bluuebunny/crossref_metadata_2025 huggingface dataset:
Pro‐inflammatory self‐reactive T cells are found within murine TCR‐αβ+CD4−CD8−PD‐1+ cells
Authors: Rodríguez‐Rodríguez Noé , Apostolidis Sokratis A. , Fitzgerald Lauren , Meehan Bronwyn S. , Corbett Alexandra J. , Martín‐Villa José Manuel , McCluskey James , Tsokos George C. , Crispín José C.
Published: April 2016

TCR‐αβ+ double negative (DN) T cells (CD3+TCR‐αβ+CD4−CD8−NK1.1−CD49b−) represent a minor heterogeneous population in healthy humans and mice. These cells have been ascribed pro‐inflammatory and regulatory capacities and are known to expand during the course of several autoimmune diseases. Importantly, previous studies have shown that self‐reactive CD8+ T cells become DN after activation by self‐antigens, suggesting that self‐reactive T cells may exist within the DN T‐cell population. Here, we demonstrate that programmed cell death 1 (PD‐1) expression in unmanipulated mice identifies a subset of DN T cells with expression of activation‐associated markers and a phenotype that strongly suggests they are derived from self‐reactive CD8+ cells. We also found that, within DN T cells, the PD‐1+ subset generates the majority of pro‐inflammatory cytokines. Finally, using a TCR‐activation reporter mouse (Nur77‐GFP), we confirmed that in the steady‐state PD‐1+ DN T cells engage endogenous antigens in healthy mice. In conclusion, we provide evidence that indicates that the PD‐1+ fraction of DN T cells represents self‐reactive cells.
The GARP/Latent TGF‐β1 complex on Treg cells modulates the induction of peripherally derived Treg cells during oral tolerance
Authors: Edwards Justin P. , Hand Timothy W. , Morais da Fonseca Denise , Glass Deborah D. , Belkaid Yasmine , Shevach Ethan M.
Published: April 2016

Treg cells can secrete latent TGF‐β1 (LTGF‐β1), but can also utilize an alternative pathway for transport and expression of LTGF‐β1 on the cell surface in which LTGF‐β1 is coupled to a distinct LTGF‐β binding protein termed glycoprotein A repetitions predominant (GARP)/LRRC32. The function of the GARP/LTGF‐β1 complex has remained elusive. Here, we examine in vivo the roles of GARP and TGF‐β1 in the induction of oral tolerance. When Foxp3− OT‐II T cells were transferred to wild‐type recipient mice followed by OVA feeding, the conversion of Foxp3− to Foxp3+ OT‐II cells was dependent on recipient Treg cells. Neutralization of IL‐2 in the recipient mice also abrogated this conversion. The GARP/LTGF‐β1 complex on recipient Treg cells, but not dendritic cell‐derived TGF‐β1, was required for efficient induction of Foxp3+ T cells and for the suppression of delayed hypersensitivity. Expression of the integrin αvβ8 by Treg cells (or T cells) in the recipients was dispensable for induction of Foxp3 expression. Transient depletion of the bacterial flora enhanced the development of oral tolerance by expanding Treg cells with enhanced expression of the GARP/LTGF‐β1 complex.
A Rhenium‐Functionalized Metal–Organic Framework as a Single‐Site Catalyst for Photochemical Reduction of Carbon Dioxide
Authors: Huang Ruiyun , Peng Yu , Wang Cheng , Shi Zhan , Lin Wenbin
Published: April 2016

A metal–organic framework (MOF) based on (bpy)Re(CO)3Cl‐containing elongated dicarboxylate ligands and Zr6(µ3‐O)4(µ3‐OH)4 clusters was synthesized and used as an effective single‐site catalyst to photochemically reduce carbon dioxide to carbon monoxide and formate and to provide mechanistic insights into the photocatalytic CO2 reduction process.
Photoinduced Homolysis of Alkyl–Cobalt(III) Bonds in a Cyclodextrin Cage
Authors: Imabeppu Kohei , Kuwano Hiroyuki , Yutani Eriko , Kitagishi Hiroaki , Kano Koji
Published: April 2016

Photodecomposition of methyl– and ethyl–CoIII complexes of meso‐tetrakis(4‐sulfonatophenyl)porphyrin (CH3– and C2H5–CoIIITPPSs) was used as a reaction probe to study the cage effect of cyclodextrin capsules formed by two per‐O‐methylated β‐cyclodextrin (TMe‐β‐CD) molecules and their covalently linked dimer, Ph2CD. The photodecomposition of CH3–CoIIITPPS under aerobic conditions was markedly suppressed in the presence of TMe‐β‐CD and Ph2CD, while C2H5–CoIIITPPS was less affected. Alkyl–CoIIITPPS formed two types of inclusion complex with Ph2CD, the alkyl groups in Type 1 being located at the opposite side of the phenyl linker of Ph2CD and those in Type 2 being located at the same side. The photodecomposition of C2H5–CoIIITPPS in Type 1 proceeded via an ethylperoxo complex, while that in Type 2 occurred via a radical pair generated in a narrow, rigid cage to form ethylene and CoIITPPS.
Generation of Tertiary and Quaternary Stereocentres through Palladium‐Catalysed Intramolecular Heck‐Type Reactions for the Stereocontrolled Synthesis of Pyrrolo[1,2‐b]isoquinolines
Authors: Azcargorta Ane Rebolledo , Coya Estíbaliz , Barbolla Iratxe , Lete Esther , Sotomayor Nuria
Published: April 2016

The generation of quaternary and tertiary stereocentres at C‐10 of the pyrroloisoquinoline skeleton through intramolecular Mizoroki–Heck reactions of 2‐alkenyl‐substituted pyrroles and pyrrolidines has been studied. The cyclizations proceeded in moderate to good yields (up to 81 %), but with low enantioselectivity when chiral phosphanes such as (R)‐BINAP were used as ligands. However, enantiomerically pure 10‐substituted pyrrolo[1,2‐b]isoquinolines were efficiently obtained by a diastereoselective approach using chiral nonracemic pyrrolidines as substrates, generating a tertiary stereocentre.
Rotationally Restricted 1,1′‐Bis­(phenylethynyl)ferrocene Subunits in Macrocycles
Authors: Hoffmann Viktor , Jenny Nicolas , Häussinger Daniel , Neuburger Markus , Mayor Marcel
Published: April 2016

The synthesis of macrocycles comprising a 1,1′‐bis(phenylethynyl)ferrocene subunit was developed to increase the structural control over the spatial arrangement of the two cyclopentadienyl ligands of the ferrocene junction. The target structures were obtained through a modular strategy that enables the assembly of varying ring sizes from a common precursor. In particular, macrocycles were either formed by an ether formation reaction or by ring‐closing metathesis reactions. The macrocycles were obtained in reasonable isolated yields, which allowed their thorough characterization by one‐ and two‐dimensional NMR spectroscopy experiments, and the identity of one macrocycle was corroborated by single‐crystal X‐ray diffraction.
Copper(II)‐Catalyzed C–S Cross‐Coupling with Thiazolidine‐2‐thiones and Boronic Acids: Synthesis of Azole Sulfides
Authors: Shanmugapriya Jayabalan , Rajaguru Kandasamy , Muthusubramanian Shanmugam , Bhuvanesh Nattamai
Published: April 2016

The copper(II)‐catalyzed C–S cross coupling of thiazolidine‐2‐thiones with organoboronic acids towards the synthesis of azole sulfides was investigated. This mild and base‐free protocol has the advantages of short reaction times and excellent yields with no need for an ancillary ligand.
Metal‐Free Direct Dehydroxytri­fluoromethylthiolation of Alcohols via the Umpolung Reactivity of Trifluoromethanesulfenamides
Authors: Glenadel Quentin , Tlili Anis , Billard Thierry
Published: April 2016

A direct dehydroxytrifluoromethylthiolation of alcohols with trifluoromethanesulfenamide has been described. This method, based on the original umpolung reactivity of trifluoromethanesulfenamides, proposes a direct “OH‐SCF3 exchange” under mild and, more especially, metal‐free conditions.
Zirconocenes vs. Alanes: a Crucial Choice of the Allyl Source for Highly Diastereoselective Allylzincation of Nonracemic Chiral Imines
Authors: Coffinet Michael , Jaroschik Florian , Vasse Jean‐Luc
Published: April 2016

An efficient in‐situ generation of allylzinc compounds from allylzirconocenes applied to the allylmetallation of phenylglycinol‐derived imines is described. The key advantage of the method lies in the concomitant formation of a zirconocene during the Zr–Zn transmetallation step, which appears to be beneficial for the stereoselectivity of the reaction. In the specific case of coupling of imines with racemic chiral allylzinc compounds, this method provides highly diastereoselective access to valuable enantiomerically enriched amines with high synthetic potential.
A Novel Impedimetric Biosensor for Detection of Lead (II) with Low‐cost Interdigitated Electrodes Made on PCB
Authors: Cui Haixia , Xiong Xingliang , Gao Bin , Chen Zhen , Luo Yiting , He Fengjie , Deng Shixiong , Chen Longcong
Published: April 2016

A novel, low‐cost, label‐free impedance biosensor based on gold interdigitated electrodes (GIE) was developed for detection of lead. This sensor was developed by immobilizing GR‐5 DNAzymes onto the GIE surface through Au‐S bonding. In the presence of lead, the substrate strand was cleaved into two parts at the RNA site (rA) and caused changes in the interfacial properties of the GIE, resulting in a corresponding decrease in the impedance magnitude. Thus, by measuring the decrease, the concentration of lead ion can be determined. And coupled the GIE with GR‐5 DNAzyme recognition, our proposed lead biosensor exhibited a high sensitivity with a detection limit of 6.61 nM, which is much lower than the 72 nM defined as the maximum contamination level (MCL) of lead ions in drinking water by The United States Environmental Protection Agency (EPA), at the same time, with a linear range from 10–100 nM and a prominent selectivity against other heavy metal ions. What's more, different from the traditional way, the GIE are made on printed circuit board (PCB), this makes the biosensor has the advantages of simplicity, low cost and easy mass production, and it can easily be widely used.
Contrasting increased levels of serum amyloid A in patients with three different bone sarcomas: An indicator of tumor malignancy?
Authors: Wan‐Ibrahim Wan Izlina , Ashrafzadeh Ali , Singh Vivek Ajit , Hashim Onn Haji , Abdul‐Rahman Puteri Shafinaz
Published: April 2016

Sarcoma is a malignant tumor that originates from the bone or soft tissue. In this study, abundances of serum amyloid A (SAA) in patients with pleomorphic sarcoma (PS), chondrosarcoma (CS), and osteosarcoma (OS) were analyzed and compared with those from their respective age‐matched healthy control subjects. Results obtained from our analysis by 2DE showed that the levels of SAA were markedly elevated in patients with PS and OS, which are highly metastatic, while in patients with CS, which is a less aggressive sarcoma, the increase appeared less pronounced. A similar trend of altered abundances was also observed when the levels of SAA in the subjects were estimated using Western blot, ELISA, and multiple‐reaction monitoring analyses. Absolute quantification using multiple‐reaction monitoring further demonstrated that the increased abundance of SAA in patients with PS, OS, and CS was mainly attributed to isoform SAA1. In view of the different degrees of tumor malignancy in PS, OS, and CS, our data suggest their apparent correlation with the levels of SAA in the patients.
MEKC‐LIF method for analysis of amino acids after on‐capillary derivatization by transverse diffusion of laminar flow profiles mixing of reactants for assessing developmental capacity of human embryos after in vitro fertilization
Authors: Celá Andrea , Mádr Aleš , Dědová Tereza , Pelcová Marta , Ješeta Michal , Žáková Jana , Crha Igor , Glatz Zdeněk
Published: April 2016

Evaluating the physiological state of an organism is of clinical importance. In assisted reproduction, knowledge of the embryo's physiology is crucial for selecting the embryo with the highest developmental capacity to ensure high pregnancy rates. Amino acids (AAs) are involved in many biochemical processes during embryo development, which means that the determination of AA fluctuations in the embryo's surroundings can determine the embryo's physiological state. Since current embryo selection methods are mainly based on visual assessment, which lacks proper accuracy, a novel method for the analysis of AAs in the embryo's surroundings was developed. AAs were analyzed by means of MEKC‐LIF after on‐capillary derivatization by naphthalene‐2,3‐dicarboxaldehyde. The reactants were injected under the three zone arrangement and mixed using the transverse diffusion of laminar flow profiles methodology. The resulting derivatives of all the standard AAs were baseline resolved in the BGE comprised of 35 mM sodium tetraborate, 55 mM SDS, 2.7 M urea, 1 mM BIS‐TRIS propane, and 23 mM NaOH within 50 min. The method was applied on an analysis of spent culture media used in assisted reproduction to culture embryos after in vitro fertilization.
Mixed thread/paper‐based microfluidic chips as a platform for glucose assays
Authors: Gonzalez Ariana , Estala Lissette , Gaines Michelle , Gomez Frank A.
Published: April 2016

A novel microfluidic thread/paper‐based analytical device (μTPAD) to detect glucose through a colorimetric assay is described. The μTPAD was fabricated from nylon thread trifurcated into three channels terminating at analysis sites comprised of circular zones of chromatography paper, which have previously been spotted with glucose of different concentrations. A solution of glucose oxidase (GOx), horseradish peroxidase (HRP), and potassium iodide (KI) is transported via capillary action to the analysis sites where a yellow‐brown color is observed indicating oxidation of iodide to iodine. The device was then dried, scanned, and analyzed yielding a correlation between yellow intensity and glucose concentrations. Both a flat platform constructed mainly of tape, and a cone platform constructed from tape and polyvinyl chloride, are described. Studies to quantitate glucose in artificial urine showed good correlation using the μTPAD.
Determination of the modes of action and synergies of xylanases by analysis of xylooligosaccharide profiles over time using fluorescence‐assisted carbohydrate electrophoresis
Authors: Gong Weili , Zhang Huaiqiang , Tian Li , Liu Shijia , Wu Xiuyun , Li Fuli , Wang Lushan
Published: April 2016

The structure of xylan, which has a 1,4‐linked β‐xylose backbone with various substituents, is much more heterogeneous and complex than that of cellulose. Because of this, complete degradation of xylan needs a large number of enzymes that includes GH10, GH11, and GH3 family xylanases together with auxiliary enzymes. Fluorescence‐assisted carbohydrate electrophoresis (FACE) is able to accurately differentiate unsubstituted and substituted xylooligosaccharides (XOS) in the heterogeneous products generated by different xylanases and allows changes in concentrations of specific XOS to be analyzed quantitatively. Based on a quantitative analysis of XOS profiles over time using FACE, we have demonstrated that GH10 and GH11 family xylanases immediately degrade xylan into sizeable XOS, which are converted into smaller XOS in a much lower speed. The shortest substituted XOS produced by hydrolysis of the substituted xylan backbone by GH10 and GH11 family xylanases were MeGlcA2Xyl3 and MeGlcA2Xyl4, respectively. The unsubstituted xylan backbone was degraded into xylose, xylobiose, and xylotriose by both GH10 and GH11 family xylanases; the product profiles are not family‐specific but, instead, depend on different subsite binding affinities in the active sites of individual enzymes. Synergystic action between xylanases and β‐xylosidase degraded MeGlcA2Xyl4 into xylose and MeGlcA2Xyl3 but further degradation of MeGlcA2Xyl3 required additional enzymes. Synergy between xylanases and β‐xylosidase was also found to significantly accelerate the conversion of XOS into xylose.
Preparation of phosphorylcholine‐based hydrophilic monolithic column and application for analysis of drug‐related impurities with capillary electrochromatography
Authors: Qiu Danye , Li Feng , Zhang Mingyu , Kang Jingwu
Published: April 2016

A hydrophilic monolithic CEC column was prepared by thermal copolymerization of zwitterionic monomer 2‐methacryloyloxyethyl phosphorylcholine (MPC), pentaerythritol triacrylate (PETA), either methacrylatoethyl trimethyl ammonium chloride (META) or sodium 2‐methylpropene‐1‐sulfonate (MPS) in a polar binary porogen consisting of methanol and THF. A typical hydrophilic interaction LC retention mechanism was observed for low‐molecular weight polar compounds including amides, nucleotides, and nucleosides in the separation mode of hydrophilic interaction CEC, when high content of ACN (>60%) was used as the mobile phase. The effect of the electrostatic interaction between the analytes and the stationary phase was found to be negligible. The poly(MPC‐co‐PETA‐co‐META or MPS) monolithic columns have an average column efficiency of 40 000 plates/m and displayed with a satisfactory repeatability in terms of migration time and peak areas. Finally, the column was successfully applied to determine the impurities of a positively charged drug pramipexole which are often separated by ion pair RP chromatography due to their high hydrophilicity. All four components can be baseline separated within 5 min with BGE consisting of ACN/20 mM ammonium formate buffer (pH 3.0; 80/20).
DNA repair variants and breast cancer risk
Authors: Grundy Anne , Richardson Harriet , Schuetz Johanna M. , Burstyn Igor , Spinelli John J. , Brooks‐Wilson Angela , Aronson Kristan J.
Published: April 2016

A functional DNA repair system has been identified as important in the prevention of tumour development. Previous studies have hypothesized that common polymorphisms in DNA repair genes could play a role in breast cancer risk and also identified the potential for interactions between these polymorphisms and established breast cancer risk factors such as physical activity. Associations with breast cancer risk for 99 single nucleotide polymorphisms (SNPs) from genes in ten DNA repair pathways were examined in a case–control study including both Europeans (644 cases, 809 controls) and East Asians (299 cases, 160 controls). Odds ratios in both additive and dominant genetic models were calculated separately for participants of European and East Asian ancestry using multivariate logistic regression. The impact of multiple comparisons was assessed by correcting for the false discovery rate within each DNA repair pathway. Interactions between several breast cancer risk factors and DNA repair SNPs were also evaluated. One SNP (rs3213282) in the gene XRCC1 was associated with an increased risk of breast cancer in the dominant model of inheritance following adjustment for the false discovery rate (P < 0.05), although no associations were observed for other DNA repair SNPs. Interactions of six SNPs in multiple DNA repair pathways with physical activity were evident prior to correction for FDR, following which there was support for only one of the interaction terms (P < 0.05). No consistent associations between variants in DNA repair genes and breast cancer risk or their modification by breast cancer risk factors were observed. Environ. Mol. Mutagen. 57:269–281, 2016. © 2016 Wiley Periodicals, Inc.
Thermoelectric Properties of Indium(III)‐Doped Copper Antimony Selenide Thin Films Deposited Using a Microwave‐Assisted Technique
Authors: Ghanwat Vishvanath B. , Mali Sawanta S. , Bagade Chaitali S. , Mane Rahul M. , Hong Chang Kook , Bhosale P. N.
Published: April 2016

The improvement of the thermoelectric performance of semiconducting chalcogenides is an important task. The principal challenge in this field is to tailor the thermoelectric properties, such as electrical conductivity, Seebeck coefficient, and thermal conductivity, to improve the figure of merit (ZT). Herein, we present an improvement in the thermoelectric properties of InIII‐doped p‐type Cu3SbSe4 thin films deposited by using a microwave‐assisted technique. The deposited thin films were characterized for their optical, structural, morphological, compositional, and electrical transport properties to show the applicability of the materials in thermoelectric energy conversion. The improvement in ZT is achieved with InIII doping because of the enhancement in the charge carrier density of Cu3SbSe4 thin films. A maximum ZT of 0.183 was achieved for Cu3(Sb0.94In0.06)Se4 at 300 K. Our results show that this deposition strategy and doping process can provide an effective solution to fabricate Cu3SbSe4‐based materials for thermoelectric applications.
Anaerobic codigestion of cow slurry with grass silage: Effect of silage duration
Authors: Osborne Homeky Billy , Adouani Nouceiba , Potier Olivier , Pons Marie‐Noëlle
Published: April 2016

The anaerobic codigestion of cow slurry with roadside grass was investigated in this study. Ensilage is known to enhance the anaerobic digestibility of grass, but the literature does not provide accurate information about the suitable silage duration needed to ensure effective codigestion. Grass was cut along roadsides and ensiled for different durations without additives. Anaerobic digestion batch tests were carried out by mixing cow slurry and grass silage. The following three silage durations were tested: 3, 8 and 36 weeks. Each mixture was tested twice and no additional inoculum was used. Compared with their respective controls (slurry only), methane yield (LCH4/kgVSadded) decreased by 14% and 5% for the 3 and 8 week silage tests, respectively, and increased by 15% for the 36 week grass silage test. The 8 week grass silage, which showed a slight decrease of 5% at the end, did not inhibit the process. Thus, we conclude that it is more appropriate to use a grass with a minimum silage duration of 8 weeks as a cosubstrate. © 2016 American Institute of Chemical Engineers Environ Prog, 35: 1374–1380, 2016
A regularized fiber element model for reinforced concrete shear walls
Authors: Vásquez Jorge A. , de la Llera Juan C. , Hube Matías A.
Published: April 2016

Reinforced concrete shear walls are used because they provide high lateral stiffness and resistance to extreme seismic loads. However, with the increase in building height, these walls have become slenderer and hence responsible of carrying larger axial and shear loads. Because 2D/3D finite element inelastic models for walls are still complex and computationally demanding, simplified but accurate and efficient fiber element models are necessary to quickly assess the expected seismic performance of these buildings. A classic fiber element model is modified herein to produce objective results under particular loading conditions of the walls, that is, high axial loads, low axial loads, and nearly constant bending moment. To make it more widely applicable, a shear model based on the modified compression field theory was added to this fiber element. Consequently, this paper shows the formulation of the proposed element and its validation with different experimental results of cyclic tests reported in the literature. It was found that in order to get objective responses in the element, the regularization techniques based on fracture energy had to be modified, and nonlinearities because of buckling and fracture of steel bars, concrete crushing, and strain penetration effects were needed to replicate the experimental cyclic behavior. Thus, even under the assumption of plane sections, which makes the element simple and computationally efficient, the proposed element was able to reproduce the experimental data, and therefore, it can be used to estimate the seismic performance of walls in reinforced concrete buildings. Copyright © 2016 John Wiley & Sons, Ltd.
Anti-anxiety drugs and fish behavior: Establishing the link between internal concentrations of oxazepam and behavioral effects
Authors: Huerta Belinda , Margiotta-Casaluci Luigi , Rodríguez-Mozaz Sara , Scholze Martin , Winter Matthew J. , Barceló Damià , Sumpter John P.
Published: April 2016

Psychoactive drugs are frequently detected in the aquatic environment. The evolutionary conservation of the molecular targets of these drugs in fish suggests that they may elicit mode of action–mediated effects in fish as they do in humans, and the key open question is at what exposure concentrations these effects might occur. In the present study, the authors investigated the uptake and tissue distribution of the benzodiazepine oxazepam in the fathead minnow (Pimephales promelas) after 28 d of waterborne exposure to 0.8 μg L−1, 4.7 μg L−1, and 30.6 μg L−1. Successively, they explored the relationship between the internal concentrations of oxazepam and the effects on fish exploratory behavior quantified by performing 2 types of behavioral tests, the novel tank diving test and the shelter-seeking test. The highest internal concentrations of oxazepam were found in brain, followed by plasma and liver, whereas muscle presented the lowest values. Average concentrations measured in the plasma of fish from the 3 exposure groups were, respectively, 8.7 ± 5.7 μg L−1, 30.3 ± 16.1 μg L−1, and 98.8 ± 72.9 μg L−1. Significant correlations between plasma and tissue concentrations of oxazepam were found in all 3 groups. Exposure of fish to 30.6 µg L−1 in water produced plasma concentrations within or just below the human therapeutic plasma concentration (HTPC) range in many individuals. Statistically significant behavioral effects in the novel tank diving test were observed in fish exposed to 4.7 μg L−1. In this group, plasma concentrations of oxazepam were approximately one-third of the lowest HTPC value. No significant effects were observed in fish exposed to the lowest and highest concentrations. The significance of these results is discussed in the context of the species-specific behavior of fathead minnow and existing knowledge of oxazepam pharmacology. Environ Toxicol Chem 2016;35:2782–2790. © 2016 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
Field assessment of the impacts of Deepwater Horizon oiling on coastal marsh vegetation of Mississippi and Alabama
Authors: Willis Jonathan M. , Hester Mark W. , Rouhani Shahrokh , Steinhoff Marla A. , Baker Mary C.
Published: April 2016

The Deepwater Horizon incident, which occurred in April 2010, resulted in significant oiling of coastal habitats throughout the northern Gulf of Mexico. Although the most substantial oiling of coastal salt marshes occurred in Louisiana, oiling of salt marshes in Mississippi and Alabama was documented as well. A field study conducted in Mississippi and Alabama salt marshes as a component of the Deepwater Horizon Natural Resource Damage Assessment determined that >10% vertical oiling of plant tissues reduced live vegetation cover and aboveground biomass (live standing crop) relative to reference sites in this region through fall 2012. This reduction of live vegetation cover and aboveground biomass appears to have largely resulted from diminished health and vigor of Juncus roemerianus, a key salt marsh species in Mississippi and Alabama. Fewer significant reductions in live vegetation cover and aboveground biomass were detected by the fall 2013 sampling, suggesting that vegetation in oiled salt marshes in this region may have begun to recover. This is corroborated by low levels of Deepwater Horizon oil contamination in these salt marsh soils. However, these findings should be interpreted in the context of the restricted sampling intensity of the present study. Environ Toxicol Chem 2016;35:2791–2797. © 2016 The Authors. Environmental Toxicology and Chemistry Published by Wiley Periodicals, Inc. on behalf of SETAC.
Chemical and biochemical characterization and in vivo safety evaluation of pharmaceuticals in drinking water
Authors: de Jesus Gaffney Vanessa , Mota-Filipe Helder , Pinto Rui Amaro , Thiemermann Chris , Loureiro Marta , Cardoso Vitor Vale , Benoliel Maria João , Almeida Cristina M.M.
Published: April 2016

The water constituents that are currently subject to legal control are only a small fraction of the vast number of chemical substances and microorganisms that may occur in both the environment and water resources. The main objective of the present study was to study the health impact resulting from exposure to a mixture of pharmaceuticals that have been detected in tap water at low doses. Analyses of atenolol, caffeine, erythromycin, carbamazepine, and their metabolites in blood, urine, feces, fat tissue, liver, and kidney after exposure to a mixture of these pharmaceuticals in treated drinking water were performed. The effects of this exposure were assessed in rats by measuring biochemical markers of organ injury or dysfunction. Simultaneously, the selected pharmaceuticals were also quantified in both physiological fluids and organ homogenates by liquid chromatography–tandem mass spectrometry (performed in multiple reaction monitoring mode and full scan mode). Following exposure of rats to a concentration of a pharmaceutical which was 10 times higher than the concentration known to be present in tap water, trace levels of some pharmaceuticals and their metabolites were detected in biological samples. This exposure did, however, not lead to significant organ injury or dysfunction. Thus, the authors report an experimental model that can be used to characterize the safety profile of pharmaceuticals in treated drinking water using a multiorgan toxicity approach. Environ Toxicol Chem 2016;35:2674–2682. © 2016 SETAC
Validation of a new standardized test method for the freshwater amphipod Hyalella azteca: Determining the chronic effects of silver in sediment
Authors: Taylor Lisa N. , Novak Lesley , Rendas Martina , Antunes Paula M.C. , Scroggins Rick P.
Published: April 2016

Environment Canada has developed a new 42-d sediment toxicity test method that includes a reproduction test endpoint with the freshwater amphipod Hyalella azteca. Because of concerns that existing standard methodologies, whereby adults are transferred to a water-only exposure before release of their first brood at day 28, will lead to internal contaminant depuration and loss of sensitivity, the Environment Canada methodology conducts the entire exposure in sediment. To demonstrate applicability of the method for assessing the toxicity of chemical-spiked sediment, H. azteca were exposed for 42 d to sediment amended with silver nitrate (AgNO3). Mortality was significantly higher at the highest sediment concentration of Ag (2088 mg/kg dry wt); however, there was no significant reduction in biomass or reproduction as a result of Ag exposure despite significant bioaccumulation. Based on Ag measurements and speciation modeling, the principle route of Ag exposure was likely through the ingestion of complexed colloidal or particulate Ag. The techniques used to recover young amphipods from sediment were critical, and although this effort can be labor intensive (20–45 min/replicate), the technicians demonstrated 91% recovery in blind trials. For the first time, Environment Canada will require laboratories to report their recovery proficiency for the 42-d test—without this information, data will not be accepted. Overall, the reproduction test will be more applicable when only a few chemical concentrations need to be evaluated in laboratory-amended sediments or for field-collected contaminated site assessments (i.e., contaminated site vs reference site comparisons). Environ Toxicol Chem 2016;35:2430–2438. © 2016 SETAC
The Prediction of Labor Force Status: Implications From International Adult Skill Assessments
Authors: Li Tongyun , von Davier Matthias , Hancock Gregory R. , Kirsch Irwin S.
Published: April 2016

This report investigates the prediction of labor force status using observed variables, such as gender, age, and immigrant status, and more importantly, measured skill variables, including literacy proficiency and a categorical rating of educational attainment based on the 1994 International Adult Literacy Survey (IALS), the 2003 Adult Literacy and Life Skills Survey (ALL), and the 2011 Programme for the International Assessment of Adult Competencies (PIAAC) projects. We explored the regression relations in the past two decades for six trend countries and subnational regions that provide data for all assessments: the United States, Norway, the Netherlands, Italy, Canada's English‐speaking region, and Canada's French‐speaking region. Probit regression models with latent predictors were used in this cross‐sectional study to investigate how those variables are structurally related to labor market outcomes. Results show the importance of literacy proficiency and education in determining individuals' labor force status across countries/regions, but with key differences among these countries/regions.
An improved Rhie–Chow interpolation scheme for the smoothed‐interface immersed boundary method
Authors: Yi Wei , Corbett Daniel , Yuan Xue‐Feng
Published: April 2016

Rhie–Chow interpolation is a commonly used method in CFD calculations on a co‐located mesh in order to suppress non‐physical pressure oscillations arising from chequerboard effects. A fully parallelized smoothed‐interface immersed boundary method on a co‐located grid is described in this paper. We discuss the necessity of modifications to the original Rhie–Chow interpolation in order to deal with a locally refined mesh. Numerical simulation with the modified scheme of Choi shows that numerical dissipation due to Rhie–Chow interpolation introduces significant errors at the immersed boundary. To address this issue, we develop an improved Rhie–Chow interpolation scheme that is shown to increase the accuracy in resolving the flow near the immersed boundary. We compare our improved scheme with the modified scheme of Choi by parallel simulations of benchmark flows: (i) flow past a stationary cylinder; (ii) flow past an oscillating cylinder; and (iii) flow past a stationary elliptical cylinder, where Reynolds numbers are tested in the range 10–200. Our improved scheme is significantly more accurate and compares favourably with a staggered grid algorithm. We also develop a scheme to compute the boundary force for the direct‐forcing immersed boundary method efficiently. Copyright © 2016 John Wiley & Sons, Ltd.
Forecasting the US Term Structure of Interest Rates Using Nonparametric Functional Data Analysis
Authors: Caldeira JoÃo , Torrent Hudson
Published: April 2016

In this paper we consider a novel procedure to forecasting the US zero coupon bond yields for a continuum of maturities by using the methodology of nonparametric functional data analysis (NP‐FDA). We interpret the US yields as curves since the term structure of interest rates defines a relation between the yield of a bond and its maturity. Within the NP‐FDA approach, each curve is viewed as a functional random variable and the dynamics present in the sample are modeled without imposing any parametric structure. In order to evaluate forecast the performance of the proposed estimator, we consider forecast horizons h = 1,3,6,12… months and the results are compared with widely known benchmark models. Our estimates with NP‐FDA present predictive performance superior to its competitors in many situations considered, especially for short‐term maturities. Copyright © 2016 John Wiley & Sons, Ltd.
Evaluation of a Two‐Stage Approach in Trans‐Ethnic Meta‐Analysis in Genome‐Wide Association Studies
Authors: Hong Jaeyoung , Lunetta Kathryn L. , Cupples L. Adrienne , Dupuis Josée , Liu Ching‐Ti
Published: April 2016

Meta‐analysis of genome‐wide association studies (GWAS) has achieved great success in detecting loci underlying human diseases. Incorporating GWAS results from diverse ethnic populations for meta‐analysis, however, remains challenging because of the possible heterogeneity across studies. Conventional fixed‐effects (FE) or random‐effects (RE) methods may not be most suitable to aggregate multiethnic GWAS results because of violation of the homogeneous effect assumption across studies (FE) or low power to detect signals (RE). Three recently proposed methods, modified RE (RE‐HE) model, binary‐effects (BE) model and a Bayesian approach (Meta‐analysis of Transethnic Association [MANTRA]), show increased power over FE and RE methods while incorporating heterogeneity of effects when meta‐analyzing trans‐ethnic GWAS results. We propose a two‐stage approach to account for heterogeneity in trans‐ethnic meta‐analysis in which we clustered studies with cohort‐specific ancestry information prior to meta‐analysis. We compare this to a no‐prior‐clustering (crude) approach, evaluating type I error and power of these two strategies, in an extensive simulation study to investigate whether the two‐stage approach offers any improvements over the crude approach. We find that the two‐stage approach and the crude approach for all five methods (FE, RE, RE‐HE, BE, MANTRA) provide well‐controlled type I error. However, the two‐stage approach shows increased power for BE and RE‐HE, and similar power for MANTRA and FE compared to their corresponding crude approach, especially when there is heterogeneity across the multiethnic GWAS results. These results suggest that prior clustering in the two‐stage approach can be an effective and efficient intermediate step in meta‐analysis to account for the multiethnic heterogeneity.
Studying the Genetics of Complex Disease With Ancestry‐Specific Human Phenotype Networks: The Case of Type 2 Diabetes in East Asian Populations
Authors: Qiu Jingya , Moore Jason H. , Darabos Christian
Published: April 2016

Genome‐wide association studies (GWAS) have led to the discovery of over 200 single nucleotide polymorphisms (SNPs) associated with type 2 diabetes mellitus (T2DM). Additionally, East Asians develop T2DM at a higher rate, younger age, and lower body mass index than their European ancestry counterparts. The reason behind this occurrence remains elusive. With comprehensive searches through the National Human Genome Research Institute (NHGRI) GWAS catalog literature, we compiled a database of 2,800 ancestry‐specific SNPs associated with T2DM and 70 other related traits. Manual data extraction was necessary because the GWAS catalog reports statistics such as odds ratio and P‐value, but does not consistently include ancestry information. Currently, many statistics are derived by combining initial and replication samples from study populations of mixed ancestry. Analysis of all‐inclusive data can be misleading, as not all SNPs are transferable across diverse populations. We used ancestry data to construct ancestry‐specific human phenotype networks (HPN) centered on T2DM. Quantitative and visual analysis of network models reveal the genetic disparities between ancestry groups. Of the 27 phenotypes in the East Asian HPN, six phenotypes were unique to the network, revealing the underlying ancestry‐specific nature of some SNPs associated with T2DM. We studied the relationship between T2DM and five phenotypes unique to the East Asian HPN to generate new interaction hypotheses in a clinical context. The genetic differences found in our ancestry‐specific HPNs suggest different pathways are involved in the pathogenesis of T2DM among different populations. Our study underlines the importance of ancestry in the development of T2DM and its implications in pharmocogenetics and personalized medicine.
Review of the Gene‐Environment Interaction Literature in Cancer: What Do We Know?
Authors: Simonds Naoko I. , Ghazarian Armen A. , Pimentel Camilla B. , Schully Sheri D. , Ellison Gary L. , Gillanders Elizabeth M. , Mechanic Leah E.
Published: April 2016

Background

Risk of cancer is determined by a complex interplay of genetic and environmental factors. Although the study of gene‐environment interactions (G×E) has been an active area of research, little is reported about the known findings in the literature.

Methods

To examine the state of the science in G×E research in cancer, we performed a systematic review of published literature using gene‐environment or pharmacogenomic flags from two curated databases of genetic association studies, the Human Genome Epidemiology (HuGE) literature finder and Cancer Genome‐Wide Association and Meta Analyses Database (CancerGAMAdb), from January 1, 2001, to January 31, 2011. A supplemental search using HuGE was conducted for articles published from February 1, 2011, to April 11, 2013. A 25% sample of the supplemental publications was reviewed.

Results

A total of 3,019 articles were identified in the original search. From these articles, 243 articles were determined to be relevant based on inclusion criteria (more than 3,500 interactions). From the supplemental search (1,400 articles identified), 29 additional relevant articles (1,370 interactions) were included. The majority of publications in both searches examined G×E in colon, rectal, or colorectal; breast; or lung cancer. Specific interactions examined most frequently included environmental factors categorized as energy balance (e.g., body mass index, diet), exogenous (e.g., oral contraceptives) and endogenous hormones (e.g., menopausal status), chemical environment (e.g., grilled meats), and lifestyle (e.g., smoking, alcohol intake). In both searches, the majority of interactions examined were using loci from candidate genes studies and none of the studies were genome‐wide interaction studies (GEWIS). The most commonly reported measure was the interaction P‐value, of which a sizable number of P‐values were considered statistically significant (i.e., <0.05). In addition, the magnitude of interactions reported was modest.

Conclusion

Observations of published literature suggest that opportunity exists for increased sample size in G×E research, including GWAS‐identified loci in G×E studies, exploring more GWAS approaches in G×E such as GEWIS, and improving the reporting of G×E findings.
Across‐Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression
Authors: Zhang Guosheng , Huang Kuan‐Chieh , Xu Zheng , Tzeng Jung‐Ying , Conneely Karen N. , Guan Weihua , Kang Jian , Li Yun
Published: April 2016

DNA methylation is a key epigenetic mark involved in both normal development and disease progression. Recent advances in high‐throughput technologies have enabled genome‐wide profiling of DNA methylation. However, DNA methylation profiling often employs different designs and platforms with varying resolution, which hinders joint analysis of methylation data from multiple platforms. In this study, we propose a penalized functional regression model to impute missing methylation data. By incorporating functional predictors, our model utilizes information from nonlocal probes to improve imputation quality. Here, we compared the performance of our functional model to linear regression and the best single probe surrogate in real data and via simulations. Specifically, we applied different imputation approaches to an acute myeloid leukemia dataset consisting of 194 samples and our method showed higher imputation accuracy, manifested, for example, by a 94% relative increase in information content and up to 86% more CpG sites passing post‐imputation filtering. Our simulated association study further demonstrated that our method substantially improves the statistical power to identify trait‐associated methylation loci. These findings indicate that the penalized functional regression model is a convenient and valuable imputation tool for methylation data, and it can boost statistical power in downstream epigenome‐wide association study (EWAS).
Testing Allele Transmission of an SNP Set Using a Family‐Based Generalized Genetic Random Field Method
Authors: Li Ming , Li Jingyun , He Zihuai , Lu Qing , Witte John S. , Macleod Stewart L. , Hobbs Charlotte A. , Cleves Mario A. ,   the National Birth Defects Prevention Study
Published: April 2016

Family‐based association studies are commonly used in genetic research because they can be robust to population stratification (PS). Recent advances in high‐throughput genotyping technologies have produced a massive amount of genomic data in family‐based studies. However, current family‐based association tests are mainly focused on evaluating individual variants one at a time. In this article, we introduce a family‐based generalized genetic random field (FB‐GGRF) method to test the joint association between a set of autosomal SNPs (i.e., single‐nucleotide polymorphisms) and disease phenotypes. The proposed method is a natural extension of a recently developed GGRF method for population‐based case‐control studies. It models offspring genotypes conditional on parental genotypes, and, thus, is robust to PS. Through simulations, we presented that under various disease scenarios the FB‐GGRF has improved power over a commonly used family‐based sequence kernel association test (FB‐SKAT). Further, similar to GGRF, the proposed FB‐GGRF method is asymptotically well‐behaved, and does not require empirical adjustment of the type I error rates. We illustrate the proposed method using a study of congenital heart defects with family trios from the National Birth Defects Prevention Study (NBDPS).
Performance of iron ore oxygen carrier modified by biomass ashes in coal‐fueled chemical looping combustion
Authors: Zhang Shuai , Xiao Rui
Published: April 2016

The modification of oxygen carrier by low‐cost biomass ash shows great potential to reduce the economic and environmental costs associated with oxygen carrier preparation and biomass ash disposal. In this study, three biomass ashes ‒ a wheat stalk ash (WSA), a corn stalk ash (CSA), and a soybean stalk ash (SSA) ‒ were selected as the modifiers to evaluate their potential to improve the reactivity of a iron ore produced from the Mining Area C (MAC) of Western Australia. A lignite coal ash‐modified MAC iron ore was also prepared to make a comparison. The reactivity performance of ash‐modified samples and the cyclic behavior of the selected best candidate were evaluated in a laboratory‐scale fluidized‐bed reactor system with coal as fuel. The results showed that MAC iron ore loaded with different ashes showed different degrees of improvement in its reactivity. SSA‐modified MAC iron ore behaved the best due to the highest K2O content and the total contents of K2O, CaO, and Na2O in SSA as well as its great resistance to melting. The higher loading content of SSA in MAC iron ore resulted in more coal gasification products converted to CO2 and H2O at a faster reaction rate. The cyclic test of MAC‐20SSA showed that it performed well both in its reactivity and physical structure. Stable outlet gas concentrations were achieved and MAC‐20SSA exhibited good resistance to sintering. It can be inferred that SSA is a promising low‐cost modifying agent to enhance the performance of oxygen carrier while reducing the environmental impact associated with its disposal. © 2016 Society of Chemical Industry and John Wiley & Sons, Ltd
Personality and reported quality of life in Parkinson's disease
Authors: Pontone Gregory M. , Mari Zoltan , Perepezko Kate , Weiss Howard D , Bassett Susan S
Published: April 2016

Objective

Personality affects an individual's ability to cope with the burden of chronic disease. However, the impact of personality on quality of life (QoL) in Parkinson's disease (PD) is not well characterized. The goal of this study is to determine the effect of personality on QoL in PD.

Methods

The study included 92 patients with idiopathic PD from Baltimore‐Washington area movement disorder neurology clinics. QoL was assessed using the 37‐item Parkinson's disease Quality of Life Questionnaire (PDQL) total score, and the Neuroticism–Extraversion–Openness Inventory was used to determine personality traits.

Results

Step‐wise regression models examined the contribution of personality, depression, demographic, and PD variables on PDQL‐assessed QoL. Neuroticism, conscientiousness, years of education, and depression explained 42% of the variance in the PDQL total score after adjusting for other disease variables. High neuroticism (β = −0.727, 95% confidence interval (CI) −1.125, −0.328, p < 0.0001) and depression (β = −9.058, 95%CI −17.46, −0.657, p = 0.035) negatively affected the PDQL, while high conscientiousness (β = 0.468, 95%CI 0.078, 0.858, p = 0.019), and years of education (β = 1.441, 95%CI 0.371, 2.510, p = 0.009) were positive factors.

Conclusions

Personality can have a positive or negative influence on QoL in PD. PD patients with otherwise similar disease burdens and depressive symptoms may experience different levels of QoL depending on the level of neurotic or conscientious personality traits. Therefore, when interpreting patient responses on the PDQL, it is important to understand whether they reflect aspects of PD, that is, motor impairment and depression, which are amenable to treatment or whether they reflect personality traits.