bluuebunny/crossref_metadata_2025 huggingface dataset:
Amorphization and thermal stability of aluminum-based nanoparticles prepared from the rapid cooling of nanodroplets: effect of iron addition
Authors: Xiao Shifang , Li Xiaofan , Deng Huiqiu , Deng Lei , Hu Wangyu
Published: January 2015

The Fe-centred ICO cluster network near the surface effectively promotes the glass formation ability of Fe–Al nanoalloy.
Stable Mn2+, Cu2+ and Ln3+ complexes with cyclen-based ligands functionalized with picolinate pendant arms
Authors: Rodríguez-Rodríguez Aurora , Garda Zoltán , Ruscsák Erika , Esteban-Gómez David , de Blas Andrés , Rodríguez-Blas Teresa , Lima Luís M. P. , Beyler Maryline , Tripier Raphaël , Tircsó Gyula , Platas-Iglesias Carlos
Published: January 2015

Cyclen-based ligands containing two picolinate pendant arms form Gd3+ complexes remarkably stable and inert with respect to metal ion dissociation.
1,2,4-Triazole-derived carbene complexes of gold: characterization, solid-state aggregation and ligand disproportionation
Authors: Guo Shuai , Bernhammer Jan Christopher , Huynh Han Vinh
Published: January 2015

Reversible ligand disproportionation of gold(i) mono-carbene complexes also works for weaker triazole-derived carbene ligand.
Direct multi-element analysis of plastic materials via solid sampling electrothermal vaporization inductively coupled plasma optical emission spectroscopy
Authors: Börno F. , Richter S. , Deiting D. , Jakubowski N. , Panne U.
Published: January 2015

How a plastic duck fits in the oven?
A Merrifield resin supported Pd–NHC complex with a spacer(Pd–NHC@SP–PS) for the Sonogashira coupling reaction under copper- and solvent-free conditions
Authors: Jadhav Sanjay N. , Kumbhar Arjun S. , Mali Sawanta S. , Hong Chang Kook , Salunkhe Rajashri S.
Published: January 2015

Synthetic applications of a polymer supported air-stable palladium NHC complex with a spacer (catalyst6, Pd–NHC@SP–PS) and without a spacer (catalyst7, Pd–NHC@PS) have been studied for the Sonogashira cross-coupling reaction.
Pd(ii)-catalyzed, controllable C–H mono-/diarylation of aryl tetrazoles: concise synthesis of Losartan
Authors: Ding Yan-Jun , Li Yan , Dai Sheng-Yu , Lan Quan , Wang Xi-Sheng
Published: January 2015

A palladium(ii)-catalyzed C–H arylation directed by tetrazole has been developed with excellent mono-/di-selectivity through adjustment of the protecting site on the tetrazole ring.
Copper(ii) bromide-catalyzed intramolecular decarboxylative functionalization to form a C(sp3)–O bond for the synthesis of furo[3,2-c]coumarins
Authors: Zhang W. L. , Yue S. N. , Shen Y. M. , Hu H. Y. , Meng Q.-H. , Wu H. , Liu Y.
Published: January 2015

Copper(ii) bromide-catalyzed intramolecular decarboxylative functionalization to form a C(sp3)–O bond has been developed.
Enantioselective synthesis of 4-substituted tetrahydroisoquinolines via palladium-catalyzed intramolecular Friedel–Crafts type allylic alkylation of phenols
Authors: Zhao Zheng-Le , Xu Qing-Long , Gu Qing , Wu Xin-Yan , You Shu-Li
Published: January 2015

Pd-catalyzed asymmetric intramolecular allylic alkylation reaction of phenols was developed, affording C4 substituted tetrahydroisoquinolines in moderate to excellent yields, enantioselectivity and regioselectivity.
Silver nanoparticles supported on silica-coated ferrite as magnetic and reusable catalysts for oxidant-free alcohol dehydrogenation
Authors: Bayat Ahmad , Shakourian-Fard Mehdi , Ehyaei Nona , Mahmoodi Hashemi Mohammad
Published: January 2015

The oxidant-free dehydrogenation of alcohols to corresponding carbonyl compounds has been performed by using silver (0) nanoparticles supported on silica-coated ferrite as an efficient and recyclable heterogeneous catalyst.
Chemical vapor infiltration tailored hierarchical porous CNTs/C composite spheres fabricated by freeze casting and their adsorption properties
Authors: Wang Junjie , Gong Qianming , Zhuang Daming , Liang Ji
Published: January 2015

CNTs/carbon composite spheres with hierarchical porous structure were prepared by freeze casting and then tailored by CVI and steam activation.
SlyD-dependent nickel delivery limits maturation of [NiFe]-hydrogenases in late-stationary phase Escherichia coli cells
Authors: Pinske Constanze , Sargent Frank , Sawers R. Gary
Published: January 2015

The metallochaperone SlyD is essential for nickel delivery to hydrogenase in stationary phaseE. colicells.
Synthesis of new generation triazolyl- and isoxazolyl-containing 6-nitro-2,3-dihydroimidazooxazoles as anti-TB agents: in vitro, structure–activity relationship, pharmacokinetics and in vivo evaluation
Authors: Munagala Gurunadham , Yempalla Kushalava Reddy , Singh Samsher , Sharma Sumit , Kalia Nitin Pal , Rajput Vikrant Singh , Kumar Sunil , Sawant Sanghapal D. , Khan Inshad Ali , Vishwakarma Ram A. , Singh Parvinder Pal
Published: January 2015

Promising nitroimidazoloxazole scaffold gives another novel triazolyl-containing 6-nitro-2,3-dihydroimidazooxazole as anti-TB lead.
All-optical switching of localized surface plasmon resonance in single gold nanosandwich using GeSbTe film as an active medium
Authors: Hira T. , Homma T. , Uchiyama T. , Kuwamura K. , Kihara Y. , Saiki T.
Published: January 2015

Localized surface plasmon resonance (LSPR) switching was investigated in a Au/GeSbTe/Au nanosandwich as a key active element for plasmonic integrated circuits and devices. Near-infrared single-particle spectroscopy was conducted to examine the interaction of a Au nanorod (AuNR) and Au film, between which a GeSbTe layer was incorporated as an active phase-change media. Numerical calculation revealed that hybridized modes of the AuNR and Au film exhibit a significant change of scattering intensity with the phase change. In particular, the antisymmetric (magnetic resonance) mode can be modulated effectively by the extinction coefficient of GST, as well as its refractive index. Experimental demonstration of the switching operation was performed by alternate irradiation with a picosecond pulsed laser for amorphization and a continuous wave laser for crystallization. Repeatable modulation was obtained by monitoring the scattering light around the LSPR peak at λ = 1070 nm.
Comparison of multi-fluid moment models with particle-in-cell simulations of collisionless magnetic reconnection
Authors: Wang Liang , Hakim Ammar H. , Bhattacharjee A. , Germaschewski K.
Published: January 2015

We introduce an extensible multi-fluid moment model in the context of collisionless magnetic reconnection. This model evolves full Maxwell equations and simultaneously moments of the Vlasov-Maxwell equation for each species in the plasma. Effects like electron inertia and pressure gradient are self-consistently embedded in the resulting multi-fluid moment equations, without the need to explicitly solving a generalized Ohm's law. Two limits of the multi-fluid moment model are discussed, namely, the five-moment limit that evolves a scalar pressures for each species and the ten-moment limit that evolves the full anisotropic, non-gyrotropic pressure tensor for each species. We first demonstrate analytically and numerically that the five-moment model reduces to the widely used Hall magnetohydrodynamics (Hall MHD) model under the assumptions of vanishing electron inertia, infinite speed of light, and quasi-neutrality. Then, we compare ten-moment and fully kinetic particle-in-cell (PIC) simulations of a large scale Harris sheet reconnection problem, where the ten-moment equations are closed with a local linear collisionless approximation for the heat flux. The ten-moment simulation gives reasonable agreement with the PIC results regarding the structures and magnitudes of the electron flows, the polarities and magnitudes of elements of the electron pressure tensor, and the decomposition of the generalized Ohm's law. Possible ways to improve the simple local closure towards a nonlocal fully three-dimensional closure are also discussed.
Additive to regulate the perovskite crystal film growth in planar heterojunction solar cells
Authors: Song Xin , Wang Weiwei , Sun Po , Ma Wanli , Chen Zhi-Kuan
Published: January 2015

We reported a planar heterojunction perovskite solar cell fabricated from MAPbI3−xClx perovskite precursor solution containing 1-chloronaphthalene (CN) additive. The MAPbI3−xClx perovskite films have been characterized by UV-vis, SEM, XRD, and steady-state photoluminescence (PL). UV-vis absorption spectra measurement shows that the absorbance of the film with CN additive is significantly higher than the pristine film and the absorption peak is red shift by 30 nm, indicating the perovskite film with additive possessing better crystal structures. In-situ XRD study of the perovskite films with additive demonstrated intense diffraction peaks from MAPbI3−xClx perovskite crystal planes of (110), (220), and (330). SEM images of the films with additive indicated the films were more smooth and homogenous with fewer pin-holes and voids and better surface coverage than the pristine films. These results implied that the additive CN is beneficial to regulate the crystallization transformation kinetics of perovskite to form high quality crystal films. The steady-state PL measurement suggested that the films with additive contained less charge traps and defects. The planar heterojunction perovskite solar cells fabricated from perovskite precursor solution containing CN additive demonstrated 30% enhancement in performance compared to the devices with pristine films. The improvement in device efficiency is mainly attributed to the good crystal structures, more homogenous film morphology, and also fewer trap centers and defects in the films with the additive.
A detailed study of magnetization reversal in individual Ni nanowires
Authors: Vilanova Vidal Enrique , Ivanov Yurii P. , Mohammed Hanan , Kosel Jürgen
Published: January 2015

Magnetic nanowires have emerged as essential components for a broad range of applications. In many cases, a key property of these components is the switching field, which is studied as a function of the angle between the field and the nanowire. We found remarkable differences of up to 100% between the switching fields of different nanowires from the same fabrication batch. Our experimental results and micromagnetic simulations indicate that the nanowires exhibit a single domain behavior and that the switching mechanism includes vortex domain wall motion across the nanowire. The differences between the switching fields are attributed to different cross-sections of the nanowires, as found by electron microscopy. While a circular cross-section yields the smallest switching field values, any deviation from this shape results in an increase of the switching field. The shape of the nanowires' cross-sections is thus a critical parameter that has not been previously taken into account.
Non-linear radial spinwave modes in thin magnetic disks
Authors: Helsen M. , Gangwar A. , De Clercq J. , Vansteenkiste A. , Weigand M. , Back C. H. , Van Waeyenberge B.
Published: January 2015

We present an experimental investigation of radial spin-wave modes in magnetic nano-disks with a vortex ground state. The spin-wave amplitude was measured using a frequency-resolved magneto-optical spectrum analyzer, allowing for high-resolution resonance curves to be recorded. It was found that with increasing excitation amplitude up to about 10 mT, the lowest-order mode behaves strongly non-linearly as the mode frequency redshifts and the resonance peak strongly deforms. This behavior was quantitatively reproduced by micromagnetic simulations. Micromagnetic simulations showed that at higher excitation amplitudes, the spinwaves are transformed into a soliton by self-focusing, and collapse onto the vortex core, dispersing the energy in short-wavelength spinwaves. Additionally, this process can lead to switching of the vortex polarization through the injection of a Bloch point.
Enhanced cryogenic magnetocaloric effect in Eu8Ga16Ge30 clathrate nanocrystals
Authors: Biswas Anis , Chandra Sayan , Stefanoski Stevce , Blázquez J. S. , Ipus J. J. , Conde A. , Phan M. H. , Franco V. , Nolas G. S. , Srikanth H.
Published: January 2015

We observe an enhanced magnetic entropy change (−ΔSM) at cryogenic temperatures (T < 20 K) in Eu8Ga16Ge30 clathrate (type-I) nanocrystals prepared by a ball milling method. With reduction in the crystal size to 15 nm, −ΔSM is enhanced at low temperatures, reaching the highest value (∼10 J/kg K) at 5 K for a field change of 5 T. For all samples investigated, there is a cross-over temperature (∼25 K) in −ΔSM (T) above which −ΔSM decreases with crystal size, opposite to that observed at low temperatures. A careful analysis of the magnetic and magnetocaloric data reveals that as the crystal size decreases the magnetic interaction between Eu2+ ions on the Eu2 site governing the primary ferromagnetic transition at ∼35 K becomes gradually weaker, in effect, altering the interaction between Eu2+ ions occupying the Eu1 and Eu2 sites responsible for the secondary ferromagnetic transition at 15 K. As a result, we have observed a strong change in magnetization and the enhancement of −ΔSM at low temperature.
VEGF-A modulates expression of inhibitory checkpoints on CD8+ T cells in tumors
Authors: Voron Thibault , Colussi Orianne , Marcheteau Elie , Pernot Simon , Nizard Mevyn , Pointet Anne-Laure , Latreche Sabrina , Bergaya Sonia , Benhamouda Nadine , Tanchot Corinne , Stockmann Christian , Combe Pierre , Berger Anne , Zinzindohoue Franck , Yagita Hideo , Tartour Eric , Taieb Julien , Terme Magali
Published: January 2015

Immune escape is a prerequisite for tumor development. To avoid the immune system, tumors develop different mechanisms, including T cell exhaustion, which is characterized by expression of immune inhibitory receptors, such as PD-1, CTLA-4, Tim-3, and a progressive loss of function. The recent development of therapies targeting PD-1 and CTLA-4 have raised great interest since they induced long-lasting objective responses in patients suffering from advanced metastatic tumors. However, the regulation of PD-1 expression, and thereby of exhaustion, is unclear. VEGF-A, a proangiogenic molecule produced by the tumors, plays a key role in the development of an immunosuppressive microenvironment. We report in the present work that VEGF-A produced in the tumor microenvironment enhances expression of PD-1 and other inhibitory checkpoints involved in CD8+ T cell exhaustion, which could be reverted by anti-angiogenic agents targeting VEGF-A–VEGFR. In view of these results, association of anti-angiogenic molecules with immunomodulators of inhibitory checkpoints may be of particular interest in VEGF-A-producing tumors.
Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering
Authors: Aibar Sara , Fontanillo Celia , Droste Conrad , De Las Rivas Javier
Published: January 2015

Summary: Functional Gene Networks (FGNet) is an R/Bioconductor package that generates gene networks derived from the results of functional enrichment analysis (FEA) and annotation clustering. The sets of genes enriched with specific biological terms (obtained from a FEA platform) are transformed into a network by establishing links between genes based on common functional annotations and common clusters. The network provides a new view of FEA results revealing gene modules with similar functions and genes that are related to multiple functions. In addition to building the functional network, FGNet analyses the similarity between the groups of genes and provides a distance heatmap and a bipartite network of functionally overlapping genes. The application includes an interface to directly perform FEA queries using different external tools: DAVID, GeneTerm Linker, TopGO or GAGE; and a graphical interface to facilitate the use.

Availability and implementation:  FGNet is available in Bioconductor, including a tutorial. URL: http://bioconductor.org/packages/release/bioc/html/FGNet.html

Contact:  jrivas@usal.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Miltefosine for Visceral and Cutaneous Leishmaniasis: Drug Characteristics and Evidence-Based Treatment Recommendations
Authors: Monge-Maillo Begoña , López-Vélez Rogelio
Published: January 2015

Miltefosine is the only recognized oral agent with potential to treat leishmaniasis. Miltefosine had demonstrated very good cure rates for visceral leishmaniasis (VL) in India, Nepal, and Bangladesh, but high rates of clinical failures have been recently reported. Moderate efficacy has been observed for VL in East Africa, whereas data from Mediterranean countries and Latin America are scarce. Results have not been very promising for patients coinfected with VL and human immunodeficiency virus. However, miltefosine's long half-life and its oral administration could make it a good option for maintenance prophylaxis. Good evidence of efficacy has been documented in Old World cutaneous leishmaniasis (CL), and different cure rates among New World CL have been obtained depending on the geographical areas and species involved. Appropriate regimens for New World mucocutaneous leishmaniasis need to be established, although longer treatment duration seems to confer better results. Strategies to prevent the development and spread of miltefosine resistance are urgently needed.
Myocardial Infarction Among Danish HIV-Infected Individuals: Population-Attributable Fractions Associated With Smoking
Authors: Rasmussen Line D. , Helleberg Marie , May Margaret T. , Afzal Shoaib , Kronborg Gitte , Larsen Carsten S. , Pedersen Court , Gerstoft Jan , Nordestgaard Børge G. , Obel Niels
Published: January 2015

Background.  Human immunodeficiency virus-infected individuals have increased risk of myocardial infarction (MI); however, the contribution from smoking and potentiating effects of HIV are controversial.

Methods.  From the Danish HIV Cohort Study and the Copenhagen General Population Study, we identified 3251 HIV-infected individuals and 13 004 population controls matched on age and gender. Data on MI were obtained from the National Hospital Registry and the National Registry of Causes of Death. We calculated adjusted incidence rate ratios (aIRR) for risk of MI and population-attributable fractions (PAF) of MI associated with smoking.

Results.  In never smokers, HIV was not associated with an increased risk of MI (aIRR, 1.01; 95% confidence interval [CI], .41–2.54). In previous and current smokers, HIV was associated with a substantially increased risk of MI (aIRR, 1.78; 95% CI, .75–4.24 and aIRR, 2.83; 95% CI, 1.71–4.70). The PAF associated with ever smoking (previous or current) was 72% (95% CI, 55%–82%) for HIV-infected individuals and 24% (95% CI, 3%–40%) for population controls. If all current smokers stopped smoking, 42% (95% CI, 21%–57%) and 21% (95% CI, 12%–28%) of all MIs could potentially be avoided in these 2 populations.

Conclusions.  Smoking is associated with a higher risk of MI in the HIV-infected population than in the general population. Approximately 3 of 4 MIs among HIV-infected individuals are associated with ever smoking compared with only 1 of 4 MIs among population controls. Smoking cessation could potentially prevent more than 40% of MIs among HIV-infected individuals, and smoking cessation should be a primary focus in modern HIV care.
Extended-Spectrum β-Lactamase–Producing Enterobacteriaceae in Children: Old Foe, Emerging Threat
Authors: Lukac Paul J. , Bonomo Robert A. , Logan Latania K.
Published: January 2015

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae present an ever-growing burden in the hospital and community settings, across all ages and demographics. Infections due to ESBL-containing pathogens continue to be associated with significant morbidity and mortality worldwide. With widespread empiric broad-spectrum β-lactam use creating selective pressure, and the resultant emergence of stable, rapidly proliferating ESBL-producing clones with continued horizontal gene transfer across genera, addressing this issue remains imperative. Although well characterized in adults, the epidemiology, risk factors, outcomes, therapies, and control measures for ESBL-producing bacteria are less appreciated in children. This analysis provides a brief summary of ESBL-producing Enterobacteriaceae in children, with a focus on recent clinical and molecular data regarding colonization and infection in nonoutbreak settings.
Depredation by killer whale (Orcinus orca) and false killer whale (Pseudorca crassidens) on the catch of the Uruguayan pelagic longline fishery in Southwestern Atlantic Ocean
Authors: Passadore Cecilia , Domingo Andrés , Secchi Eduardo R.
Published: January 2015

This study analyses depredation by killer whales (Orcinus orca) and false killer whales (Pseudorca crassidens) on catches of the Uruguayan pelagic longline fishery in the Southwestern Atlantic Ocean between 1998 and 2007. Data were collected by scientific observers from the National Observer Program of the Tuna Fleet operating in the area between 19°–40.5°S and 20°–54°W. Depredation occurred in 67 of the 1029 sets and was restricted to the area from 25°–40.5°S to 27°–53°W, though larger proportions of depredation (DP: percentage of total fish caught damaged by cetaceans) were observed in the Brazil–Malvinas (Falkland) Confluence area (34°–37°S and 51°–53°W) where most of the fishing effort was concentrated. Depredation occurred year-round though intra-annual variability in its intensity was recorded. The overall DP was 0.37% and was slightly higher in autumn. The spatial analysis showed that DP within grids of 1 × 1° was homogeneous and generally <2.5%. Ten out of 57 fish species caught by the fishery were depredated by cetaceans. Swordfish (Xiphias gladius) showed the highest DP per species (1.17%). Using the frequency of resources selectivity index of Ivlev, it was determined that swordfish was selected as a preferred prey in 43.9% of the sets with depredation. Generalized linear models indicated that distance to coast, year, and vessel were significant variables in explaining the number of fish depredated per fishing event. The presence of killer whales in the fishing ground seems not to affect the catch per unit effort by the longline fishery. The losses caused by depredation of cetaceans on the catch are low with probably minor economic effects to the Uruguayan longline fishing industry.
Fast cold gas in hot AGN outflows
Authors: Costa Tiago , Sijacki Debora , Haehnelt Martin G.
Published: January 2015

Observations of the emission from spatially extended cold gas around bright high-redshift quasars (QSOs) reveal surprisingly large velocity widths exceeding 2000 km s− 1, out to projected distances as large as 30 kpc. The high-velocity widths have been interpreted as the signature of powerful AGN-driven outflows. Naively, these findings appear in tension with hydrodynamic models in which AGN-driven outflows are energy-driven and thus very hot with typical temperatures T ≳ 106–7 K. Using the moving-mesh code arepo, we perform ‘zoom-in’ cosmological simulations of a z ∼ 6 QSO and its environment, following black hole growth and feedback via energy-driven outflows. In the simulations, the QSO host galaxy is surrounded by a clumpy circumgalactic medium pre-enriched with metals due to supernovae-driven galactic outflows. As a result, part of the AGN-driven hot outflowing gas can cool radiatively, leading to large amounts ( ≳ 109 Mȯ) of cold gas comoving with the hot bipolar outflow. This results in velocity widths of spatially extended cold gas similar to those observed. We caution, however, that gas inflows, random motions in the deep potential well of the QSO host galaxy and cooling of supernovae-driven winds contribute significantly to the large velocity width of the cold gas in the simulations, complicating the interpretation of observational data.
Hot ammonia in the center of the Seyfert 2 galaxy NGC 3079
Authors: Miyamoto Yusuke , Nakai Naomasa , Seta Masumichi , Salak Dragan , Hagiwara Kenzaburo , Nagai Makoto , Ishii Shun , Yamauchi Aya
Published: January 2015

We present the results of ammonia observations toward the center of NGC 3079. The NH3(J, K) = (1, 1) and (2, 2) inversion lines were detected in absorption with the Tsukuba 32 m telescope, and the NH3(1, 1) through (6, 6) lines with the VLA, although the profile of NH3(3, 3) was in emission in contrast to the other transitions. The background continuum source, whose flux density was ∼ 50 mJy, could not be resolved with the VLA beam of ≲ 0${^{\prime\prime}_{.}}$09 × 0${^{\prime\prime}_{.}}$08. All ammonia absorption lines have two distinct velocity components: one is at the systemic velocity and the other is blueshifted, and both components are aligned along the nuclear jets. For the systemic components, the relatively low temperature gas is extended more than the high temperature gas. The blueshifted NH3(3, 3) emission can be regarded as ammonia masers associated with shocks by strong winds probably from newly formed massive stars or supernova explosions in dense clouds in the nuclear megamaser disk. Using para-NH3(1, 1), (2, 2), (4, 4), and (5, 5) lines with VLA, we derived the rotational temperature Trot = 120 ± 12 K and 157 ± 19 K for the systemic and blueshifted components, respectively. The total column densities of NH3(0, 0)–(6, 6), assuming Tex ≈ Trot, were (8.85 ± 0.70) × 1016 cm−2 and (4.47 ± 0.78) × 1016 cm−2 for the systemic and blueshifted components, respectively. The fractional abundance of NH3 relative to molecular hydrogen H2 for the systemic and blueshifted was [NH3]/[H2] = 1.3 × 10−7 and 6.5 × 10−8, respectively. We also found the F = 4–4 and F = 5–5 doublet lines of OH 2Π3/2J = 9/2 in absorption, which could be fitted by two velocity components, systemic and redshifted components. The rotational temperature of OH was estimated to be Trot, OH ≥ 175 K, tracing hot gas associated with the interaction of the fast nuclear outflow with dense molecular material around the nucleus.
Long-term Outcomes and Complications in Pediatric Ewing Sarcoma
Authors: Hamilton Sarah N. , Carlson Ryan , Hasan Haroon , Rassekh Shahrad R. , Goddard Karen
Published: January 2015

Objectives:

The objective of this study was to determine treatment outcomes and long-term complications in pediatric patients with Ewing Sarcoma treated at the British Columbia Cancer Agency (BCCA).

Methods:

A retrospective chart review of 101 pediatric patients (<19 y old) with Ewing Sarcoma diagnosed between 1960 and 2005 was performed. The Kaplan-Meier survival analysis and Cox regression multivariate analysis were used to assess prognostic factors for overall survival (OS) and event-free survival (EFS).

Results:

The median age at diagnosis was 11 years and the median follow-up for nondeceased patients was 13.5 years. The most common primary tumor locations were lower extremity (33%), pelvis (24%), and thorax (18%). Fifty percent of patients received surgery, 79% radiotherapy and 94% chemotherapy. The 5-year OS and EFS for patients with localized disease was 85% and 73% and for metastatic disease was 27% (P<0.0001) and 28% (P<0.0001), respectively. Metastatic disease was an independent predictor of lower OS (hazard ratio [HR], 9.5; 95% confidence interval [CI],4.7-19.4; P<0.0001) and EFS (HR, 4.9; 95% CI, 2.7-8.8; P<0.0001). Extremity tumor location was an independent predictor for improved OS (HR, 0.4; 95% CI, 0.2-0.9; P=0.03). The majority (77%) of long-term survivors (≥5 y) had long-term complications; the most common were musculoskeletal abnormalities (50%) and cardiac toxicity (28%). The actuarial second neoplasm risk was 5% at 10 years.

Conclusions:

Ewing sarcoma patients with localized disease had excellent treatment outcomes at the BCCA. However, the majority of patients had chronic complications from treatment. This study validates the need for long-term follow-up of Ewing Sarcoma survivors for management of late effects.
Brain ontogeny and life history in Pleistocene hominins
Authors: Hublin Jean-Jacques , Neubauer Simon , Gunz Philipp
Published: January 2015

A high level of encephalization is critical to the human adaptive niche and emerged among hominins over the course of the past 2 Myr. Evolving larger brains required important adaptive adjustments, in particular regarding energy allocation and life history. These adaptations included a relatively small brain at birth and a protracted growth of highly dependent offspring within a complex social environment. In turn, the extended period of growth and delayed maturation of the brain structures of humans contribute to their cognitive complexity. The current palaeoanthropological evidence shows that, regarding life history and brain ontogeny, the Pleistocene hominin taxa display different patterns and that one cannot simply contrast an ‘ape-model’ to a ‘human-model’. Large-brained hominins such as Upper Pleistocene Neandertals have evolved along their own evolutionary pathway and can be distinguished from modern humans in terms of growth pattern and brain development. The life-history pattern and brain ontogeny of extant humans emerged only recently in the course of human evolution.
Uterine artery blood flow, fetal hypoxia and fetal growth
Authors: Browne Vaughn A. , Julian Colleen G. , Toledo-Jaldin Lillian , Cioffi-Ragan Darleen , Vargas Enrique , Moore Lorna G.
Published: January 2015

Evolutionary trade-offs required for bipedalism and brain expansion influence the pregnancy rise in uterine artery (UtA) blood flow and, in turn, reproductive success. We consider the importance of UtA blood flow by reviewing its determinants and presenting data from 191 normotensive (normal,
n
= 125) or hypertensive (preeclampsia (PE) or gestational hypertension (GH),
n
= 29) Andean residents of very high (4100–4300 m) or low altitude (400 m,
n
= 37). Prior studies show that UtA blood flow is reduced in pregnancies with intrauterine growth restriction (IUGR) but whether the IUGR is due to resultant fetal hypoxia is unclear. We found higher UtA blood flow and Doppler indices of fetal hypoxia in normotensive women at high versus low altitude but similar fetal growth. UtA blood flow was markedly lower in early-onset PE versus normal high-altitude women, and their fetuses more hypoxic as indicated by lower fetal heart rate, Doppler indices and greater IUGR. We concluded that, despite greater fetal hypoxia, fetal growth was well defended by higher UtA blood flows in normal Andeans at high altitude but when compounded by lower UtA blood flow in early-onset PE, exaggerated fetal hypoxia caused the fetus to respond by decreasing cardiac output and redistributing blood flow to help maintain brain development at the expense of growth elsewhere. We speculate that UtA blood flow is not only an important supply line but also a trigger for stimulating the metabolic and other processes regulating feto-placental metabolism and growth. Studies using the natural laboratory of high altitude are valuable for identifying the physiological and genetic mechanisms involved in human reproductive success.
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
Authors: Baym Michael , Kryazhimskiy Sergey , Lieberman Tami D. , Chung Hattie , Desai Michael M. , Kishony Roy
Published: January 2015

Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for the rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnecessary steps, we achieve a cost of library preparation of $8 per sample, approximately 6 times cheaper than the widely-used Nextera XT protocol. Furthermore, our procedure takes less than 5 hours for 96 samples and uses nanograms of genomic DNA. Many hundreds of samples can then be pooled on the same HiSeq lane via custom barcodes. Our method is especially useful for re-sequencing of large numbers of full microbial or viral genomes, including those from evolution experiments, genetic screens, and environmental samples.
Identification of an Arabidopsis Aminotransferase that Facilitates Tryptophan and Auxin Homeostasis
Authors: Pieck Michael , Yuan Youxi , Godfrey Jason , Fisher Christopher , Zolj Sanda , Thomas Nicholas , Wu Connie , Ramos Julian , Lee Norman , Normanly Jennifer , Celenza John
Published: January 2015

IAA plays a critical role in regulating numerous aspects of plant growth and development. While there is much genetic support for tryptophan-dependent (Trp-D) IAA synthesis pathways, there is little genetic evidence for tryptophan-independent (Trp-I) IAA synthesis pathways. Using Arabidopsis, we identified two mutant alleles ofISS1(IndoleSevereSensitive) that display indole-dependent IAA overproduction phenotypes including leaf epinasty and adventitious rooting. Stable isotope labeling showed thatiss1, but not WT, uses primarily Trp-I IAA synthesis when grown on indolesupplemented medium. In contrast, bothiss1and WT use primarily Trp-D IAA synthesis when grown on unsupplemented medium.iss1seedlings produce 8-fold higher levels of IAA when grown on indole and surprisingly have a 174-fold increase in Trp. These findings indicate that theiss1mutant’s increase in Trp-I IAA synthesis is due to a loss of Trp catabolism.ISS1was identified as At1g80360, a predicted aromatic aminotransferase, and in vitro and in vivo analysis confirmed this activity. At1g80360 was previously shown to primarily carry out the conversion of indole-3-pyruvic acid to Trp as an IAA homeostatic mechanism in young seedlings. Our results suggest that in addition to this activity, in more mature plantsISS1has a role in Trp catabolism and possibly in the metabolism of other aromatic amino acids. We postulate that this loss of Trp catabolism impacts the use of Trp-D and/or Trp-I IAA synthesis pathways.
Phylesystem: a git-based data store for community curated phylogenetic estimates
Authors: McTavish Emily Jane B. , Hinchliff Cody E. , Allman James F. , Brown Joseph W. , Cranston Karen A. , Holder Mark T. , Rees Jonathan A. , Smith Stephen A.
Published: January 2015

Phylogenetic estimates from published studies can be archived using general platforms like Dryad or TreeBASE. Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. Because the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work, and making errors introduced during curation easier to correct. Here we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating, and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git's version control features. Hosting this data store on GitHub provides open access to the data store using tools familiar to many developers. We have deployed a server running the "phylesystem-api", which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements.
The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly
Authors: Pepe-Ranney Charles , Hall Edward
Published: January 2015

The influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. Heterotrophic bacteria derive some to all of their organic carbon (C) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (P) or nitrogen (N). Therefore, C inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more C) while decreasing the resource space available to photoautotrophs (less mineral nutrients due to increased competition from heterotrophs). To test how resource dynamics affect membership of planktonic communities and assembly of biofilm communities we amended a series of flow-through mesocosms with C to alter the availability of C among treatments. Each mesocosm was fed with unfiltered seawater and incubated with sterilized microscope slides as surfaces for biofilm formation. The highest C treatment had the highest planktonic heterotroph abundance, lowest planktonic photoautotroph abundance, and highest biofilm biomass. We surveyed bacterial 16S rRNA genes and plastid 23S rRNA genes to characterize biofilm and planktonic community membership and structure. Regardless of resource additions, biofilm communities had higher alpha diversity than planktonic communities in all mesocosms. Heterotrophic plankton communities were distinct from heterotrophic biofilm communities in all but the highest C treatment where heterotrophic plankton and biofilm communities resembled each other after 17 days. Unlike the heterotrophs, photoautotrophic plankton communities were different than photoautotrophic biofilm communities in composition in all treatments including the highest C treatment. Our results suggest that although resource amendments affect community membership and structure, microbial lifestyle (biofilm versus planktonic) has a stronger influence on community composition.
A Transient Receptor Potential Ion Channel in Chlamydomonas Shares Key Features with Sensory Transduction-Associated TRP Channels in Mammals
Authors: Arias-Darraz Luis , Cabezas Deny , Colenso Charlotte K. , Alegría-Arcos Melissa , Bravo-Moraga Felipe , Varas-Concha Ignacio , Almonacid Daniel E. , Madrid Rodolfo , Brauchi Sebastian
Published: January 2015

Sensory modalities are essential for navigating through an ever-changing environment. From insects to mammals, transient receptor potential (TRP) channels are known mediators for cellular sensing. Chlamydomonas reinhardtii is a motile single-celled freshwater green alga that is guided by photosensory, mechanosensory, and chemosensory cues. In this type of alga, sensory input is first detected by membrane receptors located in the cell body and then transduced to the beating cilia by membrane depolarization. Although TRP channels seem to be absent in plants, C. reinhardtii possesses genomic sequences encoding TRP proteins. Here, we describe the cloning and characterization of a C. reinhardtii version of a TRP channel sharing key features present in mammalian TRP channels associated with sensory transduction. In silico sequence-structure analysis unveiled the modular design of TRP channels, and electrophysiological experiments conducted on Human Embryonic Kidney-293T cells expressing the Cr-TRP1 clone showed that many of the core functional features of metazoan TRP channels are present in Cr-TRP1, suggesting that basic TRP channel gating characteristics evolved early in the history of eukaryotes.
Deficiency of the Arabidopsis Helicase RTEL1 Triggers a SOG1-Dependent Replication Checkpoint in Response to DNA Cross-Links
Authors: Hu Zhubing , Cools Toon , Kalhorzadeh Pooneh , Heyman Jefri , De Veylder Lieven
Published: January 2015

To maintain genome integrity, DNA replication is executed and regulated by a complex molecular network of numerous proteins, including helicases and cell cycle checkpoint regulators. Through a systematic screening for putative replication mutants, we identified an Arabidopsis thaliana homolog of human Regulator of Telomere Length 1 (RTEL1), which functions in DNA replication, DNA repair, and recombination. RTEL1 deficiency retards plant growth, a phenotype including a prolonged S-phase duration and decreased cell proliferation. Genetic analysis revealed that rtel1 mutant plants show activated cell cycle checkpoints, specific sensitivity to DNA cross-linking agents, and increased homologous recombination, but a lack of progressive shortening of telomeres, indicating that RTEL1 functions have only been partially conserved between mammals and plants. Surprisingly, RTEL1 deficiency induces tolerance to the deoxynucleotide-depleting drug hydroxyurea, which could be mimicked by DNA cross-linking agents. This resistance does not rely on the essential replication checkpoint regulator WEE1 but could be blocked by a mutation in the SOG1 transcription factor. Taken together, our data indicate that RTEL1 is required for DNA replication and that its deficiency activates a SOG1-dependent replication checkpoint.
Cognitive behavioral therapy for adolescents with 22q11.2 deletion syndrome
Authors: Fjermestad Krister W. , Vatne Torun M. , Gjone Helene
Published: January 2015

Purpose

– 22q11.2 deletion syndrome (22q11.2DS) is a rare genetic syndrome involving high risk of psychiatric disorders with average intellectual functioning in the lower borderline range. Due to the cognitive and social problems many adolescents with 22q11.2DS experience, adaptions may be needed to teach these adolescents cognitive behavioral therapy (CBT) skills. The purpose of this paper is to assess psychosocial functioning in adolescents with 22q11.2DS and to adapt CBT with this group.

Design/methodology/approach

– Totally twelve adolescents (M age=14.5 years, SD=1.4, range 12-17 years; 25 percent boys) with 22q11.2DS were recruited from a competence center for rare disorders. Their parents completed the Child Behavior Checklist and the Kiddie SADS screening interview. The adolescents participated in 7×45-minute CBT group sessions, comprising emotional awareness, cognitive restructuring tasks, and problem-solving skills.

Findings

– Adolescents had poor parent-reported social and school functioning at onset. The most frequent disorders indicated by screening interviews were attention deficit hyperactivity disorder (92 percent), anxiety (58 percent), depression (50 percent), autism spectrum disorders (50 percent), and potential post traumatic stress disorder (50 percent).

Practical implications

– The main adaptions made to CBT groups were shorter sessions, frequent breaks, and repetition of main points, limited use of written materials and items that could distract participants (e.g. balloons, papers), extensive and explicit use of turn taking, and two adult group facilitators per group.

Originality/value

– Offers practical advice on teaching CBT skills to adolescents with 22q11.2DS, which may also be applicable to other adolescents with lower borderline intellectual functioning or intellectual disabilities.
The effects of price consciousness and sale proneness on purchase intention towards expiration date-based priced perishable foods
Authors: Konuk Faruk Anıl
Published: January 2015

Purpose

– The purpose of this paper is to examine the effects of price consciousness and sale proneness on purchase intentions regarding with expiration date-based priced perishable foods.

Design/methodology/approach

– Data were collected from a convenience sample of consumers with structured questionnaires. Structural equation modeling was used in order to test the proposed hypotheses.

Findings

– Results of a structural model reveal positive relationship between price consciousness and sale proneness. The findings also confirm the effect of price consciousness on purchase intentions toward expiration date-based priced perishable foods. On the other hand, the results have not support the positive effect of sale proneness on purchase intentions.

Originality/value

– To the knowledge, this is the first study which has examined the relationships between price consciousness, sale proneness and purchase intentions in the context of expiration date-based pricing.
The Brazilian population consumes larger serving sizes than those informed on labels
Authors: Kraemer Mariana Vieira dos Santos , Machado Priscila Pereira , Kliemann Nathalie , González Chica David Alejandro , Proença Rossana Pacheco da Costa
Published: January 2015

Purpose

– The purpose of this paper is to relate average serving size intake by the Brazilian population and declared serving size, the presence of trans fat and household measure fractioning declared on labels of processed, and ultra-processed food products.

Design/methodology/approach

– Cross-sectional study that analyzed the food labelling of all processed and ultra-processed food products sold in a supermarket in southern Brazil.

Findings

– A total of 1,071 processed and ultra-processed food products were analyzed. In 88 per cent of food groups, the average serving size consumed was larger than what was declared on labels. Consumed serving size was up to 9.2 times larger than the declared ones in food products with trans fat among their ingredients list and in false negatives and up to 9.9 times larger in foods with fractioned household measure (p<0.001). The Brazilian population consumes, on average, larger serving sizes than those declared on labels, which may represent a significant intake of trans fats without the consumers’ noticing.

Originality/value

– This study has been performed with the use of a national database on food consumption, as well as the information from a large number of processed and ultra-processed food labels marketed in Brazil. This study is also proven to be important and novel, contributing with information as to the manner in which nutrition labelling has been presented to Brazilian consumers, discussing its possible consequences for food choices, intake, and the guarantee of consumer rights.
Dynamic food demand in urban China
Authors: Zhou De , Yu Xiaohua , Herzfeld Thomas
Published: January 2015

Purpose

– The purpose of this paper is to investigate dynamic food demand in urban China, with use of a complete dynamic demand system – dynamic linear expenditure system-linear approximate dynamic almost ideal demand system (DLES-LA/DAIDS), which pushes forward the techniques of demand analysis.

Design/methodology/approach

– The authors employ a transitionary demand process and develop a new approach of complete demand system with a two-stage dynamic budgeting: a strongly separable DLES in the first stage and a LA/DAIDS in the second stage. Employing provincial aggregate data (1995-2010) from the China urban household surveys, The authors estimated the demand elasticities for primary food products in urban China.

Findings

– The results indicate that most primary food products are necessities and price inelastic for urban households in China. The authors also found that the dynamic model tends to yield relatively smaller expenditure elasticities in magnitude than the static models do due to the friction effect of dynamic adjusting costs, such as habit formation, switching costs, and learning process. However, the dynamic effects on own price elasticities are inconclusive due to the add-up restriction.

Practical implications

– The research contributes to the demand analysis methodologically, and can be used for better projections in policy simulation models.

Originality/value

– This paper methodologically relaxes the restrictive assumption of instant adjustment in static models and allows consumers to make a dynamic decision in food consumption. Empirically, the authors introduce a new complete dynamic demand model and carry out a case study with the use of urban household data in China.