bluuebunny/crossref_metadata_2025 huggingface dataset:
Poly(3-imidazolyl-2-hydroxypropyl methacrylate) – a new polymer with a tunable upper critical solution temperature in water
Authors: Zhang Ganwei , Wang Yu , Liu Guojun
Published: October 2016

A novel imidazole-bearing polymer is synthesized and its solubility in water increases as the solution temperature rises or pH increases.
A novel spirocyclic triterpenoid and a new taraxerane triterpenoid from Teucrium viscidum
Authors: Li Zheng-Yu , Qi Feng-Ming , Zhi De-Juan , Hu Qiao-Ling , Liu Ying-Hong , Zhang Zhan-Xin , Fei Dong-Qing
Published: October 2016

Two new triterpenoids, teuviscins A (1) and B (2), were isolated from the whole plants of Teucrium viscidum. Compound 2 showed anti-AD bioactivity which delayed animals paralysis of transgenic AD C. elegans.
Nickel-catalyzed alkyl-zincation and carboxylation of diynes
Authors: Cao Tao , Ma Shengming
Published: October 2016

A nickel-catalyzed carbo-carboxylation of diynes with ZnR2 is realized with the help of ester functionality demonstrating excellent chemo-, regio- and stereoselectivity.
Microstructure investigation, optical properties and magnetic phase transition of Tm3+ substituted nanocrystalline ZnO (Zn0.95Tm0.05O)
Authors: Bandyopadhyay A. , Bhakta N. , Sutradhar S. , Sarkar B. J. , Deb A. K. , Kobayashi S. , Yoshimura K. , Chakrabarti P. K.
Published: October 2016

The onset of ferromagnetic ordering with high value of magnetization of Zn0.95Tm0.05O at, and below 30 K.
Interaction between dendrimers and regulatory proteins. Comparison of effects of carbosilane and carbosilane–viologen–phosphorus dendrimers
Authors: Szwed A. , Milowska K. , Ionov M. , Shcharbin D. , Moreno S. , Gomez-Ramirez R. , de la Mata F. J. , Majoral J. P. , Bryszewska M. , Gabryelak T.
Published: October 2016

For nanoparticles to be used successfully in biomedical application, their interactions with biological fluids need to be investigated, in which they will react with proteins and other macromolecules.
Rutin phospholipid complexes confer neuro-protection in ischemic-stroke rats
Authors: Ahmad Hafsa , Arya Abhishek , Agrawal Satish , Mall Prachi , Samuel Sheeba Saji , Sharma Komal , Singh Pankaj Kumar , Singh Sandeep Kumar , Valicherla Guru Raghavendra , Mitra Kalyan , Gayen Jiaur Rehman , Paliwal Sarvesh , Shukla Rakesh , Dwivedi Anil Kumar
Published: October 2016

Rutin, a natural flavonol glycoside is known to possess significant radical scavenging properties which might have beneficial effects in cerebral ischemia.
Effect of carbon nanosheets with different graphitization degrees as a support of noble metals on selective hydrogenation of cinnamaldehyde
Authors: Han Qing , Liu Yunfei , Wang Dong , Yuan Fulong , Niu Xiaoyu , Zhu Yujun
Published: October 2016

Effect of carbon nanosheets with different graphitization degrees on the catalytic activity of Pt/CNS and Pd/CNS was investigated in selective hydrogenation of cinnamaldehyde.
Self-assembly behavior of gels composed of dibenzylidene sorbitol derivatives and poly(ethylene glycol)
Authors: Lai Wei-Chi , Lee Yi-Chin
Published: October 2016

The strongest intermolecular interactions between DBS molecules in the DBS/PEG systems led to the more regular structure compared with the DMDBS/PEG and TBPMN/PEG systems.
Isolation of multiantennary N-glycans from glycoproteins for hepatocyte specific targeting via the asialoglycoprotein receptor
Authors: Witzigmann Dominik , Detampel Pascal , Porta Fabiola , Huwyler Jörg
Published: October 2016

The asialoglycoprotein receptor (ASGPR) expressed on parenchymal liver cells specifically binds multivalent carbohydrates from desialylated glycoproteins.
Crystallization and temperature-dependent structure deflection of C6mimBr ionic liquid intercalated in LAPONITE®
Authors: Jiang Fangling , Li Cheng , Guo Xiaojing , Fu Haiying , Wu Guozhong , Chen Shimou
Published: October 2016

The physicochemical properties of large molecules confined in nanopores are expected to be different from those of the bulk.
The layer boundary effect on multi-layer mesoporous TiO2 film based dye sensitized solar cells
Authors: Xu Feng , Zhu Kai , Zhao Yixin
Published: October 2016

The layer boundary in the multi-layer TiO2 based DSSC slows down the electron transfer.
The critical zeta potential of polymer membranes: how electrolytes impact membrane fouling
Authors: Breite D. , Went M. , Prager A. , Schulze A.
Published: October 2016

The zeta potential of membrane surfaces and the resulting electrostatic interactions are determining factors of membrane fouling. This publication presents the impact of salt concentration and pH value on these interactions.
Preparation and performance of spherical FeF2.5·0.5H2O nanoparticles wrapped by MWCNTs as cathode material of lithium ion batteries
Authors: Wei Shuangying , Wang Xianyou , Zhang Rui , Hu Hai , Shen Yongqiang , Liu Jia
Published: October 2016

Fabrication of spherical FeF2.5·0.5H2O–MWCNTs nanocomposites as cathode material for lithium ion batteries.
Cryptochiral binaphthyl–bipyrene luminophores linked with alkylene esters: intense circularly polarised luminescence, but ultraweak circular dichroism
Authors: Nakanishi Shoma , Nakabayashi Kazuki , Mizusawa Takaya , Suzuki Nozomu , Guo Sibo , Fujiki Michiya , Imai Yoshitane
Published: October 2016

A C2-symmetric binaphthyl-based luminophore with two luminescent pyrenes was designed to express cryptochirality, as proven by the ultraweak circular dichroisms in the ground state.
Rapid and selective separation of molybdenum ions using a novel magnetic Mo(vi) ion imprinted polymer: a study of the adsorption properties
Authors: Hassanpour Samaneh , Taghizadeh Majid
Published: October 2016

In this work, we have developed a convenient method for the rapid and selective separation of Mo(vi) from aqueous solution by using a novel magnetic Mo(vi) ion imprinted polymer (Mo(vi)-MIIP) as the sorbent.
Promising field electron emission performance of vertically aligned one dimensional (1D) brookite (β) TiO2nanorods
Authors: Devan Rupesh S. , Ma Yuan-Ron , More Mahendra A. , Khare Ruchita T. , Antad Vivek V. , Patil Ranjit A. , Thakare Vishal P. , Dhayal Rajendra S. , Schmidt-Mende Lukas
Published: October 2016

The vertically aligned and uniformly dispersed β-TiO2nanorods injected electrons direct toward emission sites, and prominently contributed to the low turn-on field of 3.9 V μm−1at a current density of 10 μA and also enhance the emission stability.
A synergetic effect of surface plasmon and ammoniation on enhancing photocatalytic activity of ZnO nanorods
Authors: Ma L. , Yang X. , Zhou Z. Q. , Lu M.
Published: October 2016

A synergetic effect of surface plasmon (SP) and ammoniation on the enhancements of both ultraviolet and visible photocatalytic activities of ZnO nanorods is reported.
Raising thermoelectric performance of n-type SnSe via Br doping and Pb alloying
Authors: Chang Cheng , Tan Qing , Pei Yanling , Xiao Yu , Zhang Xiao , Chen Yue-Xing , Zheng Lei , Gong Shengkai , Li Jing-Feng , He Jiaqing , Zhao Li-Dong
Published: October 2016

High ZT value of ∼1.2 at 773 K was achieved in n-type polycrystalline SnSe.
Zn2−aGeO4:aRE and Zn2Ge1−aO4:aRE (RE = Ce3+, Eu3+, Tb3+, Dy3+): 4f–4f and 5d–4f transition luminescence of rare earth ions under different substitution
Authors: Bai Qiongyu , Wang Zhijun , Li Panlai , Xu Shuchao , Li Ting , Yang Zhiping
Published: October 2016

Generally, luminescent properties of rare earth ions doped host can be tuned by controlling the host composition, that is, when substituted for different cations of host, the rare earths ions can present different characteristics.
Strain-induced Curie temperature variation in La0.9Sr0.1MnO3thin films
Authors: Yin Lu , Wang Chuanbin , Shen Qiang , Zhang Lianmeng
Published: October 2016

In this paper, La0.9Sr0.1MnO3thin films were grown epitaxially on SrTiO3, LaAlO3and MgO substrates, and the strain effects on their structural, electrical and magnetic properties were investigated.
Acceptor–donor–acceptor small molecules based on derivatives of 3,4-ethylenedioxythiophene for solution processed organic solar cells
Authors: Antwi B. Y. , Taylor R. G. D. , Cameron J. , Owoare R. B. , Kingsford-Adaboh R. , Skabara P. J.
Published: October 2016

Investigation into the use of EDOT as a central donor unit in A–D–A small molecules for OPV devices.
Preparation of nitrogen-doped microporous modified biochar by high temperature CO2–NH3 treatment for CO2 adsorption: effects of temperature
Authors: Zhang Xiong , Wu Jing , Yang Haiping , Shao Jingai , Wang Xianhua , Chen Yingquan , Zhang Shihong , Chen Hanping
Published: October 2016

Nitrogen-rich agricultural waste, soybean straw, was used as a raw material to prepare high efficiency CO2 adsorbents (nitrogen-doped porous modified biochars).
A greener process for flow C–H chlorination of cyclic alkanes using in situ generation and on-site consumption of chlorine gas
Authors: Fukuyama Takahide , Tokizane Masashi , Matsui Akihiro , Ryu Ilhyong
Published: October 2016

Photo-chlorination of C–H bonds by gaseous chlorine in situ generated from HCl and NaOCl proceeded smoothly using a photo microreactor.
Elucidating the charge carrier transport and extraction in planar heterojunction perovskite solar cells by Kelvin probe force microscopy
Authors: Chang Jingjing , Xiao Juanxiu , Lin Zhenhua , Zhu Hai , Xu Qing-Hua , Zeng Kaiyang , Hao Yue , Ouyang Jianyong
Published: October 2016

KPFM study of various structures with a perovskite layer indicates unbalanced charge-carrier transport and extraction.
Plasticization resistant crosslinked polyurethane gas separation membranes
Authors: Isfahani Ali Pournaghshband , Ghalei Behnam , Wakimoto Kazuki , Bagheri Rouhollah , Sivaniah Easan , Sadeghi Morteza
Published: October 2016

We generate crosslinked PU membranes that retain high separation performance and provide enhanced plasticization resistance under realistic industrial separation conditions.
Advances in non-enzymatic glucose sensors based on metal oxides
Authors: Zhu Hua , Li Li , Zhou Wei , Shao Zongping , Chen Xianjian
Published: October 2016

This review summarizes the advances in non-enzymatic glucose sensors based on different metal oxides (ZnO, CuO/Cu2O, NiO,etc.) and their composites.
Selective metallization of alumina ceramics by inkjet printing combined with electroless copper plating
Authors: Chen Jin-ju , Guo Yan-long , Wang Yan , Zhang Jing , Li Huo-jun , Feng Zhe-sheng
Published: October 2016

A convenient and efficient approach for selective metallization of alumina ceramics via inkjet printing followed by electroless plating was developed.
Preparation of nano‐MgO by ionic liquid‐assisted solid‐state reaction
Authors: Chen Hukui , Luo Zhuxi , Chen Xiaogong , Kang Fang
Published: October 2016

Nanocrystalline MgO particles with a cubic phase structure have been synthesised via ionic liquid (IL)‐assisted solid‐state reaction. The necessary characterisations such as XRD, EDS, FTIR, SEM and TEM have been carried out to investigate the obtained materials. The results show that the synthesised MgO consisted of a large quantity of sphere‐like nanocrystals with average particle size of ∼26.3 nm, and had high crystallinity and narrow particle size distribution. Compared with solid‐state reaction method, this method has the advantages of fast reaction rate and high yield. This indicates that IL‐assisted solid‐state reaction appears to be a promising method for the manufacture of nanometre MgO in industry.
P ‐doping decrease and mobility increase of graphene in atmosphere
Authors: Zhang Qingwei , Li Ping , Wang Gang
Published: October 2016

An approach to decrease the P ‐doping density of graphene and increase the mobility of graphene field‐effect transistors (GFETs) is reported. With a layer of natural aluminium oxide (natural‐AlOx) thin film covered on the surface of graphene, the Dirac point voltage of the GFETs decreases 25 V while it experiences the mobility increase of 42 cm2/(V s) after exposure in the atmosphere for 1 month. To understand this phenomenon, other two situations are researched, the Dirac point voltage of the identical GFETs with no thin film on graphene increases more than 15 V and its mobility decreases 90 cm2/(V s) after 1 month. The last situation is that the Dirac point voltage and the mobility have no significant changes with an AlOx deposited by electron beam evaporation (Al2O3‐EBE) on graphene. These phenomena indicate that the natural‐AlOx thin film is capable of reducing p ‐type impurities on the graphene and bringing the better reliability to the GFETs.
Role of Glioblastoma Craniotomy Related to Patient Survival: A 10-Year Survey in a Tertiary Care Hospital in Pakistan
Authors: Shahid Saman , Hussain Kamran
Published: October 2016

A total of 270 glioblastoma patients were treated for tumor resection during 2004 to 2014. The following variables were examined: patient age group (PAG) and percent of the extent of resection (EOR) in four types of resections: gross total resection (GTR), subtotal resection (STR), partial resection (PR), and biopsy/decompression (BD). The Karnofsky performance scale (KPS) was used and the average survival time noted. The least survival time (7 months) was noticed in the patient age group 18 to 35 years with biopsy only, whereas, the maximum survival time (14.5 months) was noted with the patient age group 54 to 71 years by gross tumor resection. The largest number of (n = 76) patients had PR (80%) and these patients had an average survival time of 10.5 months. Total 190 patients out of 270, with EOR (100–80%) had a KPS score “0” (80 and above) and total 80 patients out of 270 patients, with EOR (50%) had a KPS score “1” (below 80). The correlation was statistically significant at (p < 0.050) for EOR (%) and KPS score (0/1) only. Correlation analysis showed that the maximum resection has a strong impact on the glioblastoma patient's survival. A lesser EOR correlated with poor quality of life and also a decreased survival of patients.
Evolution of turbulence and in-plane vortices in the near field flow behind multi-scale planar grids
Authors: Gan L. , Krogstad P.-Å.
Published: October 2016

In this experimental work, we carry out detailed two-dimensional particle image velocimetry investigations for the near field wakes behind a conventional and two multi-scale planar grids, using stitched camera fields of view. Statistical independent measurements are conducted focusing on the first few mesh distances downstream of the grid. It is found that the multiple integral length scales originated from the grids loose their importance on the turbulence development after about three mesh distances downstream, much earlier than the distance where the turbulence becomes homogeneous. The largest eddy size, represented by the integral length scales, does not show clear differences in its growth rate among the three grids after an initial development of three times the largest grid size downstream. Nevertheless, when examining individual vortex behaviours using conditional averaging and filtering processes, clear differences are found. The grids are found to have different decay rates of peak vorticity and projected vortex strengths. Despite these differences, the in-plane vorticity correlation function reveals that the mean vortex shape of all the grids shows a universal near-Gaussian pattern which does not change much as the turbulence decays.
Indirect coupling between two cavity modes via ferromagnetic resonance
Authors: Hyde Paul , Bai Lihui , Harder Michael , Match Christophe , Hu Can-Ming
Published: October 2016

We experimentally realize an indirect coupling between two cavity modes via strong coupling with ferromagnetic resonance in Yttrium Iron Garnet. We find that some indirectly coupled modes of this system can have a higher microwave transmission than the individual uncoupled modes. Using a coupled harmonic oscillator model, the influence of the oscillation phase difference between the two cavity modes on the nature of the indirect coupling is revealed. The properties of the indirectly coupled modes can be controlled using an external magnetic field or by tuning the cavity height. The relation between cavity transmission and the relative phase difference between cavity modes should be useful for developing tunable optical devices and improved information processing technologies.
Communication: Polymer entanglement dynamics: Role of attractive interactions
Authors: Grest Gary S.
Published: October 2016

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes to the late time diffusive regime, highly coarse grained models with purely repulsive interactions between monomers are widely used since they are computationally the most efficient. Here using large scale molecular dynamics simulations, the effect of including the attractive interaction between monomers on the dynamics of entangled polymer melts is explored for the first time over a wide temperature range. Attractive interactions have little effect on the local packing for all temperatures T and on the chain mobility for T higher than about twice the glass transition Tg. These results, across a broad range of molecular weight, show that to study the dynamics of entangled polymer melts, the interactions can be treated as pure repulsive, confirming a posteriori the validity of previous studies and opening the way to new large scale numerical simulations.
Electron transport and dielectric breakdown in silicon nitride using a charge transport model
Authors: Ogden Sean P. , Lu Toh-Ming , Plawsky Joel L.
Published: October 2016

Silicon nitride is an important material used in the electronics industry. As such, the electronic transport and reliability of these materials are important to study and understand. We report on a charge transport model to predict leakage current and failure trends based on previously published data for a stoichiometric silicon nitride dielectric. Failure occurs when the defect density increases to a critical value of approximately 6 × 1025 traps/m3. The model's parameters are determined using voltage ramp data only, and yet, the model is also able to predict constant voltage stress failure over a time scale ranging from minutes to months. The successful fit of the model to the experimental data validates our assumption that the dominant defect in the dielectric is the Si dangling bond, located approximately 2.2 eV below the conduction band. A comparison with previous SiCOH simulations shows SiN and SiCOH have similar defect-related material properties. It is also speculated that, based on the estimated parameter values of 2.75 eV for the defect formation activation energy, the materials' TDDB wear-out are caused by broken Si-H bonds, resulting in Si dangling bond defects.
Factors affecting the survival of Indus River dolphin and species tolerance towards anthropogenic pressures
Authors: Khan Mohd Shahnawaz
Published: October 2016

There is broad consensus among ecosystem experts that river dolphins, as top predators, can structure riverine ecosystems and benefit biodiversity. The effects of dolphins on rivers and vice versa do not operate in isolation, but are context dependent, being conditioned by other factors such as human interference. Based on the aforesaid presumption, the focus of the present study was on quantifying the factors responsible for the decline of the Indus River dolphin and species tolerance towards these factors in the upper sub-basin of the Indus River system (River Beas, India). Dolphins avoided (r=–0.667; P=0.001) the study section with higher disturbance, until some other factors, such as prey availability, came into play. Species occupancy was significantly different for different flow seasons and was associated with deep pools, eddy currents, and low disturbance index. The results indicated a marked decrease in species occurrence above a disturbance index level of 44. The findings of the present study contribute towards a better understanding of the complex ecological interactions of river dolphins with their environment and provide valuable insights into the wider conservation status of other threatened components of sympatric freshwater biodiversity that can further help in designing effective conservation measures for the ecosystem as a whole.
Community structure of reef fishes in shallow waters of the Fernando de Noronha archipelago: effects of different levels of environmental protection
Authors: Ilarri M. I. , Souza A. T. , Rosa R. S.
Published: October 2016

Marine protected areas (MPAs) are important tools for the evaluation of the biodiversity and status of marine systems. However, not all MPAs are equal in their design and management; therefore, it is important to understand how different levels of protection affect the fish communities. In the present study, the shallow reef-area fishes of seven areas in Fernando de Noronha archipelago (north-eastern Brazil) with dissimilar habitat characteristics and different levels of environmental protection (no-take MPA and MPA) were compared. In total, 140 visual censuses were performed, in which 12958 fishes of 27 families and 50 species were recorded. Differences were recorded between no-take MPAs and MPAs in the benthic composition, abiotic data and fish-community structure and composition. These differences were associated with a higher diversity, richness, density of larger fishes and top target fish families, and biomass per census (nearly 2-fold higher in the no-take MPA). Our findings suggested that the differences in the ichthyofauna were probably more related to the different levels of protection than to dissimilarities in the habitat structure among areas, and that the local no-take MPA (National Marine Park of Fernando de Noronha) is effective in maintaining the shallow reef-area fish communities healthy and diverse.
The composition of organic phosphorus in soils of the Snowy Mountains region of south-eastern Australia
Authors: Doolette Ashlea L. , Smernik Ronald J. , McLaren Timothy I.
Published: October 2016

Few studies have considered the influence of climate on organic phosphorus (P) speciation in soils. We used sodium hydroxide–ethylenediaminetetra-acetic acid (NaOH–EDTA) soil extractions and solution 31P nuclear magnetic resonance spectroscopy to investigate the soil P composition of five alpine and sub-alpine soils. The aim was to compare the P speciation of this set of soils with those of soils typically reported in the literature from other cold and wet locations, as well as those of other Australian soils from warmer and drier environments. For all alpine and sub-alpine soils, the majority of P detected was in an organic form (54–66% of total NaOH–EDTA extractable P). Phosphomonoesters comprised the largest pool of extractable organic P (83–100%) with prominent peaks assigned to myo- and scyllo-inositol hexakisphosphate (IP6), although trace amounts of the neo- and d-chiro-IP6 stereoisomers were also present. Phosphonates were identified in the soils from the coldest and wettest locations; α- and β-glycerophosphate and mononucleotides were minor components of organic P in all soils. The composition of organic P in these soils contrasts with that reported previously for Australian soils from warm, dry environments where inositol phosphate (IP6) peaks were less dominant or absent and humic-P and α- and β-glycerophosphate were proportionally larger components of organic P. Instead, the soil organic P composition exhibited similarities to soils from other cold, wet environments. This provides preliminary evidence that climate is a key driver in the variation of organic P speciation in soils.
Nitrification potential in the rhizosphere of Australian native vegetation
Authors: Chowdhury Saikat , Thangarajan Ramya , Bolan Nanthi , O'Reilly-Wapstra Julianne , Kunhikrishnan Anitha , Naidu Ravi
Published: October 2016

The rhizosphere influences nutrient dynamics in soil mainly by altering microbial activity. The objective of this study was to evaluate the rhizosphere effect on nitrogen transformation in Australian native vegetation in relation to nitrification potential (NP). Microbial activity, NP, and nitrifiers (ammonia-oxidising bacteria, AOB) were compared between rhizosphere and non-rhizosphere soils of several Australian native vegetation under field conditions. These parameters were also measured with increasing distance from the rhizosphere of selected plant species using plant growth experiments. To examine the persistence of nitrification inhibitory activity of rhizosphere soil on non-rhizosphere soil, the soils were mixed at various ratios and examined for NP and AOB populations. The rhizosphere soil from all native vegetation (29 species) had higher microbial activity than non-rhizosphere soil, whereas 13 species showed very low NP in the rhizosphere when compared with non-rhizosphere soil. Nitrification potential and AOB populations obtained in the soil mixture were lower than the predicted values, indicating the persistence of a nitrification inhibitory effect of the rhizosphere soils on non-rhizosphere soils. In plant growth experiments the microbial activity decreased with increasing distance from rhizosphere, whereas the opposite was observed for NP and AOB populations, indicating the selective inhibition of nitrification process in the rhizosphere of the Australian native plants Scaevola albida, Chrysocephalum semipapposum, and Enteropogon acicularis. Some Australian native plants inhibited nitrification in their rhizosphere. We propose future studies on these selected plant species by identifying and characterising the nitrification inhibiting compounds and also the potential of nitrification inhibition in reducing nitrogen losses through nitrate leaching and nitrous oxide emission.
Large‐Scale Changes in Bloater Growth and Condition in Lake Huron
Authors: Prichard Carson G. , Roseman Edward F. , Keeler Kevin M. , O'Brien Timothy P. , Riley Stephen C.
Published: October 2016

Native BloatersCoregonus hoyihave exhibited multiple strong year‐classes since 2005 and now are the most abundant benthopelagic offshore prey fish in Lake Huron, following the crash of nonnative AlewivesAlosa pseudoharengusand substantial declines in nonnative Rainbow SmeltOsmerus mordax. Despite recent recoveries in Bloater abundance, marketable‐size (>229 mm) Bloaters remain scarce. We used annual survey data to assess temporal and spatial dynamics of Bloater body condition and lengths at age in the main basin of Lake Huron from 1973 to 2014. Basinwide lengths at age were modeled by cohort for the 1973–2003 year‐classes using a von Bertalanffy growth model with time‐varying Brody growth coefficient (k) and asymptotic length () parameters. Median Bloater weights at selected lengths were estimated to assess changes in condition by modeling weight–length relations with an allometric growth model that allowed growth parameters to vary spatially and temporally. Estimated Bloater lengths at age declined 14–24% among ages 4–8 for all year‐classes between 1973 and 2004. Estimates ofdeclined from a peak of 394 mm (1973 year‐class) to a minimum of 238 mm (1998 year‐class). Observed mean lengths at age in 2014 were at all‐time lows, suggesting that year‐classes comprising the current Bloater population would have to follow growth trajectories unlike those characterizing the 1973–2003 year‐classes to attain marketable size. Furthermore, estimated weights of 250‐mm Bloaters (i.e., a large, commercially valuable size‐class) declined 17% among all regions from 1976 to 2007. Decreases in body condition of large Bloaters are associated with lower lipid content and may be linked to marked declines in abundance of the amphipodsDiporeiaspp. in Lake Huron. We hypothesize that since at least 1976, large Bloaters have become more negatively buoyant and may have incurred an increasingly greater metabolic cost performing diel vertical migrations to prey upon the opossum shrimpMysis diluvianaand zooplankton.

Received March 4, 2016; accepted July 12, 2016 Published online October 7, 2016
Family Dominance at the Fry Stage Weakly Influences Mean Family Body Length at Smolting in Hatchery‐Reared Steelhead
Authors: Thompson Neil F. , Blouin Michael S.
Published: October 2016

Steelhead Oncorhynchus mykiss reared in hatcheries rapidly adapt to captivity. However, the traits under selection in captivity are not well understood. Hatchery‐reared salmonids are generally more aggressive than wild fish. Therefore, it is possible that selection in hatcheries favors increased aggressiveness because aggressive fish may dominate food resources and grow larger, resulting in a fitness advantage at release. We tested whether family dominance at the fry stage correlates with mean family fork length at smolting of the same families raised in a parallel experiment. Family dominance was assessed when families were first interacting with each other as fry. Juveniles in the parallel experiment were raised at high or low density to determine whether the effect of family dominance on mean family fork length was stronger at low density. More‐dominant families were slightly larger at smolting, and the effect changed little between density treatments. Although the effect we observed was modest, these data are consistent with the hypothesis that dominance as fry is a trait under selection in hatcheries.

Received April 8, 2016; accepted July 28, 2016 Published online October 7, 2016
Using a stakeholder-engaged approach to develop and validate electronic clinical quality measures
Authors: Herndon Jill Boylston , Aravamudhan Krishna , Stephenson Ronald L , Brandon Ryan , Ruff Jesley , Catalanotto Frank , Le Huong
Published: October 2016

Objective: To describe the stakeholder-engaged processes used to develop, specify, and validate 2 oral health care electronic clinical quality measures.

Materials and Methods: A broad range of stakeholders were engaged from conception through testing to develop measures and test feasibility, reliability, and validity following National Quality Forum guidance. We assessed data element feasibility through semistructured interviews with key stakeholders using a National Quality Forum–recommended scorecard. We created test datasets of synthetic patients to test measure implementation feasibility and reliability within and across electronic health record (EHR) systems. We validated implementation with automated reporting of EHR clinical data against manual record reviews, using the kappa statistic.

Results: A stakeholder workgroup was formed and guided all development and testing processes. All critical data elements passed feasibility testing. Four test datasets, representing 577 synthetic patients, were developed and implemented within EHR vendors’ software, demonstrating measure implementation feasibility. Measure reliability and validity were established through implementation at clinical practice sites, with kappa statistic values in the “almost perfect” agreement range of 0.80–0.99 for all but 1 measure component, which demonstrated “substantial” agreement. The 2 validated measures were published in the United States Health Information Knowledgebase.

Conclusion: The stakeholder-engaged processes used in this study facilitated a successful measure development and testing cycle. Engaging stakeholders early and throughout development and testing promotes early identification of and attention to potential threats to feasibility, reliability, and validity, thereby averting significant resource investments that are unlikely to be fruitful.
Matched-filtering line search methods applied to Suzaku data
Authors: Miyazaki Naoto , Yamada Shin'ya , Enoto Teruaki , Axelsson Magnus , Ohashi Takaya
Published: October 2016

A detailed search for emission and absorption lines and an assessment of their upper limits are performed for Suzaku data. The method utilizes a matched-filtering approach to maximize the signal-to-noise ratio for a given energy resolution, which could be applicable to many types of line search. We first applied it to well-known active galactic nuclei spectra that have been reported to have ultra-fast outflows, and find that our results are consistent with previous findings at the ∼3σ level. We proceeded to search for emission and absorption features in two bright magnetars 4U 0142+61 and 1RXS J1708−4009, applying the filtering method to Suzaku data. We found that neither source showed any significant indication of line features, even using long-term Suzaku observations or dividing their spectra into spin phases. The upper limits on the equivalent width of emission/absorption lines are constrained to be a few eV at ∼1 keV and a few hundreds of eV at ∼10 keV. This strengthens previous reports that persistently bright magnetars do not show proton cyclotron absorption features in soft X-rays and, even if they exist, they would be broadened or much weaker than below the detection limit of X-ray CCD.
Fitness-valley crossing in subdivided asexual populations
Authors: McLaren Michael R.
Published: October 2016

Adaptations may require multiple mutations that are beneficial only in combination. To adapt, a lineage must acquire mutations that are individually neutral or deleterious before gaining the beneficial combination, thereby crossing a plateau or valley, respectively, in the mapping from genotype to fitness. Spatial population structure can facilitate plateau and valley crossing by allowing neutral and deleterious lineages to survive longer and produce more beneficial mutants. Here, we analyze adaptation across a two-mutation plateau or valley in an asexual population that is subdivided into discrete subpopulations, or demes, connected by migration. We describe how subdivision alters the dynamics of adaptation from those in an equally sized unstructured population and give a complete quantitative description of these dynamics for the island migration model. Subdivision can significantly decrease the waiting time for the adaptation if demes and migration rates are small enough that single-mutant lineages fix in one or more demes before producing the beneficial double mutant. But, the potential decrease is small in very large populations and may also be limited by the slow spread of the beneficial mutant in extremely subdivided populations. Subdivision has a smaller effect on the probability that the population adapts very quickly than on the mean time to adapt, which has important consequences in some applications, such as the development of cancer. Our results provide a general and intuitive framework for predicting the effects of spatial structure in other models and in natural populations.
TatA complexes exhibit a marked change in organisation in response to expression of the TatBC complex
Authors: Smith Sarah M. , Yarwood Andrew , Fleck Roland A. , Robinson Colin , Smith Corinne J.
Published: October 2016

The twin arginine translocation (Tat) system is an integral membrane protein complex that accomplishes the remarkable feat of transporting large, fully-folded polypeptides across the inner membrane of bacteria, into the periplasm. InEscherichia coliTat is comprised of three membrane proteins: TatA, TatB and TatC. How these proteins arrange themselves in the inner membrane to permit passage of Tat substrates, whilst maintaining membrane integrity, is still poorly understood. TatA is the most abundant component of this complex and facilitates assembly of the transport mechanism. We have utilised immunogold labelling in combination with array tomography to gain insight into the localisation and distribution of the TatA protein inE. colicells. We show that TatA exhibits a uniform distribution throughout the inner membrane ofE. coliand that altering the expression of TatBC shows a previously uncharacterised distribution of TatA in the inner membrane. Array tomography was used to provide our first insight into this altered distribution of TatA in 3D space, revealing that this protein forms linear clusters in the inner membrane ofE.coli upon increased expression of TatBC. This is the first indication that TatA organisation in the inner membrane alters in response to changes in Tat subunit stoichiometry.

Summary statement

The volumetric electron-microscopy technique, array tomography, revealed a novel distribution of TatA protein (from the twin arginine translocase complex), inEscherichia coli.
Comparative transcriptome analysis by deep RNA sequencing at early stage of skin pigmentation in goats (Capra hircus)
Authors: Ren Hangxing , Wang Gaofu , Jiang Jing , Liu Liangjia , Li Nianfu , Li Jie , Fu Lin , Zhang Haiyan , Na Risu , Huang Yongfu , Zhang Li , Chen Lei , Huang Yong , Zhou Peng
Published: October 2016

Although specific genes have been found to be associated with skin pigmentation, the global gene expression profile for the early stage of skin pigmentation and development in mammals is still not well understood. Here we reported a rare natural group of goat (Youzhou dark goat) featuring the dark skin of body including the visible mucous membranes, which may be an exclusive kind of large mammalian species with this special phenotype so far. In the present study, we characterized the 100-day-old fetal skin transcriptome in hyperpigmented (dark-skinned) and wild-type (white-skinned) goats using deep RNA-sequencing. A total of 923,013,870 raw reads from 6 libraries were obtained, and a large number of alternative splicing events were identified in the transcriptome of fetal skin, including the well-known melanogenic genesASIP,TYRP1, andDCT, which were differentially expressed in the skin between the dark-skinned and white-skinned goats. Further analysis demonstrated that differential genes includingASIP,TYRP1,DCT,WNT2,RAB27A,FZD4, andCREB3L1were significantly overrepresented in themelanogenesispathway and several biological process associated with pigmentation. On the other hand, we identified 1616 novel transcripts in goat skin based on the characteristics of their expression level and gene composition. These novel transcripts may represent two distinct groups of nucleic acid molecules. Our findings contribute to the understanding of the characteristics of global gene expression at early stages of skin pigmentation and development, as well as describe an animal model for human diseases associated with pigmentation.
Optimal foraging models reveal barriers and stepping stones to the evolution of host-range generalism in bacteriophage
Authors: Draghi Jeremy
Published: October 2016

The nature and stability of coexistence of specialist species with more generalized competitors present theoretical questions that have been difficult to resolve. Recent surveys of bacteriophage host-ranges suggest that generalist phage often coexistent with specialists. However, previous theoretical work has explained this coexistence only in terms of strict genetic trade-offs, which are not consistently observed when phage are challenged to evolve to multiple hosts in laboratory environments. Here we use the framework of optimal foraging to identify conditions that might prevent generalists from outcompeting specialist relatives. Our analysis shows that heterogeneities in phage life-history properties make host-range specialist more viable, and that endogenous fluctuations in host density permit a narrow window of stable coexistence between specialists and generalists without the need for genetic trade-offs. These results are especially relevant for understanding the barriers to the evolution of broader host-ranges in bacteriophage and other pathogens with similar life-cycles.
GW-CALL: Accurate Genome-Wide Variant Caller
Authors: Ghareghani M. , Motahari S. A. , Khazaei S. , Tavassolipour M.
Published: October 2016

The main challenge in reliable variant calling using DNA reads is to extract information from reads mappable to multiple locations on the reference genome. Conventional approaches ignore these reads and rely on reads mappable uniquely to the reference genome. These approaches fail to perform satisfactorily in variant calling within repeat regions which are abundant in many species including homo sapiens. This, in turn, lowers the reliability of any downstream analysis including poor performance in genome-wide association studies. GW-CALL, a fast and accurate variant caller, is proposed. GW-CALL exploits information of all reads in a genome-wide decision making process. In particular, it partitions the genome into several independent regions called clusters and incorporates an efficient algorithm to use all reads belonging to a cluster in calling variants within that cluster.

Availability

GW-CALL is implemented in C++ and is freely available at URL:brl.ce.sharif.edu/gwcall.
Exploratory bioinformatics analysis reveals importance of “junk” DNA in early embryo development
Authors: Ge Steven Xijin
Published: October 2016

Background

Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to investigate how the early mouse embryos develop from fertilized eggs through a complex, poorly understood process.

Results

Starting with a single-cell RNA-seq dataset of 259 mouse embryonic cells from zygote to blastocyst stages, we reconstructed the temporal and spatial dynamics of gene expression. Our analyses revealed similarities in the expression patterns of regular genes and those of retrotransposons, and the enrichment of transposable elements in the promoters of corresponding genes. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. The presence of B1 and B2 SINEs (Short Interspersed Nuclear Elements) in promoters is highly correlated with broad upregulation of intracellular genes in a dosage-and distance-dependent manner. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. Promoters for genes specifically expressed in embryonic stem cells (ESCs) are rich in B1 and B2 SINEs, but low in CpG islands.

Conclusions

Our results provide evidence that transposable elements may play a significant role in establishing the expression landscape in early embryos and stem cells. This study also demonstrates that open-ended, exploratory analysis aimed at a broad understanding of a complex process can pinpoint specific mechanisms for further study.

Major finding

Single-cell RNA-seq data enables estimation of retrotransposon expression during PD

Similar expression dynamics of retrotransposons and regular genes during PD

Long terminal repeats may be essential for the 1stwave of gene expression

Obox homeobox factors are possible regulators of PD, upstream of Zscan4

SINE repeats predict expression of nearby genes in murine, human and bovine embryos

Exploratory analysis of large single-cell data pinpoints developmental pathways
Research article, Biological Sciences - Anthropology, Genetics Of cats and men: the paleogenetic history of the dispersal of cats in the ancient world
Authors: Ottoni Claudio , Van Neer Wim , De Cupere Bea , Daligault Julien , Guimaraes Silvia , Peters Joris , Spassov Nikolai , Prendergast Mary E. , Boivin Nicole , Morales Arturo , Bălăşescu Adrian , Becker Cornelia , Benecke Norbert , Boronenanţ Adina , Buitenhuis Hijlke , Chahoud Jwana , Crowther Alison , Llorente Laura , Manaseryan Nina , Monchot Hervé , Onar Vedat , Osypińska Marta , Putelat Olivier , Studer Jacqueline , Wierer Ursula , Decorte Ronny , Grange Thierry , Geigl Eva-Maria
Published: October 2016

The origin and dispersal of the domestic cat remain elusive despite its importance to human societies around the world. Archaeological evidence for domestication centers in the Near East and in Egypt is contested, and genetic data on modern cats show thatFelis silvestris lybica, the subspecies of wild cat inhabiting at present the Near East and Northern Africa, is the only ancestor of the domestic cat. Here we provide the first broad geographic and chronological dataset of ancient cat mtDNA sequences, drawing on archaeological specimens from across western Eurasia and northern and eastern Africa, dating from throughout the Holocene and spanning ~9,000 years. We characterized the ancient phylogeography ofF. s. lybica,showing that it expanded up to southeastern Europe prior to the Neolithic, and reconstructed the subsequent movements that profoundly transformed its distribution and shaped its early cultural history. We found that maternal lineages from both the Near East and Egypt contributed to the gene pool of the domestic cat at different historical times, with the Near Eastern population providing the first major contribution during the Neolithic and the Egyptian cat spreading efficiently across the Old World during the Classical period. This expansion pattern and range suggest dispersal along maritime and terrestrial routes of trade and connectivity. Late trait selection is suggested by the first occurrence in our dataset of the major allele for blotched-tabby body marking not earlier than during the Late Middle Ages.

Significance

The cat has long been important to human societies as a pest-control agent, object of symbolic value, and companion animal, but little is known about its domestication process and early anthropogenic dispersal. Our DNA analyses of geographically and temporally widespread archaeological cat remains show that while the cat’s world-wide conquest began in prehistoric times, when tamed cats accompanied humans on their journeys over land and sea, it gained momentum during the Classical period, when the Egyptian cat successfully spread throughout the ancient world. The appearance of a new coat pattern at the end of the Middle Ages suggests late breeding control that might explain the semi-domestic status of the cat. This distinguishes the domestication process of cats from that of most other domesticates.
Energy subtraction angiography is comparable to digital subtraction angiography in terms of iodine Rose SNR
Authors: Burton Christiane S. , Mayo John R. , Cunningham Ian A.
Published: October 2016

Purpose

X‐ray digital subtraction angiography (DSA) is widely used for vascular imaging. However, motion artifacts render it largely unsuccessful for some applications including cardiac imaging. Dual‐energy imaging using fast kV switching was proposed in the past to provide the benefits of DSA with fewer motion artifacts, but image quality was inferior to DSA. This study compares the iodine Rose SNR that can be achieved using dual‐energy methods, called energy‐subtraction angiography (ESA), with that of DSA and examines the technical conditions required to achieve near‐optimal SNR.

Methods

A Rose SNR model is described, experimentally validated, and used to compare ESA with DSA. The model considers detector quantum efficiency, readout noise (quantum‐limit exposure), and scatter‐to‐primary ratio.

Results

The theoretical Rose SNR showed excellent agreement with experimental results for both ESA and DSA images, and shows that near‐optimal SNR is harder to achieve with ESA than DSA. In comparison to DSA, ESA requires: (1) high detector quantum efficiency at a higher energy (120 kV); (2) lower detector readout noise by a factor of four (approximately 0.005 μGy air KERMA or lower); and (3) lower scatter‐to‐primary ratio by a factor of three (approximately 0.05 or lower). These conditions were not achievable in the past, and remain difficult but not impossible to achieve at present.

Conclusions

ESA and DSA can provide similar iodine Rose SNR for the same patient exposure, but only when satisfying the above conditions. This may explain why dual‐energy methods have been unsuccessful in the past and suggests ESA methods may offer a viable alternative to DSA when implemented under optimal conditions.