bluuebunny/crossref_metadata_2025 huggingface dataset:
Redox Linked Flavin Sites in Extracellular Decaheme Proteins Involved in Microbe-Mineral Electron Transfer.
Authors: Edwards Marcus J. , White Gaye F. , Norman Michael , Tome-Fernandez Alice , Ainsworth Emma , Shi Liang , Fredrickson Jim K. , Zachara John M. , Butt Julea N. , Richardson David J. , Clarke Thomas A.
Published: July 2015

Extracellular microbe-mineral electron transfer is a major driving force for the oxidation of organic carbon in many subsurface environments. Extracellular multi-heme cytochromes of the Shewenella genus play a major role in this process but the mechanism of electron exchange at the interface between cytochrome and acceptor is widely debated. The 1.8 Å x-ray crystal structure of the decaheme MtrC revealed a highly conserved CX8C disulfide that, when substituted for AX8A, severely compromised the ability of S. oneidensis to grow under aerobic conditions. Reductive cleavage of the disulfide in the presence of flavin mononucleotide (FMN) resulted in the reversible formation of a stable flavocytochrome. Similar results were also observed with other decaheme cytochromes, OmcA, MtrF and UndA. The data suggest that these decaheme cytochromes can transition between highly reactive flavocytochromes or less reactive cytochromes and that this transition is controlled by a redox active disulfide that responds to the presence of oxygen.
A systematic analysis of human lipocalin family and its expression in esophageal carcinoma
Authors: Du Ze-Peng , Wu Bing-Li , Wu Xuan , Lin Xuan-Hao , Qiu Xiao-Yang , Zhan Xiao-Fen , Wang Shao-Hong , Shen Jin-Hui , Zheng Chun-Peng , Wu Zhi-Yong , Xu Li-Yan , Wang Dong , Li En-Min
Published: July 2015

The lipocalin proteins (lipocalins) are a large family of small proteins characterized by low sequence similarity and highly conserved crystal structures. Lipocalins have been found to play important roles in many human diseases. For this reason, a systemic analysis of the molecular properties of human lipocalins is essential. In this study, human lipocalins were found to contain four structurally conserved regions (SCRs) and could be divided into two subgroups. A human lipocalin protein-protein interaction network (PPIN) was constructed and integrated with their expression data in esophageal carcinoma. Many lipocalins showed obvious co-expression patterns in esophageal carcinoma. Their subcellular distributions also suggested these lipocalins may transfer signals from the extracellular space to the nucleus using the pathway-like paths. These analyses also expanded our knowledge about this human ancient protein family in the background of esophageal carcinoma.
Hierarchical Core/Shell NiCo2O4@NiCo2O4 Nanocactus Arrays with Dual-functionalities for High Performance Supercapacitors and Li-ion Batteries
Authors: Cheng Jinbing , Lu Yang , Qiu Kangwen , Yan Hailong , Xu Jinyou , Han Lei , Liu Xianming , Luo Jingshan , Kim Jang-Kyo , Luo Yongsong
Published: July 2015

We report the synthesis of three dimensional (3D) NiCo2O4@NiCo2O4nanocactus arrays grown directly on a Ni current collector using a facile solution method followed by electrodeposition. They possess a unique 3D hierarchical core-shell structure with large surface area and dual-functionalities that can serve as electrodes for both supercapacitors (SCs) and lithium-ion batteries (LIBs). As the SC electrode, they deliver a remarkable specific capacitance of 1264 F g−1at a current density of 2 A g−1and ~93.4% of capacitance retention after 5000 cycles at 2 A g−1. When used as the anode for LIBs, a high reversible capacity of 925 mA h g−1is achieved at a rate of 120 mA g−1with excellent cyclic stability and rate capability. The ameliorating features of the NiCo2O4core/shell structure grown directly on highly conductive Ni foam, such as hierarchical mesopores, numerous hairy needles and a large surface area, are responsible for the fast electron/ion transfer and large active sites which commonly contribute to the excellent electrochemical performance of both the SC and LIB electrodes.
Comment on “Sensitive marker bands for the detection of spin states of heme in surface-enhanced resonance Raman scattering spectra of metmyoglobin” by Y. Kitahama, M. Egashira, T. Suzuki, I. Tanabe and Y. Ozaki
Authors: Feis A. , Smulevich G.
Published: July 2015

We contrast recently reported surface-enhanced resonance Raman spectra (SERRS) of myoglobin on silver nanoparticles with established knowledge about this complex.
Self-assembly induced solubilization of drug-like molecules in nanostructured ionic liquids
Authors: Jin Wenbin , Yang Qiwei , Zhang Zhiguo , Bao Zongbi , Ren Qilong , Yang Yiwen , Xing Huabin
Published: July 2015

The self-assembly induced solubilization strategy features the formation of highly ordered mesoscopic structures, such as liquid crystals, through self-assembly of a solute in nanostructured ILs via H-bond interactions, resulting in unprecedented solubility for drug molecules.
Removal of chlorine gas by an amine functionalized metal–organic framework via electrophilic aromatic substitution
Authors: DeCoste Jared B. , Browe Matthew A. , Wagner George W. , Rossin Joseph A. , Peterson Gregory W.
Published: July 2015

Chlorine gas is removed from airstreams with an amine functionalized metal–organic framework via an electrophilic aromatic substitution reaction producing HCl, which is subsequently neutralized by the substrate.
Reaction-based phosphorescent nanosensor for ratiometric and time-resolved luminescence imaging of fluoride in live cells
Authors: Liu Shujuan , Zhang Jie , Shen Danfeng , Liang Hua , Liu Xiangmei , Zhao Qiang , Huang Wei
Published: July 2015

A two-channel phosphorescent nanosensor has been designed for use in ratiometric and time-resolved luminescence imaging of intracellular F−.
One-pot microfluidic fabrication of graphene oxide-patched hollow hydrogel microcapsules with remarkable shell impermeability
Authors: Byun Aram , Shim Jongwon , Han Sang Woo , Kim Bohyun , Chae Pil Seok , Shin Hyeong Seok , Kim Jin Woong
Published: July 2015

Uniform hollow hydrogel microcapsules, composed of a graphene oxide platelet-patched hydrogel shell, are fabricated in one step in a capillary-based microfluidic device.
An ultraselective and ultrasensitive TEA sensor based on α-MoO3 hierarchical nanostructures and the sensing mechanism
Authors: Sui Lili , Song Xiaoxiao , Cheng Xiaoli , Zhang Xianfa , Xu Yingming , Gao Shan , Wang Ping , Zhao Hui , Huo Lihua
Published: July 2015

Flower-like α-MoO3 hierarchical nanostructures were successfully synthesized via a single-step solvothermal route. A sensor based on α-MoO3 flowers manifested superior gas sensing performance towards TEA at 170 °C.
Dissecting kinetic pathways to formation of the fibrillar objects in molecular gels using synchrotron FT-IR
Authors: Rogers Michael A. , Liu Xia , Mallia V. Ajay , Weiss Richard G.
Published: July 2015

Infra-red synchrotron radiation is used to monitor the formation of fibrillar networks as sols of simple gelators become gels.
Probing keto–enol tautomerism using photoelectron spectroscopy
Authors: Capron Nathalie , Casier Bastien , Sisourat Nicolas , Piancastelli Maria Novella , Simon Marc , Carniato Stéphane
Published: July 2015

We theoretically investigate the mechanism of tautomerism in the gas-phase acetylacetone molecule.
How does bile salt penetration affect the self-assembled architecture of pluronic P123 micelles? – light scattering and spectroscopic investigations
Authors: Roy Arpita , Kundu Niloy , Banik Debasis , Kuchlyan Jagannath , Sarkar Nilmoni
Published: July 2015

The triblock copolymer of the type (PEO)20–(PPO)70–(PEO)20 (P123) forms a mixed supramolecular aggregate with different bile salts, sodium deoxycholate (NaDC) and sodium taurocholate (NaTC), having different hydrophobicity.
Solar energy utilization in the direct photocarboxylation of 2,3-dihydrofuran using CO2
Authors: Aresta Michele , Dibenedetto Angela , Baran Tomasz , Wojtyła Szymon , Macyk Wojciech
Published: July 2015

The conversion of CO2 into high energy products (fuels) and the direct carboxylation of C–H bonds require a high energy input. Energy cannot be derived from fossil carbon, in this case. Solar energy can be used instead, with a low environmental impact and good profit. We have studied the use of white light or solar energy in the photoreduction of CO2 and in photocarboxylation reactions, using different semiconductors modified at their surface. Two examples of reduction of CO2 to methanol and CO will be shortly discussed, and two cases of carboxylation of organic substrates. The case of carboxylation of 2,3-dihydrofuran will be discussed in detail.
Shell decoration of hydrothermally obtained colloidal carbon spheres with base metal nanoparticles
Authors: Hoekstra Jacco , Beale Andrew M. , Soulimani Fouad , Versluijs-Helder Marjan , Geus John W. , Jenneskens Leonardus W.
Published: July 2015

Carbothermal formation of first-row transition metal nanoparticles onto colloidal carbon supports from hydrothermal treatment of sucrose followed by catalytic graphitization.
Double substitution induced tunable photoluminescence in the Sr2Si5N8:Eu phosphor lattice
Authors: Chuang Wang , Shuangyu Xin , Xicheng Wang , Ge Zhu , Quansheng Wu , Yuhua Wang
Published: July 2015

The incorporation of La3+–Al3+ ion pairs into Sr1.95Eu0.05Si5N8 leads to an additional emission band with maximum at about 760 nm.
Hydrogen production by aqueous-phase reforming of ethylene glycol over a Ni/Zn/Al derived hydrotalcite catalyst
Authors: Chen Guanyi , Xu Ningge , Li Xiangping , Liu Qingling , Yang Huijun , Li Wanqing
Published: July 2015

The article presented the aqueous-phase reforming of ethylene glycol over Ni/Zn/Al hydrotalcite. The results showed that the H2 yield and selectivity were 73% and 96%, respectively. The conversion of ethylene glycol was >99%.
Combined effect of ether and siloxane substituents on imidazolium ionic liquids
Authors: Chavan Santosh N. , Mandal Debaprasad
Published: July 2015

The combined effect of ether and siloxane substituents on imidazolium cations helps overcome the Coulombic attraction, van der Waals forces, size factor and conformational degree of freedom, and exerts an impact on viscosity, density and thermal properties of ionic liquids.
Colorimetric and fluorescent detection of GSH with the assistance of CTAB micelles
Authors: Song Lun , Tian Haiyu , Pei Xiaoliang , Zhang Ziyou , Zhang Weibing , Qian Junhong
Published: July 2015

Two fluorescent probesSTP1–2for GSH and mercapto-containing proteins were designed. Both probes have potential application in fluorescence imaging of GSH within living cells.
Enhanced power factor in the promising thermoelectric material SnPbxTe prepared via zone-melting
Authors: He Jun , Xu Jingtao , Liu Guoqiang , Tan Xiaojian , Shao Hezhu , Liu Zhu , Xu Jiaqiang , Jiang Jun , Jiang Haochuan
Published: July 2015

Tin telluride (SnTe) has recently attracted much attention as a promising thermoelectric material. By alloying with Pb using a zone-melting method, the maximum power factor of SnTe alloys reaches 30.5 μW cm−1 K−2, and a ZT of 0.81 has been obtained.
White organic light emitting diodes based on a yellow thermally activated delayed fluorescent emitter and blue fluorescent emitter
Authors: Meng Lingqiang , Wang Hui , Wei Xiaofang , Lv Xiaopeng , Wang Ying , Wang Pengfei
Published: July 2015

Multi-emissive layered white organic light-emitting diodes (WOLEDs) based on a blue fluorescent emitter and a yellow thermally activated delayed fluorescent emitter were constructed with the co-host of mCP.
Graphene oxide nanoparticle attachment and its toxicity on living lung epithelial cells
Authors: Ahlinder Linnea , Henych Jiří , Lindström Susanne Wiklund , Ekstrand-Hammarström Barbro , Stengl Václav , Österlund Lars
Published: July 2015

Since its discovery graphene and its oxidized form graphene oxide have attracted interest in a wide range of applications, which calls for scrutinized studies about their possible toxicity.
Magnetic CuO@Fe3O4 nanocomposite as a highly active heterogeneous catalyst of persulfate for 2,4-dichlorophenol degradation in aqueous solution
Authors: Sun Chao , Zhou Rui , E Jianan , Sun Jiaqiang , Ren Hejun
Published: July 2015

Fe3O4@CuO nanocomposite was fabricated through a novel impregnation method. Both sulfate radicals and hydroxyl radicals can be produced effectively in the activated persulfate system by the composite to degrade the 2,4-dichlorophenol.
A porous nitrogen and phosphorous dual doped graphene blocking layer for high performance Li–S batteries
Authors: Gu Xingxing , Tong Chuan-jia , Lai Chao , Qiu Jingxia , Huang Xiaoxiao , Yang Wenlong , Wen Bo , Liu Li-min , Hou Yanglong , Zhang Shanqing
Published: July 2015

A porous N and P dual doped graphene interlayer was fabricated for improved conductivity and polysulfide capture in Li–S batteries, supported by first-principles DFT calculations.
Differential sub-cellular processing of single-wall carbon nanotubes via interfacial modifications
Authors: Holt Brian D. , Dahl Kris Noel , Islam Mohammad F.
Published: July 2015

Real-space and fluorescence lifetime imaging reveal that non-covalently attached dispersing agents influence sub-cellular trafficking and localization of carbon nanotubes.
Properties and reactivity of polyoxazoline plasma polymer films
Authors: Macgregor-Ramiasa Melanie N. , Cavallaro Alex A. , Vasilev Krasimir
Published: July 2015

Nanoscale polyoxazoline coatings generatedviaa single step plasma deposition process are investigated. The complex functionality of the film can be controlled by varying the deposition conditions. Partial retention of the oxazoline ring facilitates covalent binding of nanoparticles and biomolecules.
Enhanced chemotherapy efficacy by co-delivery of shABCG2 and doxorubicin with a pH-responsive charge-reversible layered graphene oxide nanocomplex
Authors: He Yuling , Zhang Lifen , Chen Zhenzhen , Liang Yong , Zhang Yushun , Bai Yanli , Zhang Jing , Li Yanfeng
Published: July 2015

pH responsive charge-reversible GO–PEI–PEG/DOX/CS-Aco/PEI/shABCG2 nanocomplexes for efficient intracellular DOX and shABCG2 co-delivery.
On-demand and negative-thermo-swelling tissue adhesive based on highly branched ambivalent PEG–catechol copolymers
Authors: Zhang Hong , Zhao Tianyu , Newland Ben , Duffy Patrick , Annaidh Aisling Ní , O'Cearbhaill Eoin D. , Wang Wenxin
Published: July 2015

A series of well-designed highly branched PEG–catechol based thermo-responsive copolymers were synthesized via a one-pot RAFT polymerization.
Chromaticity-tunable phosphor-in-glass for long-lifetime high-power warm w-LEDs
Authors: Chen Hui , Lin Hang , Xu Ju , Wang Bo , Lin Zebin , Zhou Jiangcong , Wang Yuansheng
Published: July 2015

This work highlights the practical applications of the PiG luminescent material in long-lifetime high-power warm w-LEDs.
New highly efficient electrochemical synthesis of dispersed Ag2O particles in the vicinity of the cathode with controllable size and shape
Authors: Pham Quoc-Thai , Huy Bui The , Lee Yong-Ill
Published: July 2015

Silver(i) oxide (Ag2O) hexapod particles were electrochemically synthesized with high efficiency in an aqueous solution of silver nitrate and sodium sulfate.
Reduced thermal degradation of the red-emitting Sr2Si5N8:Eu2+ phosphor via thermal treatment in nitrogen
Authors: Zhang Chenning , Uchikoshi Tetsuo , Xie Rong-Jun , Liu Lihong , Cho Yujin , Sakka Yoshio , Hirosaki Naoto , Sekiguchi Takashi
Published: July 2015

Thermal degradation of the Sr2Si5N8:Eu2+ phosphor reduced by the formation of a passivation surface layer around the phosphor particle, which inhibits Eu2+ oxidation.
Soaking based invisible photonic print with a fast response and high resolution
Authors: Ye Siyun , Ge Jianping
Published: July 2015

High-resolution invisible patterns printed on uncrosslinked SiO2/PEGMA photonic paper can be quickly revealed by water soaking and hidden by drying.
Loss of DNase II function in the gonad is associated with a higher expression of antimicrobial genes in Caenorhabditis elegans
Authors: Yu Hsiang , Lai Huey-Jen , Lin Tai-Wei , Chen Chang-Shi , Lo Szecheng J.
Published: July 2015

Three waves of apoptosis shape the development of Caenorhabditis elegans. Although the exact roles of the three DNase II genes (nuc-1, crn-6 and crn-7), which are known to mediate degradation of apoptotic DNA, in the embryonic and larval phases of apoptosis have been characterized, the DNase II acting in the third wave of germ cell apoptosis remains undetermined. In the present study, we performed in vitro and in vivo assays on various mutant nematodes to demonstrate that NUC-1 and CRN-7, but not CRN-6, function in germ cell apoptosis. In addition, in situ DNA-break detection and anti-phosphorylated ERK (extracellular-signal-regulated kinase) staining illustrated the sequential and spatially regulated actions of NUC-1 and CRN-7, at the pachytene zone of the gonad and at the loop respectively. In line with the notion that UV-induced DNA fragment accumulation in the gonad activates innate immunity responses, we also found that loss of NUC-1 and CRN-7 lead to up-regulation of antimicrobial genes (abf-2, spp-1, nlp-29, cnc-2, and lys-7). Our observations suggest that an incomplete digestion of DNA fragments resulting from the absence of NUC-1 or CRN-7 in the gonad could induce the ERK signalling, consequently activating antimicrobial gene expression. Taken together, the results of the present study demonstrate for the first time that nuc-1 and crn-7 play a role in degrading apoptotic DNA in distinct sites of the gonad, and act as negative regulators of innate immunity in C. elegans.
Tone mapping based on fast image decomposition and multi‐layer fusion
Authors: Fang Huameng , Yi Benshun , Zhang Yongqin , Xie Qiuying
Published: July 2015

To solve the problem of low efficiency and colour distortion in several typical tone mapping operators for high dynamic range (HDR) images, the authors propose a novel tone mapping algorithm based on fast image decomposition and multi‐layer fusion. An input HDR image is firstly decomposed into a base layer and a detail layer by an improved guided filtering method. For the base layer, its dynamic range is compressed by the simulated camera response function. For the detail layer, it is enhanced to produce more fine structures and reduce halo effect by applying the guided image filter. The colour balance correction method is adopted to suppress colour distortion. The experiments on HDR images demonstrate that the proposed technique could bring better brightness, contrast, and visibility with less halo effect than other state‐of‐the‐art methods both qualitatively and quantitatively in most cases.
Microwave flexible transistors on cellulose nanofibrillated fiber substrates
Authors: Seo Jung-Hun , Chang Tzu-Hsuan , Lee Jaeseong , Sabo Ronald , Zhou Weidong , Cai Zhiyong , Gong Shaoqin , Ma Zhenqiang
Published: July 2015

In this paper, we demonstrate microwave flexible thin-film transistors (TFTs) on biodegradable substrates towards potential green portable devices. The combination of cellulose nanofibrillated fiber (CNF) substrate, which is a biobased and biodegradable platform, with transferrable single crystalline Si nanomembrane (Si NM), enables the realization of truly biodegradable, flexible, and high performance devices. Double-gate flexible Si NM TFTs built on a CNF substrate have shown an electron mobility of 160 cm2/V·s and fT and fmax of 4.9 GHz and 10.6 GHz, respectively. This demonstration proves the microwave frequency capability and, considering today's wide spread use of wireless devices, thus indicates the much wider utility of CNF substrates than that has been demonstrated before. The demonstration may also pave the way toward portable green devices that would generate less persistent waste and save more valuable resources.
The Effect of Quantum-Mechanical Interference on Precise Measurements of the n = 2 Triplet P Fine Structure of Helium
Authors: Marsman A. , Horbatsch M. , Hessels E. A.
Published: July 2015

For many decades, improvements in both theory and experiment of the fine structure of the n = 2 triplet P levels of helium have allowed for an increasingly precise determination of the fine-structure constant. Recently, it has been observed that quantum-mechanical interference between neighboring resonances can cause significant shifts, even if such neighboring resonances are separated by thousands of natural widths. The shifts depend in detail on the experimental method used for the measurement, as well as the specific experimental parameters employed. Here, we review how these shifts apply for the most precise measurements of the helium 23P fine-structure intervals.
A modified Lax-Phillips scattering theory for quantum mechanics
Authors: Strauss Y.
Published: July 2015

The Lax-Phillips scattering theory is an appealing abstract framework for the analysis of scattering resonances. Quantum mechanical adaptations of the theory have been proposed. However, since these quantum adaptations essentially retain the original structure of the theory, assuming the existence of incoming and outgoing subspaces for the evolution and requiring the spectrum of the generator of evolution to be unbounded from below, their range of applications is rather limited. In this paper, it is shown that if we replace the assumption regarding the existence of incoming and outgoing subspaces by the assumption of the existence of Lyapunov operators for the quantum evolution (the existence of which has been proved for certain classes of quantum mechanical scattering problems), then it is possible to construct a structure analogous to the Lax-Phillips structure for scattering problems for which the spectrum of the generator of evolution is bounded from below.
Automatic differentiation method for numerical construction of the rotational-vibrational Hamiltonian as a power series in the curvilinear internal coordinates using the Eckart frame
Authors: Yachmenev Andrey , Yurchenko Sergei N.
Published: July 2015

We present a new numerical method to construct a rotational-vibrational Hamiltonian of a general polyatomic molecule in the Eckart frame as a power series expansion in terms of curvilinear internal coordinates. The expansion of the kinetic energy operator of an arbitrary order is obtained numerically using an automatic differentiation (AD) technique. The method is applicable to molecules of arbitrary size and structure and is flexible for choosing various types of internal coordinates. A new way of solving the Eckart-frame equations for curvilinear coordinates also based on the AD technique is presented. The resulting accuracy of the high-order expansion coefficients for the kinetic energy operator using our numerical technique is comparable to that obtained by symbolic differentiation, with the advantage of being faster and less demanding in memory. Examples for H2CO, NH3, PH3, and CH3Cl molecules demonstrate the advantages of the curvilinear internal coordinates and the Eckart molecular frame for accurate ro-vibrational calculations. Our results show that very high accuracy and quick convergence can be achieved even with moderate expansions if curvilinear coordinates are employed, which is important for applications involving large polyatomic molecules.
Quantum chemical ab initio prediction of proton exchange barriers between CH4 and different H-zeolites
Authors: Tuma Christian , Sauer Joachim
Published: July 2015

A hybrid MP2:DFT (second-order Møller–Plesset perturbation theory–density functional theory) method that combines MP2 calculations for cluster models with DFT calculations for the full periodic structure is used to localize minima and transition structures for proton jumps at different Brønsted sites in different frameworks (chabazite, faujasite, ferrierite, and ZSM-5) and at different crystallographic positions of a given framework. The MP2 limit for the periodic structures is obtained by extrapolating the results of a series of cluster models of increasing size. A coupled-cluster (CCSD(T)) correction to MP2 energies is calculated for cluster models consisting of three tetrahedra. For the adsorption energies, this difference is small, between 0.1 and 0.9 kJ/mol, but for the intrinsic proton exchange barriers, this difference makes a significant (10.85 ± 0.25 kJ/mol) and almost constant contribution across different systems. The total values of the adsorption energies vary between 22 and 34 kJ/mol, whereas the total proton exchange energy barriers fall in the narrow range of 152–156 kJ/mol. After adding nuclear motion contributions (harmonic approximation, 298 K), intrinsic enthalpy barriers between 134 and 141 kJ/mol and apparent energy barriers between 105 and 118 kJ/mol are predicted for the different sites examined for the different frameworks. These predictions are consistent with experimental results available for faujasite, ferrierite, and ZSM-5.
BEOL compatible high tunnel magneto resistance perpendicular magnetic tunnel junctions using a sacrificial Mg layer as CoFeB free layer cap
Authors: Swerts J. , Mertens S. , Lin T. , Couet S. , Tomczak Y. , Sankaran K. , Pourtois G. , Kim W. , Meersschaut J. , Souriau L. , Radisic D. , Van Elshocht S. , Kar G. , Furnemont A.
Published: July 2015

Perpendicularly magnetized MgO-based tunnel junctions are envisaged for future generation spin-torque transfer magnetoresistive random access memory devices. Achieving a high tunnel magneto resistance and preserving it together with the perpendicular magnetic anisotropy during BEOL CMOS processing are key challenges to overcome. The industry standard technique to deposit the CoFeB/MgO/CoFeB tunnel junctions is physical vapor deposition. In this letter, we report on the use of an ultrathin Mg layer as free layer cap to protect the CoFeB free layer from sputtering induced damage during the Ta electrode deposition. When Ta is deposited directly on CoFeB, a fraction of the surface of the CoFeB is sputtered even when Ta is deposited with very low deposition rates. When depositing a thin Mg layer prior to Ta deposition, the sputtering of CoFeB is prevented. The ultra-thin Mg layer is sputtered completely after Ta deposition. Therefore, the Mg acts as a sacrificial layer that protects the CoFeB from sputter-induced damage during the Ta deposition. The Ta-capped CoFeB free layer using the sacrificial Mg interlayer has significantly better electrical and magnetic properties than the equivalent stack without protective layer. We demonstrate a tunnel magneto resistance increase up to 30% in bottom pinned magnetic tunnel junctions and tunnel magneto resistance values of 160% at resistance area product of 5 Ω.μm2. Moreover, the free layer maintains perpendicular magnetic anisotropy after 400 °C annealing.
A comparative study of transport properties of monolayer graphene and AlGaN-GaN heterostructure
Authors: Ozdemir M. D. , Atasever O. , Ozdemir B. , Yarar Z. , Ozdemir M.
Published: July 2015

The electronic transport properties of monolayer graphene are presented with an Ensemble Monte Carlo method where a rejection technique is used to account for the occupancy of the final states after scattering. Acoustic and optic phonon scatterings are considered for intrinsic graphene and in addition, ionized impurity and surface roughness scatterings are considered for the case of dirty graphene. The effect of screening is considered in the ionized impurity scattering of electrons. The time dependence of drift velocity of carriers is obtained where overshoot and undershoot effects are observed for certain values of applied field and material parameters for intrinsic graphene. The field dependence of drift velocity of carriers showed negative differential resistance and disappeared as acoustic scattering becomes dominant for intrinsic graphene. The variation of electron mobility with temperature is calculated for intrinsic (suspended) and dirty monolayer graphene sheets separately and they are compared. These are also compared with the mobility of two dimensional electrons at an AlGaN/GaN heterostructure. It is observed that interface roughness may become very effective in limiting the mobility of electrons in graphene.
Fatty acid composition and mRNA expression levels of lipid-metabolic genes in the muscles of ovariectomised young goats
Authors: Zhang Lei , Wang Yan-yan , Zhou Zhan-qin , Fu Ming-zhe , Li Guang , Peng Fang , Wan Lu
Published: July 2015

This study investigated the fatty acid composition and mRNA levels of acetyl-coenzyme A carboxylase (ACC), fatty acid synthase (FAS), hormone-sensitive lipase (HSL) and lipoprotein lipase (LPL) genes in the Longissimus dorsi muscle (LD) and Biceps femoris muscle (BF) of nine ovariectomised young goats, 50 days after ovariectomy at 5 months of age, relative to nine Control goats. Ovariectomy resulted in faster growth rates (130 vs 110 g/days; P = 0.027), more intramuscular fat (3.37% vs 1.62%; P = 0.009) and heavier final weights (28.3 vs 26.6 kg; P = 0.035). The total saturated fatty acid, C15:0 in the LD and C6:0, C11:0, C12:0, C15:0 and C21:0 in the BF were lower in ovariectomised goats than that in the Control goats (P < 0.05). Ovariectomy increased the total monounsaturated fatty acids in the LD (P < 0.05) and BF (P < 0.01). In the BF, the total polyunsaturated fatty acids and C18:2 of ovariectomised goats were lower than those of the Control goats (P < 0.05), and the C20:2 content significantly decreased in the LD (P < 0.05). The LD of the ovariectomised goats expressed significantly higher FAS but lower HSL mRNA levels than those of Control goats (P < 0.01). Significantly higher ACC, FAS and LPL and lower HSL mRNA levels were observed in the BF of the ovariectomised goats than in the BF of Controls (P < 0.05). These data suggest that ovariectomy affects fatty acid composition potentially by altering the expression of lipid-metabolic genes in the muscles of young goats.
Novel protein Callipygian defines the back of migrating cells
Authors: Swaney Kristen F. , Borleis Jane , Iglesias Pablo A. , Devreotes Peter N.
Published: July 2015

Significance

Though the asymmetric distribution of proteins is a crucial first step in establishing polarity and guiding cell migration, the molecular mechanisms regulating many of these localizations are unknown. Our study reports on the novel protein Callipygian (CynA), which localizes to the rear of cells during symmetry breaking, thereby promoting polarity and increasing migration efficiency. Our data indicate that CynA localization is mediated by two distinct mechanisms, which may be important for segregating proteins in other polarized cell types including epithelial cells, neurons, and immune cells. Thus, our findings have implications for tissue formation during embryonic development, the migration of immune cells during wound healing and infection, and the aberrant migrations associated with arthritis, asthma, atherosclerosis, cancer metastasis, and other diseases.
Recreational Fishing Effort, Catch, and Harvest for Murray Cod and Golden Perch in the Murrumbidgee River, Australia
Authors: Forbes Jamin P. , Watts Robyn J. , Robinson Wayne A. , Baumgartner Lee J. , Steffe Aldo S. , Murphy Jeff J.
Published: July 2015

Recreational fishery management aims to prevent species decline and provide sustainable fisheries. Overfishing has been frequently suggested as a cause of historic fishery declines within the Murray–Darling Basin (MDB), Australia, but there have been few quantitative surveys for providing fishery-dependent data to gauge status. The Murray Cod Maccullochella peelii and the Golden Perch Macquaria ambigua are important species targeted by recreational fishers across the MDB. The fisheries are controlled by size and bag limits and gear restrictions (both species) as well as a closed season (Murray Cod only). A complemented fisher survey design was used to assess the recreational fishery for both species in a 76-km reach of the Murrumbidgee River in 2012–2013. Progressive counts were used to quantify boat- and shore-based fishing effort. Catch and harvest rate information was obtained from shore-based fishers via roving surveys and from boat-based fishers via bus route surveys. Murray Cod catch rates (fish/angler-hour) were 0.228 ± 0.047 (mean ± SE; boat based) and 0.092 ± 0.023 (shore based), and harvest rates (fish/angler-hour) were 0.013 ± 0.006 (boat based) and 0.003 ± 0.001 (shore based). Golden Perch catch rates were 0.018 ± 0.009 (shore based) and 0.002 ± 0.001 (boat based), and harvest rates were 0.006 ± 0.002 (shore based) and 0.001 ± <0.001 (boat based). The Murray Cod fishery had maximal catch and harvest during the 5-month period after the closed season ended. The closed season aims to protect spawning Murray Cod, but this strategy's effectiveness may have been influenced by high fishing effort and deliberate bycatch during the closure period. To sustain and improve these MDB fisheries, we suggest quantification of catch-and-release impacts on spawning Murray Cod, provision of fish passage, re-stocking of Golden Perch, and education on fishing techniques that minimize Murray Cod bycatch during the closed season.

Received October 22, 2014; accepted March 6, 2015
Smartphones Reveal Angler Behavior: A Case Study of a Popular Mobile Fishing Application in Alberta, Canada
Authors: Papenfuss Jason T. , Phelps Nicholas , Fulton David , Venturelli Paul A.
Published: July 2015

Successfully managing fisheries and controlling the spread of invasive species depends on the ability to describe and predict angler behavior. However, finite resources restrict conventional survey approaches and tend to produce retrospective data that are limited in time or space and rely on intentions or attitudes rather than actual behavior. In this study, we used three years of angler data from a popular mobile fishing application in Alberta, Canada, to determine province-wide, seasonal patterns of (1) lake popularity that were consistent with conventional data and (2) anthropogenic lake connectivity that has not been widely described in North America. Our proof-of-concept analyses showed that mobile apps can be an inexpensive source of high-resolution, real-time data for managing fisheries and invasive species. We also identified key challenges that underscore the need for further research and development in this new frontier that combines big data with increased stakeholder interaction and cooperation.

El manejo exitoso de las pesquerías y el control de la dispersión de especies invasivas depende de la habilidad para describir y predecir el comportamiento de los pescadores. Sin embargo, la limitación de recursos restringe el uso de muestreos convencionales y tiende a producir datos históricos incompletos en tiempo y espacio, y se fundamenta en intenciones o actitudes más que en el comportamiento real de los pescadores. En este trabajo se utilizan tres años de datos sobre pescadores obtenidos mediante una aplicación para teléfonos móviles en Alberta, Canadá, para determinar, a nivel provincie, los patrones estacionales de: 1) popularidad del lago de acuerdo a los datos convencionales, y 2) conectividad antropogénica del lago que no ha sido ampliamente descrita en Norteamérica. El análisis para poner a prueba el concepto mostró que las aplicaciones para teléfono celular pueden representar una fuente de datos barata, de alta resolución y que opera en tiempo real para manejo de pesquerías y de especies invasivas. También se identificaron retos clave que resaltan la necesidad de realizar investigación en el futuro y desarrollar información acerca de esta nueva frontera tecnológica que combina grandes cantidades de datos y mayor interés y cooperación por parte de los inversionistas.
Use of foreign-educated nurses and patient satisfaction in U.S. hospitals
Authors: Mazurenko Olena , Menachemi Nir
Published: July 2015

Purpose:

In the context of value-based purchasing, this study examines the association between the utilization of foreign-educated registered nurses (RNs) and patient satisfaction among U.S. acute care hospitals.

Data Sources/Study Setting:

We utilized data from the Hospital Consumer Assessment of Healthcare Providers and Systems to measure patient satisfaction and data from the American Hospital Association regarding the utilization of foreign-educated RNs in 2012.

Methodology/Approach:

In this study, a cross-sectional design with propensity score adjustment to examine the relationship between use of foreign-educated nurses and 10 patient satisfaction outcome measures. Control variables include hospital size, ownership, geographic location, teaching status, system membership, a high-technology index, and U.S. region based on census categories.

Findings:

The utilization of foreign-educated RNs was negatively and significantly related to six patient satisfaction measures. Specifically, hospitals with foreign-educated RNs scored, on average, lower on measures related to nurse communication (β = −0.649, p = .01), doctor’s communication (β = −0.837, p ≤ .001), communication about administered drugs (β = −0.539, p = .81), and communication about what to do during their recovery at home (β = −0.571, p = .01). Moreover, hospitals utilizing foreign-educated RNs scored, on average, lower on overall satisfaction measures including rating the hospital as 9 or 10 overall (β = −1.20, p = .005), and patients would definitely recommend the hospital (β = −1.32, p = .006).

Practice Implications:

Utilization of foreign-educated RNs is negatively associated with measures of patient satisfaction pertaining to communication and overall perceptions of care. Hospitals that utilize foreign-educated RNs should consider strategies that enhance communication competency and aid improving perception of care among patients.
Terriglobus albidus sp. nov., a member of the family Acidobacteriaceae isolated from Namibian semiarid savannah soil
Authors: Pascual Javier , Wüst Pia K. , Geppert Alicia , Foesel Bärbel U. , Huber Katharina J. , Overmann Jörg
Published: July 2015

A novel aerobic, chemo-organoheterotrophic bacterium, strain Ac_26_B10T, was isolated from a semiarid savannah soil collected in northern Namibia (Mashare, Kavango region). Based on analysis of its nearly full-length 16S rRNA gene sequence, the isolate belongs to the genus Terriglobus (family Acidobacteriaceae, order Acidobacteriales, class Acidobacteria) and shares 98.3 and 96.9 % 16S rRNA gene sequence similarity with its closest relatives, Terriglobus tenax DRP 35T and T. aquaticus O3SUJ4T. Cells were Gram-negative, coccoid to rod-shaped, non-motile and divided by binary fission. Strain Ac_26_B10T showed weak catalase activity and, in contrast to the other described species of the genus Terriglobus, was oxidase-positive. Compared with the already established species of the genus Terriglobus, the novel strain used a larger range of sugars and sugar alcohols for growth, lacked α-mannosidase activity and exhibited a higher temperature optimum of growth. DNA–DNA hybridization studies with its closest phylogenetic relative, T. tenax DSM 28898T, confirmed that strain Ac_26_B10T represents a distinct genomospecies. Its most abundant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Dominant polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The predominant menaquinone was MK-8; minor amounts of MK-7 and MK-8(H2) were also recorded. The G+C content of the genomic DNA was 58.5 mol%. On the basis of our polyphasic analysis, Ac_26_B10T represents a novel species of the genus Terriglobus, for which the name Terriglobus albidus sp. nov. is proposed. The type strain is Ac_26_B10T ( = DSM 26559T = LMG 27984T).
Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins
Authors: Kim Jin Ho , Kang Hyung Jun , Yu Byung Jo , Kim Sun Chang , Lee Pyung Cheon
Published: July 2015

Taxonomic studies were performed on a novel carotenoid-producing strain, designated AJ003T, isolated from faeces of Antarctic penguins. Cells of strain AJ003T were aerobic, Gram-stain-positive, cocci-shaped and orange. Strain AJ003T was capable of growing in a broad temperature range, including sub-zero growth (below − 20 to 30 °C). 16S rRNA gene sequence analysis revealed that strain AJ003T was closely related to Planococcus halocryophilus Or1T (97.4 % similarity), Planococcus antarcticus DSM 14505T (97.3 %), Planococcus kocurii NCIMB 629T (97.3 %), and Planococcus donghaensis JH1T (97.1 %). The predominant cellular fatty acids were anteiso-C15 : 0, and iso-C16 : 0.MK-7 and MK-8 were the quinones identified, and the major pigment was glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid. The major polar lipid was phosphatidylglycerol. DNA–DNA relatedness of strain AJ003T with respect to its closest phylogenetic neighbours was 38.2 ± 0.5 % for Planococcus halocryophilus DSM 24743T, 32.2 ± 0.2 % for Planococcus antarcticus DSM 14505T, 21.0 ± 0.3 % for Planococcus kocurii DSM 20747T and 18.6 ± 1.4 % for Planococcus donghaensis KCTC 13050T. The DNA G+C content of strain AJ003T was 40.0 ± 0.6 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain AJ003T is concluded to represent a novel species of the genus Planococcus, for which the name Planococcus faecalis sp. nov. is proposed. The type strain is AJ003T ( = KCTC 33580T = CECT 8759T).
SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees
Authors: Mallo Diego , Oliveira Martins Leonardo de , Posada David
Published: July 2015

We present here a fast and flexible software –SimPhy– for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer –all three potentially leading to the species tree/gene tree discordance– and gene conversion.SimPhyimplements a hierarchical phylogenetic model in which the evolution of species, locus and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled froma prioristatistical distributions.SimPhyalso incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validateSimPhy’s output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate howSimPhycan be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods.SimPhyis available athttps://github.com/adamallo/SimPhy, where users can find the source code, pre-compiled executables, a detailed manual and example cases.
Cooperative Binding Mitigates the High-Dose Hook Effect
Authors: Roy Ranjita Dutta , Rosenmund Christian , Stefan Melanie I
Published: July 2015

Background

The high-dose hook effect (also called prozone effect) refers to the observation that if a multivalent protein acts as a linker between two parts of a protein complex, then increasing the amount of linker protein in the mixture does not always increase the amount of fully formed complex. On the contrary, at a high enough concentration range the amount of fully formed complex actually decreases. It has been observed that allosterically regulated proteins seem less susceptible to this effect. The aim of this study was two-fold: First, to investigate the mathematical basis of how allostery mitigates the prozone effect. And second, to explore the consequences of allostery and the high-dose hook effect using the example of calmodulin, a calcium-sensing protein that regulates the switch between long-term potentiation and long-term depression in neurons.

Results

We use a combinatorial model of a “perfect linker protein” (with infinite binding affinity) to mathematically describe the hook effect and its behaviour under allosteric conditions. We show that allosteric regulation does indeed mitigate the high-dose hook effect. We then turn to calmodulin as a real-life example of an allosteric protein. Using kinetic simulations, we show that calmodulin is indeed subject to a hook effect. We also show that this effect is stronger in the presence of the allosteric activator Ca2+/calmodulin-dependent kinase II (CaMKII), because it reduces the overall cooperativity of the calcium-calmodulin system. It follows that, surprisingly, there are conditions where increased amount of allosteric activator actuallydecreasethe activity of a protein.

Conclusions

We show that cooperative binding can indeed act as a protective mechanism against the hook effect. This will have implicationsin vivowhere the extent of cooperativity of a protein can be modulated, for instance, by allosteric activators or inhibitors. This can result in counterintuitive effects of decreased activity with increased concentrations of both the allosteric protein itself and its allosteric activators.
Chromatin interactions correlate with local transcriptional activity inSaccharomyces cerevisiae
Authors: Scholl Zackary , Zhong Jianling , Hartemink Alexander J.
Published: July 2015

Genome organization is crucial for efficiently responding to DNA damage and regulating transcription. In this study, we relate the genome organization ofSaccharomyces cerevisiae(budding yeast) to its transcription activity by analyzing published circularized chromosome conformation capture (4C) data in conjunction with eight separate datasets describing genome-wide transcription rate or RNA polymerase II (Pol II) occupancy. We find that large chromosome segments are more likely to interact in areas that have high transcription rate or Pol II occupancy. Additionally, we find that groups of genes with similar transcription rates or similar Pol II occupancy are more likely to have higher numbers of chromosomal interactions than groups of random genes. We hypothesize that transcription localization occurs around sets of genes with similar transcription rates, and more often around genes that are highly transcribed, in order to produce more efficient transcription. Our analysis cannot discern whether gene co-localization occurs because of similar transcription rates or whether similar transcription rates are a consequence of co-localization.
Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform
Authors: Chen Rui , Im Hogune , Snyder Michael
Published: July 2015

Multiple platforms are available for whole-exome enrichment and sequencing (WES). This protocol is based on the Illumina TruSeq Exome Enrichment platform, which captures ∼62 Mb of the human exonic regions using 95-base DNA probes. In addition to covering the RefSeq and Ensembl coding sequences, the enriched sequences also include ∼28 Mb of RefSeq untranslated regions (UTR). The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.
Studying Apoptosis in Drosophila
Authors: Denton Donna , Kumar Sharad
Published: July 2015

The apoptotic machinery is highly conserved throughout evolution, and central to the regulation of apoptosis is the caspase family of cysteine proteases. Insights into the regulation and function of apoptosis in mammals have come from studies using model organisms. Drosophila provides an exceptional model system for identifying the function of conserved mechanisms regulating apoptosis, especially during development. The characteristic patterns of apoptosis during Drosophila development have been well described, as has the apoptotic response following DNA damage. The focus of this discussion is to introduce methodologies for monitoring apoptosis during Drosophila development and also in Drosophila cell lines.