bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Analysis of 16 NMR‐Lipoprotein Fractions in Humans, the GOLDN Study
Authors: Kraja Aldi T. , Borecki Ingrid B. , Tsai Michael Y. , Ordovas Jose M. , Hopkins Paul N. , Lai Chao‐Qiang , Frazier‐Wood Alexis C. , Straka Robert J. , Hixson James E. , Province Michael A. , Arnett Donna K.
Published: November 2012

Sixteen nuclear magnetic resonance (NMR) spectroscopy lipoprotein measurements of more than 1,000 subjects of GOLDN study, at fasting and at 3.5 and 6 h after a postprandial fat (PPL) challenge at visits 2 and 4, before and after a 3 weeks Fenofibrate (FF) treatment, were included in 6 time‐independent multivariate factor analyses. Their top 1,541 unique SNPs were assessed for association with GOLDN NMR‐particles and classical lipids. Several SNPs with −log10p > 7.3 and MAF ≥ 0.10, mostly intergenic associated with NMR‐single traits near genes FAM84B (8q24.21), CRIPT (2p21), ACOXL (2q13), BCL2L11 (2q13), PCDH10 (4q28.3), NXPH1 (7p22), and SLC24A4 (14q32.12) in association with NMR‐LDLs; HOMER1 (5q14.2), KIT (4q11–q12), VSNL1 (2p24.3), QPRT (16p11.2), SYNPR (3p14.2), NXPH1 (7p22), NELL1 (11p15.1), and RUNX3 (1p36) with NMR‐HDLs; and DOK5‐CBLN4‐MC3R (20q13), NELL1 (11p15.1), STXBP6 (14q12), APOB (2p24‐p23), GPR133 (12q24.33), FAM84B (8q24.21) and NR5A2 (1q32.1) in association with NMR‐VLDLs particles. NMR single traits associations produced 75 % of 114 significant candidates, 7 % belonged to classical lipids and 18 % overlapped, and 16 % matched for time of discovery between NMR‐ and classical traits. Five proxy genes, (ACOXL, FAM84B, NXPH1, STK40 and VAPA) showed pleiotropic effects. While tagged for significant associations in our study and with some extra evidence from the literature, candidates as CBNL4, FAM84B, NXPH1, SLC24A4 remain unclear for their functional relation to lipid metabolism. Although GOLDN study is one of the largest in studying PPL and FF treatment effects, the relatively small samples (over 700–1,000 subjects) in association tests appeals for a replication of such a study. Thus, further investigation is needed.
Weight gain during external fixation
Authors: Culotta Brad A. , Gilbert Shawn R. , Sawyer Jeffrey R. , Ruch Alice , Sellers Thomas
Published: November 2012

Background/purpose

In our clinical practice we found that some patients treated with external fixation, especially those with Blount disease, had notable weight gain. We hypothesized that correction of Blount disease using external fixation would be associated with weight gain and that the weight gain would be greater than that seen in other patients.

Methods

This was a retrospective chart review of patients with Blount disease at two children's hospitals. Patients with Blount disease were compared to patients treated with external fixation for fracture or other deformity. The data recorded included initial and post-treatment weight and time in external fixation. Within each group pre-operative weight was compared with post-treatment weight, and weight gain was compared between groups.

Results

The study cohort comprised 39 patients with Blount disease and 13 control patients. The average age and weight of the patients with Blount disease and the controls were 12.8 years and 106.4 kg (1.7 × the 95th percentile weight for age) and 12.2 years and 52.4 kg (0.89 × the 95th percentile weight for age), respectively. Patients with Blount disease gained an average of 3.7 kg (range −12.5 to +43.1 kg) during 18 weeks of treatment (0.19 kg/week), and the controls gained an average of 4.1 kg (range −4.4 to +19 kg) over 17 weeks (0.247 kg/week). The weight gain during treatment was statistically significant for both groups, but was not statistically different between groups.

Conclusion

Patients with Blount disease as well as those with other conditions treated with prolonged external fixation experience significant weight gain which could complicate rehabilitation or return to previous activity.
Quantitative ergodic theorems for weakly integrable functions
Authors: HAYNES ALAN
Published: November 2012

Under suitable hypotheses we establish a quantitative pointwise ergodic theorem which applies to trimmed Birkhoff sums of weakly integrable functions.
Portfolio Allocation and the Vote of No Confidence
Authors: Golder Sona N. , Thomas Jacquelyn A.
Published: November 2012

There is a contradiction between theory and empirics with respect to portfolio allocation in parliamentary democracies. While the canonical model of legislative bargaining predicts the existence of a ‘formateur bonus’, empirical studies show that portfolios are allocated in a manner that favours smaller parties. This article argues that the difference between the empirical pattern and the theoretical predictions can be explained by the vote of no confidence, which provides an incentive for large formateur parties to overcompensate smaller coalition partners in exchange for their sustained support over time. This argument is tested by exploiting variations in the presence of no confidence votes across national and regional levels in France. As predicted, we find that larger formateur parties receive a greater share of portfolios if the vote of no confidence is absent than if it is present.
Tensor-based morphometry of cannabis use on brain structure in individuals at elevated genetic risk of schizophrenia
Authors: Welch K. A. , Moorhead T. W. , McIntosh A. M. , Owens D. G. C. , Johnstone E. C. , Lawrie S. M.
Published: November 2012

Background

Schizophrenia is associated with various brain structural abnormalities, including reduced volume of the hippocampi, prefrontal lobes and thalami. Cannabis use increases the risk of schizophrenia but reports of brain structural abnormalities in the cannabis-using population have not been consistent. We used automated image analysis to compare brain structural changes over time in people at elevated risk of schizophrenia for familial reasons who did and did not use cannabis.

Method

Magnetic resonance imaging (MRI) scans were obtained from subjects at high familial risk of schizophrenia at entry to the Edinburgh High Risk Study (EHRS) and approximately 2 years later. Differential grey matter (GM) loss in those exposed (n = 23) and not exposed to cannabis (n = 32) in the intervening period was compared using tensor-based morphometry (TBM).

Results

Cannabis exposure was associated with significantly greater loss of right anterior hippocampal (pcorrected = 0.029, t = 3.88) and left superior frontal lobe GM (pcorrected = 0.026, t = 4.68). The former finding remained significant even after the exclusion of individuals who had used other drugs during the inter-scan interval.

Conclusions

Using an automated analysis of longitudinal data, we demonstrate an association between cannabis use and GM loss in currently well people at familial risk of developing schizophrenia. This observation may be important in understanding the link between cannabis exposure and the subsequent development of schizophrenia.
Reflecting on the implications, problems and possibilities raised by the entrance of ‘world musics’ in music education
Authors: Wu Sinae
Published: November 2012

Since the 1960s, there has been a growing awareness of the need for cultural plurality in Europe (Drummond et al., 2005). Globalisation and technological development stimulate rapid exchanges between today's diverse and hybrid societies.
Genetic diversity among INERA-Mulungu (DR Congo) Musa spp. germplasm and their relatedness to those in Tanzania using numerical taxonomy
Authors: Nzawele D. B. , Rweyemamu C. L. , Maerere A. P.
Published: November 2012

Bananas and plantains (Musa spp.) constitute staple food for over 20 million people in Democratic Republic of Congo (DRC). Since 1960, DRC is considered as a secondary centre of plantain diversification with few unknown accessions kept in the INERA-Mulungu genebank. Through similarity coefficients, cluster (unweighted pair group method with arithmetic mean, single, complete, sequential, agglomerative, hierarchical and nested design/clustering procedure) and/or multivariate analyses, numerical morpho-taxonomy has established that this diversity is composed of 37 different accessions. Each accession expressed 98 characters among the 401 possible character states, thus providing 39,298 feature patterns (data points). The 98 characters included 32 vegetative and 66 male and female inflorescences. The accessions were clustered into three genomic groups (AAA, AAB and AABB). Subjective classification ascertained nine subgroups: AAB-Silk, AAB-Pome, AAB-Plantain, AABB-Pisang Awak, AAA-Cavendish, AAA-Ibota, AAA-Gros Michel, AAA-Green-Red and AAA-Lujugira-Mutika. Three subgroups were further divided into nine clone sets which consisted of: Dwarf and Giant Cavendish, French and Horn Plantains, and Musakala, Nfuuka, Nakitembe, Nakabululu and Beer/Mbidde within Lujugira-Mutika. Numerical morpho-taxonomy effectively indicated a relationship between the DRC and Tanzania's Musa diversity. For example, the accessions ‘Kamaramasengi’ and ‘Isangi’ were found to be similar to ‘Kisukari’ (AAB-Silk) and ‘Ngego I’ (AAB-French) common in the Tanzanian Southern Highland. Likewise, the accessions Kimalindi-fupi, Kimalindi-ndefu and Jamaica of Tanzania were duplicates of Bakurura (Kigurube), Cavendish of Butuza and Gros Michel in DRC, respectively. Moreover, numerical morpho-taxonomy confirmed the pedigree of AAB-Prata (Cibwalo) in FHIA 17 and FHIA 23 and the closeness of the ancestors of Yangambi Km5 and Gros Michel. Furthermore, numerical morpho-taxonomy established AA-Mshale malembo as one of the AAA-Lujugira-Mutika parents. Molecular investigations are finally required to confirm the genomes.
Seismic imaging of the Alpine Fault near Inchbonnie, New Zealand
Authors: Carpentier S. F. A. , Green A. G. , Langridge R. , Hurter F. , Kaiser A. , Horstmeyer H. , Finnemore M.
Published: November 2012

The transpressive Alpine Fault is the boundary between the Pacific and Australian plates across the South Island of New Zealand. Earthquakes on the Alpine Fault and related structures pose a serious risk to many urban centers, including the city of Christchurch. Although it is a major feature on satellite images, the Alpine Fault is a difficult target for surface studies along much of its length; it mostly traverses densely forested and mountainous terrain and where it occurs in the lowlands it is usually covered by recent sediments. To investigate the Alpine Fault at a rare accessible location (Inchbonnie), we have acquired high‐resolution seismic reflection data along five 380–1200 m long lines. Images produced from these data reveal a glacially overdeepened valley containing a thick sequence of diverse glacigenic sediments that have been disrupted by three en echelon strands of the principal Alpine Fault and several secondary fault strands. Based on their seismic facies, the sedimentary sequence is interpreted to comprise basal lacustrine beds overlain successively by alluvial‐colluvial deposits that possibly include the remnants of large landslides, deltaic‐fan units, and braided river gravels. Whereas the principal Alpine Fault strands disrupt the entire post‐glacial sedimentary section and likely offset basement at depths up to 400 m, most of the secondary faults either merge with the principal fault strands at shallow depths or are surficial features limited to the sedimentary section.
Constraining ozone‐precursor responsiveness using ambient measurements
Authors: Digar Antara , Cohan Daniel S. , Xiao Xue , Foley Kristen M. , Koo Bonyoung , Yarwood Greg
Published: November 2012

This study develops probabilistic estimates of ozone (O3) sensitivities to precursor emissions by incorporating uncertainties in photochemical modeling and evaluating model performance based on ground‐level observations of O3 and oxides of nitrogen (NOx). Uncertainties in model formulations and input parameters are jointly considered to identify factors that strongly influence O3 concentrations and sensitivities in the Dallas‐Fort Worth region in Texas. Weightings based on a Bayesian inference technique and screenings based on model performance and statistical tests of significance are used to generate probabilistic representation of O3 response to emissions and model input parameters. Adjusted (observation‐constrained) results favor simulations using the sixth version of the carbon bond chemical mechanism (CB6) and scaled‐up emissions of NOx, dampening the overall sensitivity of O3 to NOx and increasing the sensitivity of O3 to volatile organic compounds in the study region. This approach of using observations to adjust and constrain model simulations can provide probabilistic representations of pollutant responsiveness to emission controls that complement the results obtained from deterministic air‐quality modeling.
Sensitivity of tropical intraseasonal variability to the pattern of climate warming
Authors: Maloney Eric D. , Xie Shang‐Ping
Published: November 2012

Key Points

Future MJO activity is sensitive to the pattern of SST change

Care should be taken in future projections of MJO

Process‐oriented diagnosis of why MJO might change in future
Spin-based Optomechanics with Carbon Nanotubes
Authors: Li Jin-Jin , Zhu Ka-Di
Published: November 2012

A simple scheme for determination of spin-orbit coupling strength in spinbased optomechanics with carbon nanotubes is introduced, under the control of a strong pump field and a weak signal field. The physical mechanism comes from the phonon induced transparency (PIT), by relying on the coherent coupling of electron spin to vibrational motion of the nanotube, which is analogous to electromagnetically induced transparency (EIT) effect in atom systems. Based on this spin-nanotube optomechanical system, we also conceptually design a single photon router and a quantum microwave transistor, with ultralow pump power (~ pW) and tunable switching time, which should provide a unique platform for the study of spin-based microwave quantum optics and quantum information processing.
Intrinsic localized modes in two-dimensional vibrations of crystalline pillars and their application for sensing
Authors: Brake Daniel , Xu Huiwen , Hollowell Andrew , Balakrishnan Ganesh , Hains Chris , Marconi Mario , Putkaradze Vakhtang
Published: November 2012

We present a complete analysis on the possibility of exciting and observing the intrinsic localized modes (ILMs) in a crystalline linear array of nano pillars. We discuss the nano-fabrication techniques for these arrays and visualization procedures to observe the real-time dynamics. As a consequence, we extend previous models to the study of two dimensional vibrations to be consistent with these restrictions. For these pillars, the elastic properties and hence the dynamics depend on the pillar's shape and the orientation of the crystal axes. We show that ILMs do form in the system, but their stability, defect pinning, and reaction to friction strongly depend on the crystals properties, with the optimal dynamics only achieved in a rather small region of the parameter space. We also demonstrate fabrication techniques for these pillars and discuss the applications of these pillar arrays to sensing.
I-V characteristics of single and clustered ligand stabilized cobalt nanoparticles on highly oriented pyrolytic graphite obtained with conducting atomic force microscopy under ambient conditions
Authors: Fetting J. , Mill N. , Hütten A. , Reiss G. , Peter M. K.-H. , Mattay J.
Published: November 2012

Cobalt nanoparticles are of large interest for applications in magnetic devices and in healthcare. We studied their properties by conducting atomic force microscopy on clusters of particles and single particles deposited on highly oriented pyrolytic graphite. Topography and conductance maps have been taken simultaneously and I-V curves were measured at predefined locations on nanoparticle clusters and single nanoparticles. The I-V curves on clusters corresponded to an energy band gap in the density of states of 3.7 eV which matches the band gap of CoO nanostructures while a single particle showed only a gap of 1.3 eV in the I-V curves which is similar to the indirect band gap of Co3O4. Moreover, we found a resistive switching, i.e., a change of the clusters’ resistance during sweeping the voltage. As a reason, we suggest a transition from CoO to Co3O4 due to heating effects.
Shape and core excited resonances in electron collisions with diazines
Authors: Mašín Zdeněk , Gorfinkiel Jimena D.
Published: November 2012

We present a comprehensive ab-initio study of electron collisions with pyrazine, pyrimidine, and pyridazine. The emphasis is placed on the identification and characterization of electron resonances in these systems. We use the R-matrix method and show that analysing the time-delay reveals resonances whose signature is not visible in the eigenphase sums. In addition to the well known π* resonances below 5 eV, we find three core-excited shape resonances in the energy range 5.5–8.5 eV and a few Feshbach resonances in the dipolar molecules. Additionally, 11 resonances with little effect on the elastic scattering from ground state diazines (but significant effect in elastic collisions with the molecules in an excited state) are found and characterized. We correlate these resonances across the three molecules and discuss their possible correspondence to resonances described in earlier studies on uracil.
Local ab initio methods for calculating optical bandgaps in periodic systems. II. Periodic density fitted local configuration interaction singles method for solids
Authors: Lorenz Marco , Maschio Lorenzo , Schütz Martin , Usvyat Denis
Published: November 2012

We present a density fitted local configuration interaction singles (CIS) method for calculating optical bandgaps in 3D-periodic systems. We employ an Ewald technique to carry out infinite lattice summations for the exciton-exciton interaction, and robust product-density specific local density fitting in direct space for the electron-hole interaction. Moreover, we propose an alternative to the usual cyclic model with Born-von Karman periodic boundary conditions, the so called Wigner-Seitz supercell truncated infinite model, which exhibits much improved convergence of the CIS excitation energy with respect to the size of the supercell. Test calculations on a series of prototypical systems demonstrate that the method at the present stage can be used to calculate the excitonic bandgaps of 3D periodic systems with up to a dozen atoms in the unit cell, ranging from wide-gap insulators to semiconductors.
Second-order many-body perturbation study of ice Ih
Authors: He Xiao , Sode Olaseni , Xantheas Sotiris S. , Hirata So
Published: November 2012

Ice Ih is arguably the most important molecular crystal in nature, yet our understanding of its structural and dynamical properties is still far from complete. We present embedded-fragment calculations of the structures and vibrational spectra of the three-dimensional, proton-disordered phase of ice Ih performed at the level of second-order many-body perturbation theory with a basis-set superposition error correction. Our calculations address previous controversies such as the one related to the O–H bond length as well as the existence of two types of hydrogen bonds with strengths differing by a factor of two. For the latter, our calculations suggest that the observed spectral features arise from the directionality or the anisotropy of collective hydrogen-bond stretching vibrations rather than the previously suggested vastly different force constants. We also report a capability to efficiently compute infrared and Raman intensities of a periodic solid. Our approach reproduces the infrared and Raman spectra, the variation of inelastic neutron scattering spectra with deuterium concentration, and the anomaly of heat capacities at low temperatures for ice Ih.
Stochastic evaluation of second-order many-body perturbation energies
Authors: Willow Soohaeng Yoo , Kim Kwang S. , Hirata So
Published: November 2012

With the aid of the Laplace transform, the canonical expression of the second-order many-body perturbation correction to an electronic energy is converted into the sum of two 13-dimensional integrals, the 12-dimensional parts of which are evaluated by Monte Carlo integration. Weight functions are identified that are analytically normalizable, are finite and non-negative everywhere, and share the same singularities as the integrands. They thus generate appropriate distributions of four-electron walkers via the Metropolis algorithm, yielding correlation energies of small molecules within a few mEh of the correct values after 108 Monte Carlo steps. This algorithm does away with the integral transformation as the hotspot of the usual algorithms, has a far superior size dependence of cost, does not suffer from the sign problem of some quantum Monte Carlo methods, and potentially easily parallelizable and extensible to other more complex electron-correlation theories.
Performance investigation of p-i-n ZnO-based thin film homojunction ultraviolet photodetectors
Authors: Lin Tzu-Shun , Lee Ching-Ting
Published: November 2012

The p-i-n ZnO-based ultraviolet (UV) photodetectors was deposited using the vapor cooling condensation system. The rejection ratio between the ultraviolet and the visible was 2.82 × 103 measured at a reverse bias of −1 V. The low-frequency noise, which was dominated by the flicker noise, exhibited the noise equivalent power of 1.70 × 10−12 W and the high detectivity of 5.53 × 1011 cm Hz1/2W−1 with the illumination wavelength of 360 nm at the reverse bias voltage of −1 V. The high performances were attributed to the low defects and interface states present in the p-i-n ZnO-based ultraviolet photodetectors prepared using the vapor cooling condensation system.
First-principles study of transition metal doped Li2S as cathode materials in lithium batteries
Authors: Luo Gaixia , Zhao Jijun , Wang Baolin
Published: November 2012

The effects of transition metal (TM) doping on Li-vacancy formation energies and electrode potentials of Li2S cathode materials for lithium batteries are investigated using first-principles calculations with density functional theory. In addition, the geometric and electronic structures for 1.56 at. % Fe-doped lithium sulfide are analyzed to further reveal the TM-doping effect. We find that Evac can be only moderately enhanced by the increasing atomic number of TM dopant. The Evac is lowered from 3.37 eV in pure Li2S to about 1.11–1.23 eV in the Fe-doped compounds. Such decrease can be mainly attributed to the electronic structures. Compared with Li2S, the downtrend of reversible electrode potential (U) value in the Cu-doped systems is indistinctive with increase in the dopant contents.
Tunable-focus liquid crystal Fresnel zone lens based on harmonic diffraction
Authors: Lou Yimin , Chen Linsen , Wang Chinhua , Shen Su
Published: November 2012

We propose and demonstrate a tunable-focus liquid crystal Fresnel zone lens (TLCFZL) based on harmonic diffraction. The physical mechanism of the focus tuning is based on a multi-order diffraction process using a shallow surface relief type harmonic diffractive structure with uniform electrodes which results in significantly reduced fabrication complexity and excellent electro-optic performances. A rapid fabrication process including imprinting technique is studied, from which a high performance TLCFZL with three switchable focus lengths and high diffraction efficiency (about 70%) is fabricated. Focusing and imaging properties of the TFLCFZL are tested. The highest resolution of the lens reaches 22.6 lp/mm with low operating voltage of less than 7.2 Vrm and response time of ∼200 ms.
Exact analysis of particle dynamics in combined field of finite duration laser pulse and static axial magnetic field
Authors: Sagar Vikram , Sengupta Sudip , Kaw Predhiman
Published: November 2012

Dynamics of a charged particle is studied in the field of a relativistically intense linearly polarized finite duration laser pulse in the presence of a static axial magnetic field. For a finite duration laser pulse whose temporal shape is defined by Gaussian profile, exact analytical expressions are derived for the particle trajectory, momentum, and energy as function of laser phase. From the solutions, it is shown that, unlike for the monochromatic plane wave case, resonant phase locking time between the particle and laser pulse is finite. The net energy transferred to the particle does not increase monotonically but tends to saturate. It is further shown that appropriate tuning of cyclotron frequency of the particle with the characteristic frequency in the pulse spectrum can lead to the generation of accelerated particles with variable energies in MeV-TeV range.
Design and performance evaluation of solar dryer for drying of large cardamom (Amomum subulatum)
Authors: Seveda M. S. , Jhajharia Deepak
Published: November 2012

A solar dryer was designed, fabricated, and evaluated for drying of large cardamom (Amomum Subulatum) at College of Agricultural Engineering and Post Harvest Technology, Central Agricultural University, Ranipool (27° 20′ N, 88° 40′ E), Gangtok, Sikkim. It was observed that on an average 55.7% of higher temperature was obtained in the solar dryer over the ambient temperature. A total drying time of 24 h (3 sunny days) was required for large cardamom drying in the solar dryer to reduce the moisture content from 75.6% (w.b.) to 10.1% (w.b.) compared to that of 48 h for the open sun drying to obtain the same level of moisture contents resulting in a net saving of about 50% of drying time for the solar dryer in comparison to the open sun drying.
Reflectance continuum removal spectral index tracking the xanthophyll cycle photoprotective reactions in Norway spruce needles
Authors: Kováč Daniel , Navrátil Martin , Malenovský Zbynĕk , Štroch Michal , Špunda Vladimír , Urban Otmar
Published: November 2012

This laboratory experiment tested the ability of the spectral index called ‘area under curve normalised to maximal band depth’ (ANMB) to track dynamic changes in the xanthophyll cycle of Norway spruce (Picea abies (L.) Karsten) needles. Four-year-old spruce seedlings were gradually acclimated to different photosynthetic photon flux densities (PPFDs) and air temperature regimes. The measurements were conducted at the end of each acclimation period lasting for 11 days. A significant decline in the chlorophylls to carotenoids ratio and the increase of the amount of xanthophyll cycle pigments indicated a higher need for carotenoid-mediated photoprotection in spruce leaves acclimated to high PPFD conditions. Similarly, the photochemical reflectance index (PRI) changed from positive to negative values after changing light conditions from low to high intensity as a consequence of the increase in carotenoid content. Systematic responses of PRI to the de-epoxidation state of xanthophyll cycle pigments (DEPS) were, however, observed only during high temperature treatments and after the exposition of needles to high irradiance. The ANMB index computed from needle reflectance between 507 and 556 nm was able to track dynamic changes in DEPS without any influence induced by changing the content of leaf photosynthetic pigments (chlorophylls, carotenoids).
β-Arrestin–biased agonism as the central mechanism of action for insulin-like growth factor 1 receptor–targeting antibodies in Ewing’s sarcoma
Authors: Zheng Huiyuan , Shen Hongchang , Oprea Iulian , Worrall Claire , Stefanescu Radu , Girnita Ada , Girnita Leonard
Published: November 2012

Owing to its essential role in cancer, insulin-like growth factor type 1 receptor (IGF-1R)–targeted therapy is an exciting approach for cancer treatment. However, when translated into clinical trials, IGF-1R–specific antibodies did not fulfill expectations. Despite promising clinical responses in Ewing’s sarcoma (ES) phase I/II trials, phase III trials were discouraging, requiring bedside-to-bench translation and functional reevaluation of the drugs. The anti-IGF-1R antibody figitumumab (CP-751,871; CP) was designed as an antagonist to prevent ligand–receptor interaction but, as with all anti-IGF-1R antibodies, it induces agonist-like receptor down-regulation. We explored this paradox in a panel of ES cell lines and found their sensitivity to CP was unaffected by presence of IGF-1, countering a ligand blocking mechanism. CP induced IGF-1R/β-arrestin1 association with dual functional outcome: receptor ubiquitination and degradation and decrease in cell viability and β-arrestin1–dependent ERK signaling activation. Controlled β-arrestin1 suppression initially enhanced CP resistance. This effect was mitigated on further β-arrestin1 decrease, due to loss of CP-induced ERK activation. Confirming this, the ERK1/2 inhibitor U0126 increased sensitivity to CP. Combined, these results reveal the mechanism of CP-induced receptor down-regulation and characteristics that functionally qualify a prototypical antagonist as an IGF-1R–biased agonist: β-arrestin1 recruitment to IGF-1R as the underlying mechanism for ERK signaling activation and receptor down-regulation. We further confirmed the consequences of β-arrestin1 regulation on cell sensitivity to CP and demonstrated a therapeutic strategy to enhance response. Defining and suppressing such biased signaling represents a practical therapeutic strategy to enhance response to anti-IGF-1R therapies.
A neuropeptide circuit that coordinates sperm transfer and copulation duration in
Drosophila
Authors: Tayler Timothy D. , Pacheco Diego A. , Hergarden Anne C. , Murthy Mala , Anderson David J.
Published: November 2012

Innate behaviors are often executed in concert with accompanying physiological programs. How this coordination is achieved is poorly understood. Mating behavior and the transfer of sperm and seminal fluid (SSFT) provide a model for understanding how concerted behavioral and physiological programs are coordinated. Here we identify a male-specific neural pathway that coordinates the timing of SSFT with the duration of copulation behavior in
Drosophila.
Silencing four abdominal ganglion (AG) interneurons (INs) that contain the neuropeptide corazonin (Crz) both blocked SSFT and substantially lengthened copulation duration. Activating these Crz INs caused rapid ejaculation in isolated males, a phenotype mimicked by injection of Crz peptide. Crz promotes SSFT by activating serotonergic (5-HT) projection neurons (PNs) that innervate the accessory glands. Activation of these PNs
in copulo
caused premature SSFT and also shortened copulation duration. However, mating terminated normally when these PNs were silenced, indicating that SSFT is not required for appropriate copulation duration. Thus, the lengthened copulation duration phenotype caused by silencing Crz INs is independent of the block to SSFT. We conclude that four Crz INs independently control SSFT and copulation duration, thereby coupling the timing of these two processes.
Rotation of the head of the 30S ribosomal subunit during mRNA translocation
Authors: Guo Zhuojun , Noller Harry F.
Published: November 2012

Elongation factor-G–catalyzed translocation of mRNA and tRNAs during protein synthesis involves large-scale conformational changes in the ribosome. Formation of hybrid-state intermediates is coupled to counterclockwise (forward) rotation of the body of the 30S subunit. Recent structural studies implicate intrasubunit rotation of the 30S head in translocation. Here, we observe rotation of the head during translocation in real time using ensemble stopped-flow FRET with ribosomes containing fluorescent probes attached to specific positions in the head and body of the 30S subunit. Our results allow ordering of the rates of movement of the 30S subunit body and head during translocation: body forward > head forward > head reverse ≥ body reverse. The rate of quenching of pyrene-labeled mRNA is consistent with coupling of mRNA translocation to head rotation.
Allometric Growth in Red Porgy Larvae: Developing Morphological Indices for Mesocosm Semi-Intensive Culture
Authors: Andrade Carlos A P , Nascimento Francisco J A , Nogueira Natacha , Pimenta Filomena , Dinis Maria T , Narciso Luís
Published: November 2012

We studied the morphological development, allometric growth, and cannibalistic behavior of Red Porgy Pagrus pagrus reared in mesocosm semi-intensive culture. The study was conducted from hatching to 32 d after hatching (DAH). Red porgy ontogeny was characterized by strong positive allometric growth of body depth at anus (BDA) to 6.7 mm total length (TL) at about 21–22 DAH. The BDA combined with standard length (SL) in a morphometric index was found to be better correlated with dry weight than TL and provided an improved method to estimate larval growth. Mouth size also exhibited strong positive allometric growth at early larval stages that, together with inflation of the swim bladder, may have contributed to improve feeding ability, in preparation for the high energy demands of metamorphosis. A predictive regression model developed for cannibalism underestimated prey size. Cannibalism coincided with the development of acidic digestion and was first evident at 27 DAH as larvae reached about 23% of their maximum size variation. We hypothesize that cannibalism is associated with larval size and condition, but is prompted by physiological and energetic factors. The bivariate morphometric index developed in this study can be used to mitigate cannibalism by controlling larval size variation and improving feed supply. The morphological measurements and morphometric indices that result from this study provide important tools for improving red porgy larvae culture.
Surface Photocatalysis-TPD Spectrometer for Photochemical Kinetics
Authors: Ren Ze-feng , Guo Qing , Xu Chen-biao , Yang Wen-shao , Xiao Chun-lei , Dai Dong-xu , Yang Xue-ming
Published: November 2012

A surface photocatalysis-TPD apparatus devoted to studying kinetics and mechanism of photocatalytic processes with various signal crystal surfaces has been constructed. Extremely high vacuum (∼0.2 nPa) in the ionization region is obtained by using multiple ultrahigh vacuum pumps. Compared with similar instruments built previously by others, the H2, CH4 background in the ionization region can be reduced by about two orders of magnitude, and other residual gases in the ionization region can be reduced by about an order of magnitude. Therefore, the signal-to-noise ratio for the temperature programmed desorption (TPD) and time of flight (TOF) spectra is substantially enhanced, making experimental studies of photocatalytic processes on surfaces much easier. In this work, we describe the new apparatus in detail and present some preliminary studies on the photo-induced oxygen vacancy defects on TiO2(110) at 266 nm by using the TPD and TOF methods. Preliminary results suggest that the apparatus is a powerful tool for studying kinetics and mechanism of photochemical processes.
Raman Scattering Study on Vibrational Modes and Structure of Lanthanum Tellurite Glasses
Authors: Kalampounias Angelos G.
Published: November 2012

Raman spectra of xLa2O3-(1−x)TeO2 (x=0, 0.05, 0.10, 0.15, 0.20, and 0.25) lanthanum tellurite glasses were measured and analyzed over the entire glass-forming region in an effort to quantitatively follow the structural changes caused by lanthanum oxide variation. For the first time, systematic intensity measurements have been performed to elucidate the composition induced structural changes in the high-frequency stretching vibration region and a possible mechanism was proposed. The network structure of the glasses is formed by mixing TeO4 trigonal bipyramid and TeO3 trigonal pyramid units. The change of the lanthanum oxide content results in conversion of the TeO4 units to TeO3 units with a varying number of non-bridging oxygen atoms. Analysis of the Raman band contours in terms of vibrations due to different oxygen bridged trigonal bipyramid and trigonal pyramid tellurite structural units, allowed to calculate the relative amounts of the species involved in the structural changes with composition. The fraction of the terminal oxygen atoms has been estimated from the Raman intensities with the aid of a structural model concerning the structure of tellurite network systems. The simulation of the experimental density of lanthanum tellurite glasses with modifier content up to 25% revealed that the short range order building units assumed here are sufficient to account for the overall structure in these glasses.
Ab initioStudy on Ionization Energies of 1-Methyl-hypoxanthine
Authors: Wang Ke-dong , Yang Da-peng , Liu Yu-fang
Published: November 2012

Six low-lying tautomers of 1-methyl-hypoxanthine have been studied at the B3LYP/aug-cc-pVDZ level. Two tautomers N7H and N9H with the comparable energies are far more stable than the others. The vertical ionization energies of the tautomers calculated with ab initio electron propagator theory in the P3/aug-cc-pVDZ approximation are in agreement with the experimental data from photoelectron spectroscopy. According to the calculated relative energies and the comparison between the simulated and the experimental photoelectron spectra, it demonstrates that there are at least two tautomers of 1-methyl-hypoxanthine in the gas-phase experiments.
Direct Visual Evidence for Neutral and Charged Hexaphyrin Aromaticity with and without Keto-Defect
Authors: Zhang Shan , Song Peng , Wang Sha , Chu Yu-ling , Li Yuan-zuo , Yang Zhong , Ding Yong , Ma Feng-cai
Published: November 2012

We use density functional theory and time-dependent together with a set of extensive multidimensional visualization techniques to characterize the influence of keto effect on charge distribution at ground state and electronic transitions for neutral and charged hexaphyrin aromaticity with and without keto-defect. It is found that the aromaticity is the key factor to influence the ground state Mulliken charges distribution properties, other than the meso-aryl-substituted effect. But with the enhancement of the keto-defect, the distribution changes of Mulliken charges on the hexaphyrin groups are larger than those on the pentafluorophenyl substituted groups, following with the aromaticity changes from nonaromatic to aromatic. Furthermore, through characterizing by transition density and charge difference density, direct visual evidence for neutral and charged aromaticity with and without ketodefect can be clearly derived, and the ability of charge transfer between units of monoradical (nonaromaticity) and singlet biradical (aromaticity) forms is much stronger than that of neutral forms.
Molecular Dynamics Study of Interaction between Acrylamide Copolymers and Alumina Crystal
Authors: Wang Feng-he , Wang Feng-yun , Gong Xue-dong
Published: November 2012

Four acrylamide polymer flocculants, anionic polyacrylamide P(AA-co-AM), cationic polyacrylamide P(DMB-co-AM), nonionic polyacrylamide P(AM), and hydrophobical polyacrylamide P(OA-co-AM) have been prepared by copolymerizing with acrylic acid, cationic monomer dimethylethyl (acryloxyethyl) ammonium bromide (DMB) and hydrophobical monomer octadecyl acrylate with acrylamide. The interactions between the flocculants with the (012) surface of alumina crystal (Al2O3) have been simulated by molecular dynamics method. All the polymers can bind tightly with Al2O3 crystal, the interaction between the O of polymers and Al of the (012) surface of Al2O3 is significantly strong. The order of binding energy is as follows: P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), implying a better flocculation performance of P(DMB-co-AM) than the others. Analysis indicates that binding energy is mainly determined by Coulomb interaction. Bonds are found between the O atoms of the polymers and the Al atoms of Al2O3. The polymers' structures deform when they combine with Al2O3 crystal, but the deformation energies are low and far less than non-bonding energies. Flocculation experiments in suspension medium of 1%Kaolin show a transmittancy of 90.8% for 6 mg/L P(DMB-co-AM) and 73.0% for P(AM). The sequence of flocculation performance of four polymers is P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), which is in excellent agreement with the simulation results of binding energy.
Pervoskite-type Ba0.5Sr0.5Al0.1Fe0.9O3−δ as Intermediate-Temperature Solid Oxide Fuel Cell Cathode
Authors: Gan Yun , Xie Kui
Published: November 2012

A cobalt-free perovskite-type Ba0.5Sr0.5Al0.1Fe0.9O3−δ (BSAF) is developed and electrochemically studied as solid oxide fuel cell (SOFC) cathode. The structures, electrical conductivity, and electrode polarizations in symmetrical cell based on mixed ion conducting electrolyte were investigated, respectively. The temperature dependence of conductivity of BSAF in air shows a typical semiconductor behavior with positive temperature coefficient up to 450 °C where the conductivity reaches 14.0 S/cm while above this temperature the negative temperature coefficient dominates the total conductivity. Electrochemical characterizations show desirable polarization resistance of BSAF cathode in a symmetric cell based on mixed ion conducting electrolyte at 650–700 °C. A single SOFC with BSAF cathode shows OCV of 1.0 V and maximum output of 420 mW/cm2 at 700 °C with humidified hydrogen fuel and static air oxidant.
Effects of Metal Oxide Modifications on Photoelectrochemical Properties of Mesoporous TiO2 Nanoparticles Electrodes for Dye-Sensitized Solar Cells
Authors: Peng Tian-you , Fan Ke , Zhao De , Yu Li-juan , Li Ren-jie
Published: November 2012

Mesoporous TiO2 (m-TiO2) nanoparticles were used to prepare the porous film electrodes for dye-sensitized solar cells, and a second metal oxide (MgO, ZnO, Al2O3, or NiO) modification was carried out by dipping the m-TiO2 electrode into their respective nitrate solution followed by annealing at 500 °C. Experimental results indicated that the above second metal oxide modifications on m-TiO2 electrode are shown in all cases to act as barrier layer for the interfacial charge transfer processes, but film electron transport and interfacial charge recombination characteristics under applied bias voltage were dependent significantly on the existing states and kinds of these second metal oxides. Those changes based on second metal oxide modifications showed good correlation with the current-voltage analyses of dye-sensitized solar cell, and all modifications were found to increase the open-circuit photo-voltage in various degrees, while the MgO, ZnO, and NiO modifications result in 23%, 13%, and 6% improvement in cell conversion efficiency, respectively. The above observations indicate that controlling the charge transport and recombination is very important to improve the photovoltaic performance of TiO2-based solar cell.
Effect of Charge, Size and Temperature on Stability of Charged Colloidal Nano Particles
Authors: Golchoobi A. , Khosravi A. , Modarress H. , Ahmadzadeh A.
Published: November 2012

Molecular simulation of charged colloidal suspension is performed in NVT canonical ensemble using Monte Carlo method and primitive model. The well-known Derjaguin-Landau-Verwey-Overbeek theory is applied to account for effective interactions between particles. Effect of temperature, valance of micro-ions and the size of colloidal particles on the phase stability of the solution is investigated. The results indicate that the suspension is more stable at higher temperatures. On the other hand, for a more stable suspension to exist, lower micro-ion valance is favorable. For micro-ions of higher charge the number of aggregates and the number of particle in each of aggregate on average is higher. However for the best of our results larger colloidal particle are less stable. Comparing the results with theoretical formula considering the influence of surface curvature shows qualitative consistency.
Inverted Organic Solar Cells with Improved Performance using Varied Cathode Buffer Layers
Authors: Guan Zhi-qiang , Yu Jun-sheng , Zang Yue , Zeng Xing-xin
Published: November 2012

Organic solar cells with inverted planar heterojunction structure based on subphthalocyanine and C60 were fabricated using several kinds of materials as cathode buffer layer (CBL), including tris-8-hydroxy-quinolinato aluminum (Alq3), bathophenanthroline (Bphen), bathocuproine, 2,3,8,9,14,15-hexakis-dodecyl-sulfanyl-5,6,11,12,17,18-hexaazatrinaphthylene (HATNA), and an inorganic compound of Cs2CO3. The influence of the lowest unoccupied molecular orbital level and the electron mobility of organic CBL on the solar cells performance was compared. The results showed that Alq3, Bphen, and HATNA could significantly improve the device performance. The highest efficiency was obtained from device with annealed HATNA as CBL and increased for more than 7 times compared with device without CBL. Furthermore, the simulation results with space charge-limited current theory indicated that the Schottky barrier at the organic/electrode interface in inverted OSC structure was reduced for 27% by inserting HATNA CBL.
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
Authors: Naeem Raeece , Rashid Mamoon , Pain Arnab
Published: November 2012

Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material).

Availability:  http://cbrc.kaust.edu.sa/readscan

Contact:  arnab.pain@kaust.edu.sa or raeece.naeem@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Submerged banks in the Great Barrier Reef, Australia, greatly increase available coral reef habitat
Authors: Harris Peter T. , Bridge Thomas C.L. , Beaman Robin J. , Webster Jody M. , Nichol Scott L. , Brooke Brendan P.
Published: November 2012

Harris, P. T., Bridge, T. C. L., Beaman, R. J., Webster, J. M., Nichol, S. L., and Brooke, B. P. 2013. Submerged banks in the Great Barrier Reef, Australia, greatly increase available coral reef habitat. – ICES Journal of Marine Science, 70: 284–293. Anthropogenic global ocean warming is predicted to cause bleaching of many near-sea-surface (NSS) coral reefs, placing increased importance on deeper reef habitats to maintain coral reef biodiversity and ecosystem function. However, the location and spatial extent of many deep reef habitats is poorly known. The question arises: how common are deep reef habitats in comparison with NSS reefs? We used a dataset from the Great Barrier Reef (GBR) to show that only about 39% of available seabed on submerged banks is capped by NSS coral reefs (16 110 km2); the other 61% of bank area (25 600 km2) is submerged at a mean depth of around 27 m and represents potential deep reef habitat that is spatially distributed along the GBR continental shelf in the same latitudinal distribution as NSS reefs. Out of 25 600 km2 of submerged bank area, predictive habitat modelling indicates that more than half (around 14 000 km2) is suitable habitat for coral communities.
Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images
Authors: Karimi Nejadasl Fatemeh , Karuppasamy Manikandan , Newman Emily R. , McGeehan John E. , Ravelli Raimond B. G.
Published: November 2012

The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.