end of the carbon–nitrogen π-bond. At the highest level of theory used in this study (G2//MP2(full)/6-31G*), energy barriers of 11.2 and 22.6 kJ mol–1 are calculated for acetyl radical addition to the carbon and nitrogen-ends of N-aminomethanimine respectively. The analogous energy barriers for the methoxycarbonyl radical are 4.9 and 25.7 kJ mol–1 at the same level of theory.
Gold Catalysis: Chemoselective Indolin Synthesis in the Presence of Acrylate Units
Authors: Hashmi A. Stephen K. , Wagner Sebastian , Rominger Frank
Published: July 2009

A sequence of an aza-Morita–Baylis–Hillman reaction, a simple sulfonamide propargylation, and a gold-catalyzed cycloisomerization delivers indoline derivatives with acrylate units in the side chain. The chemoselectivity in the last step is very high; out of the two C–C double bonds that are in equal distance to the alkyne, only the furan reacts, the acrylate neither participates in nor interferes with the gold catalysis.
Formal Total Synthesis of (+)-Citrafungin A
Authors: Tsegay Sammi , Hügel Helmut , Rizzacasa Mark A.
Published: July 2009

The formal total synthesis of the fungal GGTase I inhibitor (+)-citrafungin A 1 is described. The key steps include a selective vinyl anion addition of the anion derived from iodide 10 to the lactone 9 and lactonization/selective deprotection of the allylic alcohols 8 and 23 to afford the citrafungin lactone. Esterification with the isocitrate 6 afforded citrafungin A tetra-t-butyl ester 5 which completed the formal total synthesis.
A Synthetic and Computational Investigation into the Direct Synthesis of ?-Hydroxymethylated Enones from ?-Keto Phosphonates
Authors: Ryan Sarah J. , Thompson Christopher D. , Lupton David W.
Published: July 2009

The synthesis of a range of α-hydroxymethylated enones has been achieved using the Villiéras modification of the Horner–Wadsworth–Emmons (HWE) reaction. Scope, limitations, and mechanistic aspects of this reaction were investigated using a combination of synthetic and computational studies. These investigations support a Schlosser–Corey type reaction mechanism that is balanced between two pathways with the outcome influenced by the steric environment of the substrate.
Yemen’s last Zaydī Imām: the shabāb al-muʾmin, the Malāzim, and ‘hizb allāh’ in the thought of Ḥusayn Badr al-Dīn al-Ḥūthī
Authors: Lux Abdullah
Published: July 2009

Excerpted from the manuscript of a forthcoming book project, this article provides essential English-language source material on Ḥusayn Badr al-Dῑn al- Ḥῡthῑ and an alternative framework to that of the mainstream media for exploring what are likely the genuine causes and nature of the wars against Ṣaꜥdah, Yemen, undertaken with backing and technical assistance from the United States, if not direct complicity in the name of then President George W. Bush’s administration’s ‘war on terror’. In addition to shedding light on the voluminous Malāzim of Ḥusayn Badr al-Dῑn and providing analysis of its various influences including Khomeini and Lebanon’s Ḥizb Allāh, while at the same time demonstrating a lack of evidence for direct support by either Ḥizb Allaāh or Iran, the article examines the distinct Jārῡdῑ Zaydῑ nature of the only contemporary Zaydῑ political discourse and formulation of its kind, which is distinct from Twelver Shῑꜥism and antithetical to the ‘wilaāyat al-faqῑ h’ in Iran. The article examines the origins of the Lebanese group known as al-Shabā b al-Muࣿmin that would later evolve into Ḥizb Allāh and the history of Yemen’s Tanẓῑm al-Shabāb al-Muࣿmin from which al-Hῡthῑ would draw his core group of supporters, and it aims to decipher the nature of the relation between al-Hῡthῑ’s thought and Khomeini’s Islamic Revolution in Iran as well as its grounding in the Jārῡdῑ Zaydῑ sect and the Zaydῑyah at large. The article includes excerpts from an interview with Ayatollah Mu ḥammad Ḥusayn Faḍlallah on the subject, new statements from the Office of Abd al-Mālik al- Hῡthῑ in Ṣaꜥdah, and in-depth analysis of the Malāzim with exhaustive citations in translation – all never before published – all of which provide essential reading for understanding the objective historical conditions as well as the political, cultural, tribal, ideological, and sectarian dimensions of the wars against Ṣaꜥdah.
Mobile DHHC palmitoylating enzyme mediates activity-sensitive synaptic targeting of PSD-95
Authors: Noritake Jun , Fukata Yuko , Iwanaga Tsuyoshi , Hosomi Naoki , Tsutsumi Ryouhei , Matsuda Naoto , Tani Hideki , Iwanari Hiroko , Mochizuki Yasuhiro , Kodama Tatsuhiko , Matsuura Yoshiharu , Bredt David S. , Hamakubo Takao , Fukata Masaki
Published: July 2009

Protein palmitoylation is the most common posttranslational lipid modification; its reversibility mediates protein shuttling between intracellular compartments. A large family of DHHC (Asp-His-His-Cys) proteins has emerged as protein palmitoyl acyltransferases (PATs). However, mechanisms that regulate these PATs in a physiological context remain unknown. In this study, we efficiently monitored the dynamic palmitate cycling on synaptic scaffold PSD-95. We found that blocking synaptic activity rapidly induces PSD-95 palmitoylation and mediates synaptic clustering of PSD-95 and associated AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid)-type glutamate receptors. A dendritically localized DHHC2 but not the Golgi-resident DHHC3 mediates this activity-sensitive palmitoylation. Upon activity blockade, DHHC2 translocates to the postsynaptic density to transduce this effect. These data demonstrate that individual DHHC members are differentially regulated and that dynamic recruitment of protein palmitoylation machinery enables compartmentalized regulation of protein trafficking in response to extracellular signals.
Neuronal activity moves protein palmitoylation into the synapse
Authors: Dalva Matthew B.
Published: July 2009

Many neuronal proteins undergo lipid modification that regulates their function and subcellular localization. One such modification is palmitoylation, which is mediated by a large class of protein palmitoyl acyltransferases (PATs). Now, a paper in this issue (Noritake et al. 2009. J. Cell Biol. doi:10.1083/jcb.200903101) demonstrates that the localization of the PAT DHHC2 is regulated by neuronal activity and thereby selectively controls the palmitoylation and subsequent accumulation of specific proteins in the synapse.
Evaluation of a High-Throughput Protocol for Detecting Blueberry shock virus in Vaccinium Using ELISA
Authors: Sedegui Mohamed (Sid) , Osterbauer Nancy K.
Published: July 2009

The Oregon Department of Agriculture's official virus testing program for Vaccinium has grown 915% since its inception. To address this increased workload, we evaluated a high-throughput ELISA protocol that uses a 96-well format for sap extraction. To verify the efficacy of the protocol, it was used to test leaves from known infected and healthy plants (positive and negative controls) and from 940 Vaccinium plants grown in a nursery with Blueberry shock virus (BlShV) problems. Each leaf collected was cut in half; one-half was macerated in an extraction buffer using mesh sample bags and a roller press (standard protocol) and the other half was placed into 10 × 96 collection microtubes and macerated in the extraction buffer using a Mixer Mill MM300 (high-throughput protocol). All sample sap extractions were then tested with a commercial ELISA kit. In experiments with the BlShV positive and negative control plants, the high-throughput protocol had high sensitivity (100%) and specificity (100%), matching the standard protocol. In experiments with the blueberry plants of unknown BlShV infection status, the high-throughput protocol had a sensitivity of 94.85% and a specificity of 96.70%, compared to the standard protocol. It is concluded the high-throughput protocol can be used successfully with ELISA to detect BlShV in Accepted for publication 17 May 2009. Published 10 July 2009.

Accepted for publication 17 May 2009. Published 10 July 2009.
Reevaluation of a Tetraploid Wheat Population Indicates that the Tsn1–ToxA Interaction Is the Only Factor Governing Stagonospora nodorum Blotch Susceptibility
Authors: Faris Justin D. , Friesen Timothy L.
Published: July 2009

The wheat Tsn1 gene on chromosome 5B confers sensitivity to a host-selective toxin produced by the pathogens that cause tan spot and Stagonospora nodorum blotch (SNB) known as Ptr ToxA and SnToxA, respectively (hereafter referred to as ToxA). A compatible Tsn1–ToxA interaction is known to play a major role in conferring susceptibility of hexaploid (common) wheat to SNB. However, a recent study by another group suggested that the Tsn1–ToxA interaction was not relevant in conferring susceptibility of the tetraploid (durum) wheat cv. Langdon (LDN). Here, we reevaluated the role of the Tsn1–ToxA interaction in governing SNB susceptibility using the same mapping population and Stagonospora nodorum isolate (Sn2000) as were used in the previous study. Results of our quantitative trait locus analysis showed that the Tsn1 locus accounted for 95% of the variation in SNB. In addition, inoculation of the mapping population with two ToxA-knockout strains of Sn2000 revealed that the entire population was resistant. Furthermore, several LDN Tsn1-disrupted mutants were evaluated and found to be resistant to SNB. Together, these results prove unequivocally that Tsn1 is the only factor present along chromosome 5B that governs response to SNB in this population and that a compatible Tsn1–ToxA interaction is necessary for the manifestation of disease. Therefore, the results from the previous study are refuted.
Differences in the prevalence of growth, endocrine and vitamin D abnormalities among the various thalassaemia syndromes in North America
Authors: Vogiatzi Maria G. , Macklin Eric A. , Trachtenberg Felicia L. , Fung Ellen B. , Cheung Angela M. , Vichinsky Elliott , Olivieri Nancy , Kirby Melody , Kwiatkowski Janet L. , Cunningham Melody , Holm Ingrid A. , Fleisher Martin , Grady Robert W. , Peterson Charles M. , Giardina Patricia J. ,   for the Thalassemia Clinical Research Network
Published: July 2009

This study aimed to determine differences in the rates of growth, endocrine‐ and calcium‐related abnormalities in the various thalassemia syndromes in North America treated with current therapies. Medical history, physical examinations and blood and urine collections were obtained from patients with all thalassemia syndromes age 6 years and older in the Thalassemia Clinical Research Network. 361 subjects, 49% male, mean age 23·2 years (range 6·1–75 years) were studied. Approximately 25% of children and adults, regardless of the thalassemia syndrome, had short stature. Overall growth in children was mildly affected. Final height was close to midparental height (z = −0·73 ± 1·24). Patients with beta thalassemia major (TM) had higher rates of hypogonadism, multiple endocrinopathies, worse hyperglycaemia, subclinical hypoparathyroidism and hypercalciuria. Hypogonadism remained the most frequent endocrinopathy and was frequently under‐treated. 12·8% of the subjects had 25 vitamin D concentrations less than 27 nmol/l and 82% less than 75 nmol/l, regardless of the thalassemia syndrome. Adolescents had lower 25 vitamin D levels than children and adults. Compared to patients with other thalassemia syndromes, those with beta TM suffered from higher rates of multiple endocrinopathies, abnormal calcium metabolism and hypercalciuria. Vitamin D abnormalities were high among adolescents.
Automated diffusion chambers to monitor diurnal and seasonal dynamics of the soil CO2 concentration profile
Authors: Albanito F. , Saunders M. , Jones M. B.
Published: July 2009

To better understand the factors controlling carbon dioxide (CO2) production and transport in soil, we developed a new method to continuously monitor soil CO2 concentration at multiple depths, by using diffusion chambers. The soil diffusion chambers are constructed from a high‐density polyethylene cylindrical frame enclosed by a micro‐polyvinylidene difluoride flat membrane (PVDF). All chambers are linked to an infrared gas analyser positioned above‐ground through a multi‐port valve system. We set up two experimental sites for long‐term measurements of soil CO2 concentration, soil temperature and soil water content at depths of 0, 10, 20, 40 and 80 cm. The system provides the following advantages : (i) the use of the PVDF combined with the small dimensions of the diffusion chambers allows rapid diffusion of soil gas into the chambers and therefore a short equilibration time of the gas phase with the surrounding soil atmosphere, (ii) the equilibrating closed loop system allows the semi‐continuous measurement of soil profile CO2 concentrations without creating a pressure differential within the chambers, thus reducing gas concentration distortions in the soil, (iii) the small size of the closed diffusion chambers reduces the initial soil disturbance during installation, (iv) it allows sampling in wet, humid soils, including ones that are waterlogged or temporarily saturated, and (v) the chambers do not require removal for maintenance purposes and are inexpensive.
Interactions among performance capacities predict male combat outcomes in the field cricket
Authors: Hall Matthew D. , McLaren Luke , Brooks Robert C. , Lailvaux Simon P.
Published: July 2009

1. There is a growing appreciation that male fighting ability is influenced by multiple traits. In particular, studies of male combat have identified a variety of performance capacities that predict victory in conflicts between conspecifics in several animal species. However, while multiple aspects of male fighting ability are often examined with a single study, the interactions among traits are rarely considered.

2. We conducted fight trials between size‐matched males in the black field cricket, Teleogryllus commodus, with the aim of testing how two whole‐organism performance traits, jumping ability and bite force, together with weight at eclosion, interact to determine combat outcomes. We then examined the relationships between these traits and the outcome of a fight using: a univariate framework, where we examined the difference between winners and losers for each trait separately; and, a multivariate framework known as response surface analysis, where we examined how the interactions among traits predict the outcome of a fight.

3. We show that males that won fights tended to exert significantly more force when biting, but were neither better jumpers nor heavier at eclosion than their rivals. However, when we examined the effects of these three traits while statistically controlling for one another in a multiple regression, we showed that overall fighting ability depends not only on contributions of individual traits to contest resolution but also on the interactions among traits and their relationship to the capabilities of rival males. We found that the probability of winning was highest for a male with the greatest positive difference from his rival in the combination of bite force, jump power and weight at eclosion.

4. These findings highlight how studying multiple performance capabilities in isolation from each other may obscure the importance of some variables. Our multivariate analyses revealed that the interactions between multiple dimensions of performance are important in male combat. We discuss the broader implications of these findings, including the potential role of whole‐organism performance in determining male quality.
Diversity, endemism and evolution in the Coral Triangle
Authors: Briggs J. C.
Published: July 2009

In a recent paper by D. R. Bellwood and C. P. Meyer (‘Searching for heat in a marine biodiversity hotspot’, Journal of Biogeography, 2009, 36, 569–576), the authors had two evident objectives: (1) to disprove the theory that the geographical origins of reef organisms could be determined by locating concentrations of endemic species, and (2) to emphasize that the high diversity of the Coral Triangle was due to an accumulation of species from outside that area. With regard to the first point, no such theory had previously been proposed to my knowledge. Second, the accumulation theory was promoted without consideration of the facts supporting the centre of origin hypothesis, except to dismiss it by saying that it had its origin in pre‐continental drift ideas. This short response outlines the properties and evidence for the operation of centres of origin in this region.
Social calls are subject to stabilizing selection in insular bats
Authors: Russo Danilo , Teixeira Sérgio , Cistrone Luca , Jesus José , Teixeira David , Freitas Tamira , Jones Gareth
Published: July 2009

Aim  Bats communicate by emitting social calls, and these often elicit reactions in conspecifics. Many such vocalizations are species‐specific so that unambiguous signals can be transmitted and interpreted by conspecifics. In species‐rich assemblages, evolutionary pressures might prompt interspecific diversification of call structure so that communication with heterospecifics is avoided. In species‐poor island communities, where no risk of miscommunication occurs, stabilizing selection should prevail and preserve call structure and function. Call structure in island bats might be inherited from colonizers from the mainland and be maintained with little change in the absence of selection from heterospecifics. To test this hypothesis we studied Pipistrellus maderensis, an insular taxon occurring on the Madeira Archipelago, the Canary Islands and the Azores. It is closely related to one of the most widespread European pipistrelles, Pipistrellus kuhlii. Pipistrellus maderensis most probably evolved from a common ancestor shared with P. kuhlii, or from founders of that taxon that colonized the islands. We hypothesized that on Madeira Island, where no risk of ambiguous communication with heterospecifics exists, the structure and function of social calls should have been preserved by stabilizing selection. Echolocation calls, subject to different selection pressures, may instead show more pronounced differences between P. maderensis and P. kuhlii.

Location  Madeira Island (Portugal, Atlantic Ocean), central and southern Italy.

Methods  We recorded social and echolocation calls from allopatric populations of the two pipistrelles and explored interspecific differences in time and frequency characteristics. We also conducted playback experiments by broadcasting recordings of social calls from P. kuhlii and P. maderensis (taken respectively in peninsular Italy and on Madeira) and monitoring the bats’ responses.

Results  Social call structure showed a strong similarity between species, whereas echolocation calls were markedly different and exhibited a mean divergence of over 6 kHz in their frequency of maximum energy. On Madeira, P. maderensis significantly reduced flight activity when we broadcast P. kuhlii signals, as did P. kuhlii in Italy in response to P. maderensis calls.

Main conclusions  Reliable interpretation of social calls provides benefits to both the signaller and the receiver because signals help to optimize food exploitation at foraging sites. In the absence of closely related species that can emit similar calls, this advantage may have acted as a strong evolutionary pressure, stabilizing social call structure in P. maderensis in insular ecosystems with limited foraging resources.
Holocene vegetation and climate change on the Colorado Great Plains, USA, and the invasion of Colorado piñon (Pinus edulis)
Authors: Anderson R. Scott , Feiler Eric
Published: July 2009

Aim  To reconstruct the last c. 7000 years of vegetation and climate change in an unusual region of modern Great Plains grassland and scarp woodland in south‐east Colorado (USA), and to determine the late Holocene biogeography of Colorado piñon (Pinus edulis) at its easternmost extent, using a series of radiocarbon‐dated packrat (Neotoma sp.) middens.

Location  The West Carrizo Canyon drains the Chaquaqua Plateau, a plateau that projects into the western extent of the southern Great Plains grasslands in south‐eastern Colorado, USA. Elevations of the study sites are 1448 to 1525 m a.s.l. Today the plateau is mostly Juniperus scopulorum–P. edulis woodland.

Methods  Plant macrofossils and pollen assemblages were analysed from 11 14C‐dated packrat middens. Ages ranged from 5990 yr bp (6839 cal. yr bp) to 280 yr bp (485 cal. yr bp).

Results  The results presented here provide information on the establishment and expansion of Juniperus–P. edulis woodland at its eastern limits. The analysis of both plant macrofossils and pollen from the 11 middens documents changes in plant communities over the last 7000 years, and the establishment of P. edulis at its easternmost limit. Though very minor amounts of P. edulis pollen occur as early as the middle Holocene, plant macrofossils were only recovered in middens dating after c. 480 cal. yr bp.

Main conclusions  Originally, midden research suggested a late glacial refuge to the north‐east of the Carrizo Canyon site, and a middle Holocene expansion of P. edulis. Results reported here are consistent with a late Holocene expansion, here at its eastern limits, but noted elsewhere at its northern and north‐eastern limits. In general, this late Holocene expansion is consistent with pollen data from sediments in Colorado and New Mexico, and suggests that P. edulis is still expanding its range at its present extremes. This has implications for further extension of its range due to changing climatic conditions in the future.
From Africa via Europe to South America: migrational route of a species‐rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae)
Authors: Erkens Roy H. J. , Maas Jan. W. , Couvreur Thomas L. P.
Published: July 2009

Aim Several recent studies have suggested that a substantial portion of today’s plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than by vicariance. In general, three routes have been documented for the dispersal of taxa onto the South American continent: (1) via the North Atlantic Land Bridge, (2) via the Bering Land Bridge, or (3) from Africa directly onto the continent. Here a species‐rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae) is used as a model to investigate these three hypotheses.

Location The Neotropics.

Methods The phylogenetic relationships within the long‐branch clade of Annonaceae were reconstructed (using maximum parsimony, maximum likelihood and Bayesian inference) in order to gain insight in the phylogenetic position ofGuatteria. Furthermore, Bayesian molecular dating and Bayesian dispersal–vicariance (Bayes‐DIVA) analyses were undertaken.

Results Most of the relationships within the long‐branch clade of Annonaceae were reconstructed and had high support. However, the relationship between theDuguetiaclade, theXylopia–Artabotrysclade andGuatteriaremained unclear. The stem node age estimate ofGuatteriaranged between 49.2 and 51.3 Ma, whereas the crown node age estimate ranged between 11.4 and 17.8 Ma. For the ancestral area ofGuatteriaand its sister group, the area North America–Africa was reconstructed in 99% of 10,000 DIVA analyses, while South America–North America was found just 1% of the time.

Main conclusions The estimated stem to crown node ages ofGuatteriain combination with the Bayes‐DIVA analyses imply a scenario congruent with an African origin followed by dispersal across the North Atlantic Land Bridge in the early to middle Eocene and further dispersal into North and Central America (and ultimately South America) in the Miocene. The phylogenetically and morphologically isolated position of the genus is probably due to extinction of the North American and European stem lineages in the Tertiary.
Climate history, human impacts and global body size of Carnivora (Mammalia: Eutheria) at multiple evolutionary scales
Authors: Diniz‐Filho José Alexandre Felizola , Rodríguez Miguel Ángel , Bini Luis Mauricio , Olalla‐Tarraga Miguel Ángel , Cardillo Marcel , Nabout João Carlos , Hortal Joaquín , Hawkins Bradford A.
Published: July 2009

Aim One of the longest recognized patterns in macroecology, Bergmann’s rule, describes the tendency for homeothermic animals to have larger body sizes in cooler climates than their phylogenetic relatives in warmer climates. Here we provide an integrative process‐based explanation for Bergmann’s rule at the global scale for the mammal order Carnivora.

Location Global.

Methods Our database comprises the body sizes of 209 species of extant terrestrial Carnivora, which were analysed using phylogenetic autocorrelation and phylogenetic eigenvector regression. The interspecific variation in body size was partitioned into phylogenetic (P) and specific (S) components, and mean P‐ and S‐components across species were correlated with environmental variables and human occupation both globally and for regions glaciated or not during the last Ice Age.

Results Three‐quarters of the variation in body size can be explained by phylogenetic relationships among species, and the geographical pattern of mean values of the P‐component is the opposite of the pattern predicted by Bergmann’s rule. Partial regression revealed that at least 43% of global variation in the mean phylogenetic component is explained by current environmental factors. In contrast, the mean S‐component of body size shows large positive deviations from ancestors across the Holarctic, and negative deviations in southern South America, the Sahara Desert, and tropical Asia. There is a moderately strong relationship between the human footprint and body size in glaciated regions, explaining 19% of the variance of the mean P‐component. The relationship with the human footprint and the P‐component is much weaker in the rest of the world, and there is no relationship between human footprint and S‐component in any region.

Main conclusions Bergmannian clines are stronger at higher latitudes in the Northern Hemisphere because of the continuous alternation of glacial–interglacial cycles throughout the late Pliocene and Pleistocene, which generated increased species turnover, differential colonization and more intense adaptive processes soon after glaciated areas became exposed. Our analyses provide a unified explanation for an adaptive Bergmann’s rule within species and for an interspecific trend towards larger body sizes in assemblages resulting from historical changes in climate and contemporary human impacts.
Endemism and evolution in the Coral Triangle: a call for clarity
Authors: Bellwood David R. , Meyer Christopher P.
Published: July 2009

In a recent paper (Bellwood & Meyer, Journal of Biogeography, 2009, 36, 569–576), we critically evaluated the utility of marine endemics for marking the geographical origins of species. In reply, Briggs (2009) identified two issues that needed clarification: (1) whether endemics are assumed to mark the geographical origins of species or areas of exceptionally high rates of origination, and (2) whether our evaluation of the role of endemics disproves the centre of origin hypothesis. Of these two issues, the first can be clearly resolved by recourse to the original literature that explicitly states that it has been assumed that endemics do indeed mark the probable sites of origin of species. The second is equally clear: our evidence does not and can not disprove the centre of origin theory. We suggest, however, that the current data, and endemics in particular, provide limited support for centre of origin theories and that they are more consistent with some centre of accumulation theories. The Indo‐Australian Archipelago (IAA; Coral Triangle) therefore appears to be an area where species persist, a centre of survival, regardless of the site of origin of species.
Understanding measurements of intestinal permeability in healthy humans with urine lactulose and mannitol excretion
Authors: Camilleri M. , Nadeau A. , Lamsam J. , Linker Nord S. , Ryks M. , Burton D. , Sweetser S. , Zinsmeister A. R. , Singh R.
Published: July 2009

Abstract  Our aim was to understand the information from differential two‐sugar excretion (2‐SE) in measuring intestinal permeability. In a crossover study in 12 healthy volunteers, we compared urinary excretion ratios of lactulose (L) to mannitol [(M) LMR] after ingestion in liquid formulation (LF) or in delayed‐release, methacrylate‐coated capsules (CAP). Both formulations were radiolabelled. Urine was collected every 2 h from 0 to 8 h, and from 8 to 24 h. Two hours after LF, gastric residual was 15.9 ± 6.2% (SEM), and the percentage in colon was 49.6 ± 7.8%; in 11/12 participants, liquid had entered colon within 2 h. Average CAP arrival time in colon was 5.16 ± 0.46 h (mode 6 h). After LF, mannitol was extensively absorbed in the first 8 h; lactulose absorption was low thoughout the 24 h. After the LF, the LMR (geometric mean, 95% CI per h) in the 0–2 h urine was [0.08 (0.05, 0.11)], which was lower than in 8–24 h urine [0.32 (0.16, 0.46); P < 0.05]. Urine LMRs at 8–24 h were similar after LF or CAP. We concluded that, after LF, sugar excretion in 0–2 h urine may reflect both SI and colon permeability. Colonic permeability is reflected by urine sugar excretion between 6 and 24 h. CAP delivery reduces mannitol excreted at 0–6 h, compared with LF. The 0–5 or 6 h 2‐SE urine likely reflects both SI and colon permeability; the higher LMR in the 8–24 h urine relative to 0–2 h urine should be interpreted with caution and does not mean that colon is more permeable than SI.
The Arabidopsis ATRIP ortholog is required for a programmed response to replication inhibitors
Authors: Sweeney Paul R. , Britt Anne B. , Culligan Kevin M.
Published: July 2009

The programmed response to replication inhibitors in eukaryotic cells requires the protein kinase ATR (ataxia telangiectasia mutated and rad3‐related), which is activated primarily through the persistence of replication protein A (RPA)‐bound single‐stranded DNA at stalled replication forks and sites of DNA damage undergoing excision repair. Once activated, ATR initiates a cascade of events, including cell‐cycle arrest and induction of DNA repair, to mitigate the mutagenic effects of DNA replication in the presence of damage and/or blockage. While many of the molecular regulators of ATR have been determined in yeast and animal cells, little is known about ATR regulation in plants. To genetically define ATR regulatory pathways in Arabidopsis, we describe here a genetic screen for identifying mutants that display a characteristic phenotype of Arabidopsis atr null mutants – hypersensitivity to the replication blocking agent hydroxyurea (HU). Employing this screen, we isolated a novel mutant, termed hus2 (hydroxyurea‐sensitive), that displays hypersensitivity to HU, aphidicolin and ionizing radiation, similar to atr mutants. In addition, cell‐cycle progression in response to replication blocks and ionizing radiation is defective in hus2, displaying a nearly identical phenotype to atr mutants. Positional cloning of hus2 reveals a gene sequence similar to yeast Rad26/Ddc2 and ATRIP (ATR interacting protein), suggesting that hus2 encodes an Arabidopsis ATRIP ortholog.