bluuebunny/crossref_metadata_2025 huggingface dataset:
Improvement in thermal barriers to intense terahertz generation from photoconductive antennas
Authors: Ropagnol X. , Bouvier Marcel , Reid M. , Ozaki T.
Published: July 2014

We study the generation of free-space terahertz (THz) pulses at low THz frequencies using 6H-SiC and 4H-SiC photoconductive antennas. We investigate the dependence of the THz electric field radiated from the biased SiC emitters on the applied bias field and on the incident optical fluence. In this work, bias fields as high as 32 kV/cm, and optical fluences up to 2.5 mJ/cm2 (for the 400 nm laser), and 7.5 mJ/cm2 (for the 800 nm laser) were used. THz generation with back- and front-side illumination of the antennas is also examined. It is found that the SiC antenna, when illuminated from the backside, generates higher THz electric fields. The performance of 6H-SiC and ZnSe photoconductive antennas are compared. We show that, taking advantage of the superior thermal properties of SiC compare with ZnSe, the THz output power generated with the 6H-SiC photoconductive antenna under optimum conditions is 2.3 times larger that with a ZnSe photoconductive antenna.
Surface enhanced Raman scattering of 4-aminothiophenol sandwiched between Ag nanocubes and smooth Pt substrate: The effect of the thickness of Pt film
Authors: Zhu Shuangmei , Fan Chunzhen , Wang Junqiao , He Jinna , Liang Erjun , Chao Mingju
Published: July 2014

Ag nanocubes (NCs)/4-aminothiophenol (p-ATP)/smooth platinum (Pt) film (Ag-NCs @ p-ATP/Pt) sandwich structure is created for surface enhanced Raman scattering (SERS). The proposed sandwich structure is shown to exhibit better performance than the Ag-NCs only as SERS substrate. The dependence of the Raman signal intensity on the thickness of the Pt films is examined. It is shown that the Raman signal increases with the thickness of the Pt films from 42 to 90 nm, suggesting the electromagnetic coupling of the localized surface plasmons of the Ag-NCs with the surface plasmon polaritons of the underneath Pt film, which is confirmed by our numerical simulations. The SERS enhancement factor in Ag-NCs @ p-ATP/Pt is estimated to be (4.1 ± 0.2) × 106 for a Pt film of 90 nm.
Ge/SiGe quantum wells on Si(111): Growth, structural, and optical properties
Authors: Gatti E. , Isa F. , Chrastina D. , Müller Gubler E. , Pezzoli F. , Grilli E. , Isella G.
Published: July 2014

The epitaxial growth of Ge/Si0.15Ge0.85 multiple quantum wells (MQWs) on Si(111) substrates is demonstrated. A 3 μm thick reverse, double-step virtual substrate with a final composition of Si0.10Ge0.90 has been employed. High resolution XRD, TEM, AFM and defect etching analysis has been used for the study of the structural properties of the buffer and of the QWs. The QW stack is characterized by a threading dislocation density of about 3 × 107 cm−2 and an interdiffusion layer at the well/barrier interface of 2.1 nm. The quantum confined energy levels of this system have been calculated using the k·p and effective mass approximation methods. The Ge/Si0.15Ge0.85 MQWs have been characterized through absorption and photoluminescence measurements. The optical spectra have been compared with those of Ge/Si0.15Ge0.85 QWs grown on Si(001) through a thick graded virtual substrate.
Communication: Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields
Authors: Craven Galen T. , Bartsch Thomas , Hernandez Rigoberto
Published: July 2014

When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product—for example, an energy barrier—becomes time-dependent. We show that for periodic forcing the rate of barrier crossing can be determined through stability analysis of the non-autonomous transition state. Specifically, strong agreement is observed between the difference in the Floquet exponents describing stability of the transition state trajectory, which defines a recrossing-free dividing surface [G. T. Craven, T. Bartsch, and R. Hernandez, “Persistence of transition state structure in chemical reactions driven by fields oscillating in time,” Phys. Rev. E 89, 040801(R) (2014)], and the rates calculated by simulation of ensembles of trajectories. This result opens the possibility to extract rates directly from the intrinsic stability of the transition state, even when it is time-dependent, without requiring a numerically expensive simulation of the long-time dynamics of a large ensemble of trajectories.
Stoichiometry determined exchange interactions in amorphous ternary transition metal oxides: Theory and experiment
Authors: Hu Shu-jun , Yan Shi-shen , Zhang Yun-peng , Zhao Ming-wen , Kang Shi-shou , Mei Liang-mo
Published: July 2014

Amorphous transition metal oxides exhibit exotic transport and magnetic properties, while the absence of periodic structure has long been a major obstacle for the understanding of their electronic structure and exchange interaction. In this paper, we have formulated a theoretical approach, which combines the melt-quench approach and the spin dynamic Monte-Carlo simulations, and based on it, we explored amorphous Co0.5Zn0.5O1−y ternary transition metal oxides. Our theoretical results reveal that the microstructure, the magnetic properties, and the exchange interactions of Co0.5Zn0.5O1−y are strongly determined by the oxygen stoichiometry. In the oxygen-deficient sample (y > 0), we have observed the long-range ferromagnetic spin ordering which is associated with the non-stoichiometric cobalt-rich region rather than metallic clusters. On the other hand, the microstructure of stoichiometric sample takes the form of continuous random networks, and no long-range ferromagnetism has been observed in it. Magnetization characterization of experimental synthesized Co0.61Zn0.39O1−y films verifies the relation between the spin ordering and the oxygen stoichiometry. Furthermore, the temperature dependence of electrical transport shows a typical feature of semiconductors, in agreement with our theoretical results.
Remote Walker breakdown and coupling breaking in parallel nanowire systems
Authors: Krishnia S. , Purnama I. , Lew W. S.
Published: July 2014

In a multiple nanowire system, we show by micromagnetic simulations that a transverse domain wall in a current-free nanowire can undergo a remote Walker breakdown when it is coupled to a nearby current-driven domain wall. Moreover, for chirality combination with the highest coupling strength, the remote Walker breakdown preceded the current-induced Walker breakdown. The Walker breakdown limit of such coupled systems has also been shifted towards higher current densities, where beyond these, the coupling is shown to be broken.
Characterizing the hohlraum radiation via one-end driven experiments
Authors: Zhao Yiqing , Zou Shiyang , Li Sanwei , Li Zhichao , Guo Liang
Published: July 2014

A new experiment is designed and performed on the Shenguang III laser facility with the first eight available beams to characterizing the hohlraum radiation, in which the hohlraum with laser entrance holes on both ends is driven through one-end only. The experiment enables us to identify the x-ray radiations originated from the hohlraum reemission wall and high-Z bubble plasmas utilizing their position and spectral characters, which provides a better test on the associated hohlraum models. The total and M-band x-ray radiation fluxes are measured with the flat response x-ray detectors and the filtered M-band x-ray detectors, respectively. Numerical simulations are conducted with the two-dimensional radiation hydrodynamic code LARED-INTEGRATION using the multi-group radiation transfer and/or diffusion models. It is found that the experimentally measured temporal profiles and angular distributions of hohlraum radiation are in good agreement with the predictions of simulation using radiation transfer models, but differ significantly from the results obtained with the multi-group radiation diffusion calculations. We thus note that to accurately represent the hohlraum radiation, a true radiation transfer model is essential.
Extracting the emitter orientation in organic light-emitting diodes from external quantum efficiency measurements
Authors: Schmidt Tobias D. , Reichardt Lukas J. , Rausch Andreas F. , Wehrmeister Sebastian , Scholz Bert J. , Mayr Christian , Wehlus Thomas , Ciarnáin Rossá Mac , Danz Norbert , Reusch Thilo C. G. , Brütting Wolfgang
Published: July 2014

Emitter orientation will play a major role in future applications of organic light-emitting diodes due to its strong impact on the efficiency of the devices. Up to now, determining the orientation of transition dipole moments required elaborate angular-dependent measurements of the light emission pattern. In this paper, we present a simplified and straightforward method to extract the emitter orientation from external quantum efficiency measurements. We demonstrate the validity of the method on three different dye-doped emitting systems.
Wideband, thin, and polarization-insensitive perfect absorber based the double octagonal rings metamaterials and lumped resistances
Authors: Li Sijia , Gao Jun , Cao Xiangyu , Li Wenqiang , Zhang Zhao , Zhang Di
Published: July 2014

By loading the lumped resistances into the double octagonal rings metamaterials, a wideband, thin, and polarization-insensitive perfect absorber is investigated theoretically and experimentally. The perfect absorber is constructed of double octagonal rings loading the eight lumped resistances and the substrate with height of 3 mm. The effects of the double octagonal rings and eight lumped resistances are explored by absorption and the electric field distributions. The simulated results indicate that the structure obtains 9.25 GHz-wide absorption from 7.93 to 17.18 GHz with absorptivity larger than 90% at the incident angles from 0° to 20° and achieves above 12.2 GHz-wide absorption from 5.8 to 18 GHz with a full width at half maximum at wide incident angles from 0° to 70°. The fabricated metamaterial absorber device was measured and analyzed. A good agreement is observed between the simulation and the measurement.
In situ monitoring of stacking fault formation and its carrier lifetime mediation in p-type 4H-SiC
Authors: Chen Bin , Chen Jun , Yao Yuanzhao , Sekiguchi Takashi , Matsuhata Hirofumi , Okumura Hajime
Published: July 2014

Using the fine control of an electron beam (e-beam) in scanning electron microscopy with the capabilities of both electrical and optical imaging, the stacking fault (SF) formation together with its tuning of carrier lifetime was in situ monitored and investigated in p-type 4H-SiC homoepitaxial films. The SFs were formed through engineering basal plane dislocations with the energy supplied by the e-beam. The e-beam intensity required for the SF formation in the p-type films was ∼100 times higher than that in the n-type ones. The SFs reduced the minority-carrier lifetime in the p-type films, which was opposite to that observed in the n-type case. The reason for the peculiar SF behavior in the p-type 4H-SiC is discussed with the cathodoluminescence results.
Metal-semiconductor-transition observed in Bi2Ca(Sr, Ba)2Co2O8+δ single crystals
Authors: Dong Song-Tao , Zhang Bin-Bin , Zhang Lun-Yong , Chen Y. B. , Yao Shu-Hua , Zhou Jian , Zhang Shan-Tao , Gu Zheng-Bin , Chen Yan-Feng
Published: July 2014

Electrical property evolution of Bi2AE2Co2O8+δ single crystals (AE = Ca, Sr and Ba) is systematically explored. When AE changes from Ca to Ba, the electrical property of Bi2Ca2Co2O8+δ and Bi2Sr2Co2O8+δ demonstrates semiconductor-like properties. But Bi2Ba2Co2O8+δ shows the metallic behavior. Analysis of temperature-dependent resistance substantiates that from metallic Bi2Ba2Co2O8+δ to semiconductor-like Bi2Sr2Co2O8+δ can be attributed to Anderson localization. However the semiconductor behaviour of Bi2Sr2Co2O8+δ and Bi2Ca2Co2O8+δ is related to electronic correlations effect that is inferred by large negative magnetoresistance (∼70%). The theoretical electronic structures and valence X-ray photoemission spectroscopy substantiate that there is a relative large density of state around Fermi level in Bi2Ba2Co2O8+δ compared with other two compounds. It suggests that Bi2Ba2Co2O8+δ is more apt to be metal in this material system.
Contactless electronic transport in a bio-molecular junction
Authors: Hossain Faruque M. , Al-Dirini Feras , Skafidas Efstratios
Published: July 2014

Molecular electronics hold promise for next generation ultra-low power, nano-scale integrated electronics. The main challenge in molecular electronics is to make a reliable interface between molecules and metal electrodes. Interfacing metals and molecules detrimentally affects the characteristics of nano-scale molecular electronic devices. It is therefore essential to investigate alternative arrangements such as contact-less tunneling gaps wherever such configurations are feasible. We conduct ab initio density functional theory and non-equilibrium Green's functions calculations to investigate the transport properties of a biocompatible glycine molecular junction. By analyzing the localized molecular orbital energy distributions and transmission probabilities in the transport-gap, we find a glycine molecule confined between two gold electrodes, without making a contact, is energetically stable and possesses high tunneling current resembling an excellent ohmic-like interface.
Application of double femtosecond pulses for plasma harmonic generation
Authors: Ganeev R. A. , Suzuki M. , Yoneya S. , Kuroda H.
Published: July 2014

We demonstrate the harmonic generation of the femtosecond pulses propagated in the vicinity of solid targets. The harmonics were observed in the case of double-pulse scheme while using different solids (metals, nanoparticle, and microparticle powders). The efficiency and cut-off of harmonic generation using double-pulse scheme were varied depending on the target and compared with the commonly used method of the laser ablation by the picosecond pulses. The simplicity of this method allows its application in the nonlinear spectroscopy of solids.
Solid-phase characterisation of an effective household sand filter for As, Fe and Mn removal from groundwater in Vietnam
Authors: Voegelin Andreas , Kaegi Ralf , Berg Michael , Nitzsche Katja Sonja , Kappler Andreas , Lan Vi Mai , Trang Pham Thi Kim , Göttlicher Jörg , Steininger Ralph
Published: July 2014

Environmental context Household sand filters are widely used in Vietnam to remove As, Fe and Mn from groundwater used as drinking water. From the solid-phase characterisation of a sand filter that has been used for 8 years, we conclude that As and Fe are retained by a combination of fast sorption reactions, surface-catalysed Fe oxidation and mediated As co-oxidation and that microbial processes are probably involved in effective Mn retention. This study contributes to a better mechanistic understanding of filter functioning as a basis for further improvements in filter design and operation. Abstract Household sand filters are widely used in Vietnam to remove As, Fe and Mn from anoxic groundwater used as a drinking water resource. To expand the mechanistic knowledge of the filter functioning, we investigated the bulk and micrometre-scale distribution of Fe, As, P and Mn and the speciation of Fe, Mn and As in a sand filter after 8 years of operation using bulk and micro-focussed X-ray fluorescence spectrometry (XRF) and X-ray absorption spectroscopy (XAS) and scanning electron microscopy coupled with energy dispersive X-ray detection (SEM-EDX). Effective oxygenation of the anoxic groundwater enables the oxidative removal of Fe, As and Mn in the filter sand. Our results show that Fe is retained in the filter as a 2-line ferrihydrite-like FeIII-precipitate that coats sand grains, and that As accumulates dominantly as pentavalent arsenate. The very close spatial correlation of accumulated As and P with Fe throughout the filter sand and down to the micrometre-scale and the effective Fe, P and As retention at an estimated average water residence time of only 30min suggest that their uptake is governed by a combination of fast sorption reactions, surface-catalysed FeII oxidation and mediated AsIII co-oxidation. In contrast, Mn is retained in separate MnIV/III-(oxyhydr)oxide coatings and concretions, probably as a result of coupled surface-catalysed and microbial MnII oxidation. Silicate sorbed to the ferrihydrite-like FeIII-coatings inhibits their crystallisation and associated remobilisation of P and As. The periodic drainage and aeration of the filter favours the oxidation of any residual FeII and AsIII and the formation of dense Fe precipitates and may thereby contribute to effective filter operation over several years.
Development of a diurnal dehydration index for spring barley phenotyping
Authors: Rischbeck Pablo , Baresel Peter , Elsayed Salah , Mistele Bodo , Schmidhalter Urs
Published: July 2014

Spectral and thermal assessments may enable the precise, high-throughput and low-cost characterisation of traits linked to drought tolerance. However, spectral and thermal measurements of the canopy water status are influenced by the crops’ soil coverage, the size of the biomass and other properties such as the leaf angle distribution. The aim of this study was to develop a referenced spectral method that would be minimally influenced by potentially perturbing factors for retrieving the water status of differing cultivars. Sixteen spring barley cultivars were grown in field trials under imposed drought stress, natural drought stress and irrigated conditions. The relative leaf water content of barley plants declines diurnally from pre-dawn until the afternoon, and other plant traits such as the biomass change little throughout the day. As an indicator of the current drought stress, pre-dawn and afternoon values of the relative leaf water content were assessed spectrally. Diurnal changes in reflectance are only slightly influenced by other perturbing factors. A new spectral index (diurnal dehydration index) was developed by using the wavelengths 730 and 457 nm collected from an active spectrometer. This index allowed the differentiation of the drought tolerance of barley plants. The diurnal dehydration index was significantly related to final biomass, grain yield and harvest index and significantly different between cultivars. Compared with other indices, the diurnal dehydration index offered a higher stability in retrieving the water status of barley plants. Due to its diurnal assessment, the index was barely influenced by the differences in cultivars biomass at the time of measurement. It may represent a valuable tool for assessing the water status or drought tolerance in breeding nurseries.
New host records for ticks (Ixodidae) from the northern quoll (Dasyurus hallucatus) in north Queensland
Authors: Weaver Haylee J.
Published: July 2014

Ticks (Ixodidae) were collected from northern quolls (Dasyurus hallucatus) from three sites on the Atherton Tableland, north Queensland. Four species of ticks (Haemaphysalis humerosa, Ixodes fecialis, I. holocyclus and I. tasmani) were collected from quolls. Prevalence of infestation of ticks varied from 44 to 92% across the three sites. The collection of the three species of Ixodes represents new host records for D. hallucatus, thus adding valuable new details to the ecology of the parasite fauna of an endangered marsupial.
Structure–function analysis of mouse Sry reveals dual essential roles of the C-terminal polyglutamine tract in sex determination
Authors: Zhao Liang , Ng Ee Ting , Davidson Tara-Lynne , Longmuss Enya , Urschitz Johann , Elston Marlee , Moisyadi Stefan , Bowles Josephine , Koopman Peter
Published: July 2014

Significance

The sex-determining factor SRY is thought to function by up-regulating expression of its key target gene SRY-box 9 (SOX9) in pre-Sertoli cells of the developing gonads, but evidence for a transactivation domain is lacking for human SRY and is limited to in vitro evidence for mouse Sry. The latter is unusual in possessing a polyglutamine tract at its C terminus. We demonstrate, using a combination of biochemical, cell-based, and transgenic mouse assays, that this domain plays essential roles in both protein stabilization and transactivation ofSox9, and is required for male sex determination in mice. Our data indicate that mouse Sry has evolved a novel bifunctional module, revealing an unexpected level of plasticity of sex-determining mechanisms even among mammals.
Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3
Authors: Tanaka Shigeru , Suto Akira , Iwamoto Taro , Kashiwakuma Daisuke , Kagami Shin-ichiro , Suzuki Kotaro , Takatori Hiroaki , Tamachi Tomohiro , Hirose Koichi , Onodera Atsushi , Suzuki Junpei , Ohara Osamu , Yamashita Masakatsu , Nakayama Toshinori , Nakajima Hiroshi
Published: July 2014

Stat3 signaling is essential for the induction of RORγt and subsequent Th17 cell differentiation. However, the downstream targets of Stat3 for RORγt expression remain largely unknown. We show here that a novel isoform of Sox5, named Sox5t, is induced in Th17 cells in a Stat3-dependent manner. In vivo, T cell–specific Sox5-deficient mice exhibit impaired Th17 cell differentiation and are resistant to experimental autoimmune encephalomyelitis and delayed-type hypersensitivity. Retrovirus-mediated induction of Sox5 together with c-Maf induces Th17 cell differentiation even in Stat3-deficient CD4+ T cells but not in RORγt-deficient CD4+ T cells, indicating that Sox5 and c-Maf induce Th17 cell differentiation as downstream effectors of Stat3 and as upstream inducers of RORγt. Moreover, Sox5 physically associates with c-Maf via the HMG domain of Sox5 and DNA-binding domain of c-Maf, and Sox5 together with c-Maf directly activates the promoter of RORγt in CD4+ T cells. Collectively, our results suggest that Sox5 and c-Maf cooperatively induce Th17 cell differentiation via the induction of RORγt as downstream targets of Stat3.
Mechanisms of action of therapeutic amyloidogenic hexapeptides in amelioration of inflammatory brain disease
Authors: Kurnellas Michael P. , Schartner Jill M. , Fathman C. Garrison , Jagger Ann , Steinman Lawrence , Rothbard Jonathan B.
Published: July 2014

Amyloid fibrils composed of peptides as short as six amino acids are effective therapeutics for experimental autoimmune encephalomyelitis (EAE). Immunosuppression arises from at least two pathways: (1) expression of type 1 IFN by pDCs, which were induced by neutrophil extracellular traps arising from the endocytosis of the fibrils; and (2) the reduced expression of IFN-γ, TNF, and IL-6. The two independent pathways stimulated by the fibrils can act in concert to be immunosuppressive in Th1 indications, or in opposition, resulting in inflammation when Th17 T lymphocytes are predominant. The generation of type 1 IFN can be minimized by using polar, nonionizable, amyloidogenic peptides, which are effective in both Th1 and Th17 polarized EAE.
Marcabru's
Estornel
: On Ventriloquists, or, The Art of Putting Words in your Belly
Authors: Bruckner Matilda Tomaryn
Published: July 2014

Marcabru's ‘starling songs’,
Estornel, cueill ta volada
and
Ges l'estornels no·n s'ublida
, set up a dialogue among multiple speakers — animal and human — who interact with the troubadour's own plural identity as poet, composer, performer, and persona. Focusing on his ventriloquistic acrobatics, I examine how Marcabru's piebald art, embedded in the interplay between performance and reception, mixes courtly seduction and sexual innuendo to stage a burlesque morality play that slips comically among shifting and elusive identities.
A Comparison of Implants Used in Open-Door Laminoplasty
Authors: Tabaraee Ehsan , Mummaneni Praveen , Abdul-Jabbar Amir , Shearer David , Roy Esha , Amin Beejal , Ames Christopher , Burch Shane , Deviren Vedat , Berven Sigurd , Hu Serena , Chou Dean , Tay Bobby K.
Published: July 2014

Study Design:

A retrospective case-controlled study.

Summary of Background Data:

Open-door laminoplasty has been successfully used to address cervical spondylotic myelopathy and ossification of the posterior longitudinal ligament. Two common implants include rib allograft struts and metallic miniplates.

Objective:

The goals of this study were to compare outcomes, complications, and costs associated with these 2 implants.

Methods:

A retrospective review was done on 51 patients with allograft struts and 55 patients with miniplates. Primary outcomes were neck visual analog scale (VAS) pain scores and Nurick scores. Secondary outcomes included length of the procedure, estimated blood loss, rates of complications, and the direct costs associated with the surgery and inpatient hospitalization.

Results:

There were no differences in demographic characteristics, diagnoses, comorbidities, and preoperative outcome scores between the 2 treatment groups. Mean follow-up was 27 months. The postoperative neck VAS scores and Nurick scores improved significantly from baseline to final follow-up for both groups, but there was no difference between the 2 groups. The average length of operation (161 vs. 136 min) and number of foraminotomies (2.7 vs. 1.3) were higher for the allograft group (P=0.007 and 0.0001, respectively). Among the miniplate group, there was no difference in complications but a trend for less neck pain for patients treated without hard collar at final follow-up (1.8 vs. 2.3, P=0.52). The mean direct costs of hospitalization for the miniplate group were 15% higher.

Conclusions:

Structural rib allograft struts and metallic miniplates result in similar improvements in pain and functional outcome scores with no difference in the rate of complications in short-term follow-up. Potential benefits of using a plate include shorter procedure length and less need for postoperative immobilization. When costs of bracing and operative time are included, the difference in cost between miniplates and allograft struts is negligible.
Defectors, not norm violators, are punished by third-parties
Authors: Bone Jonathan , Silva Antonio S. , Raihani Nichola J.
Published: July 2014

Punishment of defectors and cooperators is prevalent when their behaviour deviates from the social norm. Why atypical behaviour is more likely to be punished than typical behaviour remains unclear. One possible proximate explanation is that individuals simply dislike norm violators. However, an alternative possibility exists: individuals may be more likely to punish atypical behaviour, because the cost of punishment generally increases with the number of individuals that are punished. We used a public goods game with third-party punishment to test whether punishment of defectors was reduced when defecting was typical, as predicted if punishment is responsive to norm violation. The cost of punishment was fixed, regardless of the number of players punished, meaning that it was not more costly to punish typical, relative to atypical, behaviour. Under these conditions, atypical behaviour was not punished more often than typical behaviour. In fact, most punishment was targeted at defectors, irrespective of whether defecting was typical or atypical. We suggest that the reduced punishment of defectors when they are common might often be explained in terms of the costs to the punisher, rather than responses to norm violators.
The cockroachBlattella germanicaobtains nitrogen from uric acid through a metabolic pathway shared with its bacterial endosymbiont
Authors: Patiño-Navarrete Rafael , Piulachs Maria-Dolors , Belles Xavier , Moya Andrés , Latorre Amparo , Peretó Juli
Published: July 2014

Uric acid stored in the fat body of cockroaches is a nitrogen reservoir mobilized in times of scarcity. The discovery of urease inBlattabacterium cuenoti, the primary endosymbiont of cockroaches, suggests that the endosymbiont may participate in cockroach nitrogen economy. However, bacterial urease may only be one piece in the entire nitrogen recycling process from insect uric acid. Thus, in addition to the uricolytic pathway to urea, there must be glutamine synthetase assimilating the released ammonia by the urease reaction to enable the stored nitrogen to be metabolically usable. None of theBlattabacteriumgenomes sequenced to date possess genes encoding for those enzymes. To test the host's contribution to the process, we have sequenced and analysedBlattella germanicatranscriptomes from the fat body. We identified transcripts corresponding to all genes necessary for the synthesis of uric acid and its catabolism to urea, as well as for the synthesis of glutamine, asparagine, proline and glycine, i.e. the amino acids required by the endosymbiont. We also explored the changes in gene expression with different dietary protein levels. It appears that the ability to use uric acid as a nitrogen reservoir emerged in cockroaches after its age-old symbiotic association with bacteria.
Solving Wiener–Hopf problems without kernel factorization
Authors: Crowdy Darren G. , Luca Elena
Published: July 2014

A new approach to solving problems of Wiener–Hopf type is expounded by showing its implementation in two concrete and typical examples from fluid mechanics. The new method adapts mathematical ideas underlying the so-called unified transform method due to A. S. Fokas and collaborators in recent years. The method has the key advantage of avoiding what is usually the most challenging part of the usual Wiener–Hopf approach: the factorization of kernel functions into sectionally analytical functions. Two example boundary value problems, involving both harmonic and biharmonic fields, are solved in detail. The approach leads to fast and accurate schemes for evaluation of the solutions.
A new anisotropic fractional model of diffusion suitable for applications of diffusion tensor imaging in biological tissues
Authors: Hanyga Andrzej , Magin Richard L.
Published: July 2014

An anomalous anisotropic diffusion equation is constructed in which the order of the spatial pseudo-differential operator is generalized to be distributed with a directionally dependent distribution. A time fractional version of this equation is also considered. First, it is proved that the equation is positivity-preserving and properly normalized. Second, the existence of a smooth Green's function solution is proved. Finally, an expression for the diffusive flux density for this new fractional order process is calculated. This approach may find utility in modelling diffusion tensor imaging data in the white matter of the human brain where both the apparent diffusion coefficient and the order of the pseudo-differential operator are anisotropic.
Heat shock protein expression enhances heat tolerance of reptile embryos
Authors: Gao Jing , Zhang Wen , Dang Wei , Mou Yi , Gao Yuan , Sun Bao-Jun , Du Wei-Guo
Published: July 2014

The role of heat shock proteins (HSPs) in heat tolerance has been demonstrated in cultured cells and animal tissues, but rarely in whole organisms because of methodological difficulties associated with gene manipulation. By comparing HSP70 expression patterns among representative species of reptiles and birds, and by determining the effect of HSP70 overexpression on embryonic development and hatchling traits, we have identified the role of HSP70 in the heat tolerance of amniote embryos. Consistent with their thermal environment, and high incubation temperatures and heat tolerance, the embryos of birds have higher onset and maximum temperatures for induced HSP70 than do reptiles, and turtles have higher onset and maximum temperatures than do lizards. Interestingly, the trade-off between benefits and costs of HSP70 overexpression occurred between life-history stages: when turtle embryos developed at extreme high temperatures, HSP70 overexpression generated benefits by enhancing embryo heat tolerance and hatching success, but subsequently imposed costs by decreasing heat tolerance of surviving hatchlings. Taken together, the correlative and causal links between HSP70 and heat tolerance provide, to our knowledge, the first unequivocal evidence that HSP70 promotes thermal tolerance of embryos in oviparous amniotes.
Matching the supply of bacterial nutrients to the nutritional demand of the animal host
Authors: Russell Calum W. , Poliakov Anton , Haribal Meena , Jander Georg , van Wijk Klaas J. , Douglas Angela E.
Published: July 2014

Various animals derive nutrients from symbiotic microorganisms with much-reduced genomes, but it is unknown whether, and how, the supply of these nutrients is regulated. Here, we demonstrate that the production of essential amino acids (EAAs) by the bacteriumBuchnera aphidicolain the pea aphidAcyrthosiphon pisumis elevated when aphids are reared on diets from which that EAA are omitted, demonstrating thatBuchnerascale EAA production to host demand. Quantitative proteomics of bacteriocytes (host cells bearingBuchnera) revealed that these metabolic changes are not accompanied by significant change inBuchneraor host proteins, suggesting that EAA production is regulated post-translationally. Bacteriocytes in aphids reared on diet lacking the EAA methionine had elevated concentrations of both methionine and the precursor cystathionine, indicating that methionine production is promoted by precursor supply and is not subject to feedback inhibition by methionine. Furthermore, methionine production by isolatedBuchneraincreased with increasing cystathionine concentration. We propose thatBuchnerametabolism is poised for EAA production at certain maximal rates, and the realized release rate is determined by precursor supply from the host. The incidence of host regulation of symbiont nutritional function via supply of key nutritional inputs in other symbioses remains to be investigated.
Adaptive value of a predatory mouth-form in a dimorphic nematode
Authors: Serobyan Vahan , Ragsdale Erik J. , Sommer Ralf J.
Published: July 2014

Polyphenisms can be adaptations to environments that are heterogeneous in space and time, but to persist they require conditional-specific advantages. The nematode
Pristionchus pacificus
is a facultative predator that displays an evolutionarily conserved polyphenism of its mouthparts. During development,
P. pacificus
irreversibly executes either a eurystomatous (Eu) or stenostomatous (St) mouth-form, which differ in the shape and number of movable teeth. The Eu form, which has an additional tooth, is more complex than the St form and is thus more highly derived relative to species lacking teeth. Here, we investigate a putative fitness trade-off for the alternative feeding-structures of
P. pacificus
. We show that the complex Eu form confers a greater ability to kill prey. When adults were provided with a prey diet, Eu nematodes exhibited greater fitness than St nematodes by several measures, including longevity, offspring survival and fecundity when followed by bacterial feeding. However, the two mouth-forms had similar fecundity when fed ad libitum on bacteria, a condition that would confer benefit on the more rapidly developing St form. Thus, the two forms show conditional fitness advantages in different environments. This study provides, to our knowledge, the first functional context for dimorphism in a model for the genetics of plasticity.
Differences in vaginal microbiome in African American women versus women of European ancestry
Authors: Fettweis Jennifer M. , Brooks J. Paul , Serrano Myrna G. , Sheth Nihar U. , Girerd Philippe H. , Edwards David J. , Strauss Jerome F. ,   the Vaginal Microbiome Consortium, Jefferson Kimberly K. , Buck Gregory A.
Published: July 2014

Women of European ancestry are more likely to harbour aLactobacillus-dominated microbiome, whereas African American women are more likely to exhibit a diverse microbial profile. African American women are also twice as likely to be diagnosed with bacterial vaginosis and are twice as likely to experience preterm birth. The objective of this study was to further characterize and contrast the vaginal microbial profiles in African American versus European ancestry women. Through the Vaginal Human Microbiome Project at Virginia Commonwealth University, 16S rRNA gene sequence analysis was used to compare the microbiomes of vaginal samples from 1268 African American women and 416 women of European ancestry. The results confirmed significant differences in the vaginal microbiomes of the two groups and identified several taxa relevant to these differences. Major community types were dominated byGardnerella vaginalisand the uncultivated bacterial vaginosis-associated bacterium-1 (BVAB1) that were common among African Americans. Moreover, the prevalence of multiple bacterial taxa that are associated with microbial invasion of the amniotic cavity and preterm birth, includingMycoplasma,Gardnerella,PrevotellaandSneathia, differed between the two ethnic groups. We investigated the contributions of intrinsic and extrinsic factors, including pregnancy, body mass index, diet, smoking and alcohol use, number of sexual partners, and household income, to vaginal community composition. Ethnicity, pregnancy and alcohol use correlated significantly with the relative abundance of bacterial vaginosis-associated species. Trends between microbial profiles and smoking and number of sexual partners were observed; however, these associations were not statistically significant. These results support and extend previous findings that there are significant differences in the vaginal microbiome related to ethnicity and demonstrate that these differences are pronounced even in healthy women.
poRe: an R package for the visualization and analysis of nanopore sequencing data
Authors: Watson Mick , Thomson Marian , Risse Judith , Talbot Richard , Santoyo-Lopez Javier , Gharbi Karim , Blaxter Mark
Published: July 2014

Motivation

The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results

Here we present poRe, a package for the statistical software R that enables users to manipulate, organize, summarise and visualize MinION nanopore sequencing data. As a packge for R, poRe has been tested on both Windows and Linux. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device

Availability

Pre-built R packages for Windows and Linux are available under a BSD license athttp://sourceforge.net/projects/rpore/

Contact

mick.watson@roslin.ed.ac.uk
4-Methyl-N-[2-(pyridin-2-yl)ethylcarbamothioyl]benzamide
Authors: Adam Farook , Ameram Nadiah , Eltayeb Naser Eltaher
Published: July 2014

In the title compound, C16H17N3OS, the dihedral angle between the planes of the benzene and pyridine rings is 71.33 (15)°. An intramolecular N—H...O hydrogen bond is present. In the crystal, weak aromatic C—H...O hydrogen bonds link the molecules into chains extending alonga.
(E)-3-Methyl-2,6-diphenylpiperidin-4-oneO-(3-methylbenzoyl)oxime
Authors: Kathiravan V. , Krishnan K. Gokula , Mohandas T. , Thanikachalam V. , Sakthivel P.
Published: July 2014

In the title compound, C26H26N2O2, the piperidine ring exhibits a chair conformation. The phenyl rings are attached to the central heterocycle in an equatorial position. The dihedral angle between the planes of the phenyl rings is 57.58 (8)°. In the crystal, C—H...O interactions connect the molecules into zigzag chains along [001].
Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing
Authors: Panini Piyush , Venugopala K. N. , Odhav Bharti , Chopra Deepak
Published: July 2014

A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (AandB) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N—H]+...Cl−and [C—H]+...Cl−hydrogen bonds mainly stabilizes the crystal packing in both formsAandB, while in the case ofB·H2O [N—H]+...Owaterand Owater—H...Cl−hydrogen bonds along with [N—H]+...Cl−and [C—H]+...Cl−provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case ofA, form (I) (monoclinic) is more stable whereas forBit is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms ofAandBand its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. TheR/E(distance–energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organicR+and Cl−) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case ofA) or the hydrates (in the case ofB) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms ofAandBand its hydrate were observed to be different.
X-ray diffraction study of oxygen-conducting compoundsLn2Mo2O9(Ln= La, Pr)
Authors: Antipin Alexander M. , Alekseeva Olga A. , Sorokina Natalia I. , Kuskova Alexandra N. , Presniakov Michail Yu. , Kharitonova Elena P. , Voronkova Valentina I.
Published: July 2014

The La2Mo2O9(LM) and Pr2Mo2O9(PM) single crystals are studied using precision X-ray diffraction and high-resolution transmission microscopy at room temperature. The crystal structures are determined in the space groupP213. La and Pr atoms, as well as Mo1 and O1 atoms, are located in the vicinity of the threefold axes rather than on the axes as in the high-temperature cubic phase. In both structures studied, the O2 and O3 positions are partially occupied. The coexistence of different configurations of the Mo coordination environment facilitates the oxygen-ion migration in the structure. Based on the X-ray data, the activation energies of O atoms are calculated and the migration paths of oxygen ions in the structures are analysed. The conductivity of PM crystals is close to that of LM crystals. The O2 and O3 atoms are the main contributors to the ion conductivity of LM and PM.
Mean bond-length variation in crystal structures: a bond-valence approach
Authors: Bosi Ferdinando
Published: July 2014

The distortion theorem of the bond-valence theory predicts that the mean bond length 〈D〉 increases with increasing deviation of the individual bond lengths from their mean value according to the equation 〈D〉 = (D′ + ΔD), whereD′ is the length found in a polyhedron having equivalent bonds and ΔDis the bond distortion. For a given atom,D′ is expected to be similar from one structure to another, whereas 〈D〉 should vary as a function of ΔD. However, in several crystal structures 〈D〉 significantly varies without any relevant contribution from ΔD. In accordance with bond-valence theory, 〈D〉 variation is described here by a new equation: 〈D〉 = (DRU + ΔDtop + ΔDiso + ΔDaniso + ΔDelec), whereDRUis a constant related to the type of cation and coordination environment, ΔDtopis the topological distortion related to the way the atoms are linked, ΔDisois an isotropic effect of compression (or stretching) in the bonds produced by steric strain and represents the same increase (or decrease) in all the bond lengths in the coordination sphere, ΔDanisois the distortion produced by compression and stretching of bonds in the same coordination sphere, ΔDelecis the distortion produced by electronic effects. If present, ΔDeleccan be combined with ΔDanisobecause they lead to the same kind of distortions in line with the distortion theorem. EachD-index, in the new equation, corresponds to an algebraic expression containing experimental and theoretical bond valences. On the basis of this study, the ΔDindex defined in bond valence theory is a result of both the bond topology and the distortion theorem (ΔD= ΔDtop + ΔDaniso + ΔDelec), andD′ is a result of the compression, or stretching, of bonds (D′ =DRU + ΔDiso). The deficiencies present in the bond-valence theory in explaining mean bond-length variations can therefore be overcome, and the observed variations of 〈D〉 in crystal structures can be described by a self-consistent model.
Sixth blind test of organic crystal-structure prediction methods
Authors: Groom Colin R. , Reilly Anthony M.
Published: July 2014

Over the past 15 years progress in predicting crystal structures of small organic molecules has been charted by a series of blind tests hosted by the Cambridge Crystallographic Data Centre. This letter announces a sixth blind test to take place between September 2014 and August 2015, giving details of the target systems and the revised procedure. We hope that as many methods as possible will be assessed and benchmarked in this new blind test.
Heterocyclic tautomerism: reassignment of two crystal structures of 2-amino-1,3-thiazolidin-4-one derivatives
Authors: Gzella Andrzej K. , Kowiel Marcin , Suseł Aneta , Wojtyra Magdalena N. , Lesyk Roman
Published: July 2014

The structures of 5-(2-hydroxyethyl)-2-[(pyridin-2-yl)amino]-1,3-thiazolidin-4-one, C10H11N3O2S, (I), and ethyl 4-[(4-oxo-1,3-thiazolidin-2-yl)amino]benzoate, C12H12N2O3S, (II), which are identical to the entries with refcodes GACXOZ [Váňaet al.(2009).J. Heterocycl. Chem.46, 635–639] and HEGLUC [Behbehani & Ibrahim (2012).Molecules,17, 6362–6385], respectively, in the Cambridge Structural Database [Allen (2002).Acta Cryst.B58, 380–388], have been redetermined at 130 K. This structural study shows that both investigated compounds exist in their crystal structures as the tautomer with the carbonyl–imine group in the five-membered heterocyclic ring and an exocyclic amine N atom, rather than the previously reported tautomer with a secondary amide group and an exocyclic imine N atom. The physicochemical and spectroscopic data of the two investigated compounds are the same as those of GACXOZ and HEGLUC, respectively. In the thiazolidin-4-one system of (I), the S and chiral C atoms, along with the hydroxyethyl group, are disordered. The thiazolidin-4-one fragment takes up two alternative locations in the crystal structure, which allows the molecule to adoptRandSconfigurations. The occupancy factors of the disordered atoms are 0.883 (2) (for theRconfiguration) and 0.117 (2) (for theSconfiguration). In (I), the main factor that determines the crystal packing is a system of hydrogen bonds, involving both strong N—H...N and O—H...O and weak C—H...O hydrogen bonds, linking the molecules into a three-dimensional hydrogen-bond network. On the other hand, in (II), the molecules are linkedviaN—H...O hydrogen bonds into chains.