bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics
Authors: Davies Hannah A. , Rigden Daniel J. , Phelan Marie M. , Madine Jillian
Published: March 2017

Aortic medial amyloid is the most prevalent amyloid found to date, but remarkably little is known about it. It is characterised by aberrant deposition of a 5.4 kDa protein called medin within the medial layer of large arteries. Here we employ a combined approach of ab initio protein modelling and 13C-direct detection NMR to generate a model for soluble monomeric medin comprising a stable core of three β-strands and shorter more labile strands at the termini. Molecular dynamics simulations suggested that detachment of the short, C-terminal β-strand from the soluble fold exposes key amyloidogenic regions as a potential site of nucleation enabling dimerisation and subsequent fibril formation. This mechanism resembles models proposed for several other amyloidogenic proteins suggesting that despite variations in sequence and protomer structure these proteins may share a common pathway for amyloid nucleation and subsequent protofibril and fibril formation.
An advanced conjugation strategy for the preparation of quantum dot-antibody immunoprobes
Authors: Dvorakova Veronika , Cadkova Michaela , Datinska Vladimira , Kleparnik Karel , Foret Frantisek , Bilkova Zuzana , Korecka Lucie
Published: March 2017

An advanced site-specific conjugation strategy for the preparation of quantum dot-based antibody probes applicable in various immunoassays from fluorescence to electrochemical biosensors is described.
Self-assembly and redox induced phase transfer of gold nanoparticles at a water–propylene carbonate interface
Authors: Smirnov Evgeny , Peljo Pekka , Girault Hubert H.
Published: March 2017

Citrate-stabilized gold nanoparticles were found to spontaneously self-assemble into a lustrous film at a bare water–propylene carbonate interface after vigorous shaking, due to the extremely low interfacial tension. The presence of the electron donor, tetrathiafulvalene, in the oil phase, led to the extraction of particles into the organic phase.
The metalation of hen egg white lysozyme impacts protein stability as shown by ion mobility mass spectrometry, differential scanning calorimetry, and X-ray crystallography
Authors: Sullivan Matthew P. , Groessl Michael , Meier Samuel M. , Kingston Richard L. , Goldstone David C. , Hartinger Christian G.
Published: March 2017

Metalation of lysozyme with anticancer organometallics results in protein destabilisation, probably relevant in metallodrug mode of action.
Synthesis and magnetic properties of new tellurate compounds Na4MTeO6 (M = Co and Ni) with a ferromagnetic spin-chain structure
Authors: He Zhangzhen , Guo Wenbin , Cui Meiyan , Tang Yingying
Published: March 2017

New tellurate compounds Na4MTeO6 (M = Co and Ni) 1D are obtained by a high-temperature solid-state reaction, showing a unique spin-chain structure.
Mono- and polynuclear Ag(i) complexes of N-functionalized bis(diphenylphosphino)amine DPPA-type ligands: synthesis, solid-state structures and reactivity
Authors: Ghisolfi Alessio , Fliedel Christophe , de Frémont Pierre , Braunstein Pierre
Published: March 2017

DPPA-type ligands (Ph2P)2N(p-Z)C6H4 (Z = H, SMe, OMe) led to Ag(i) complexes of various nuclearities and an unexpected influence of the para-substituent Z is observed, including for CH2Cl2 activation.
Ultrahigh capacity and superior stability of three-dimensional porous graphene networks containing in situ grown carbon nanotube clusters as an anode material for lithium-ion batteries
Authors: Huang Shizhi , Wang Jingyan , Pan Zhiyi , Zhu Jinliang , Shen Pei Kang
Published: March 2017

Three-dimensional porous graphene networks containing in situ grown carbon nanotube clusters (CNTs@3DG) exhibited an ultrahigh capacity, remarkable rate performance and excellent cycling stability for lithium-ion batteries.
Redox/pH dual-sensitive hybrid micelles for targeting delivery and overcoming multidrug resistance of cancer
Authors: Yin Mingxing , Bao Yuling , Gao Xueqin , Wu Yupei , Sun Yu , Zhao Xinyuan , Xu Hongzhe , Zhang Zhiping , Tan Songwei
Published: March 2017

A three-step approach was used to enhance anticancer activity via targeted delivery, intracellular drug burst release, and depressed drug efflux.
A two-photon fluorescent probe for nitroreductase imaging in living cells, tissues and zebrafish under hypoxia conditions
Authors: Zhai Baoping , Hu Wei , Sun Jinyu , Chi Siyu , Lei Yidi , Zhang Fang , Zhong Cheng , Liu Zhihong
Published: March 2017

A two-photon fluorescent probe FNTR, constructed for nitroreductase by using a fluorine derivative as a TP fluorophore and a p-nitrobenzyl carbamate group as a recognition domain, was successfully applied to detect endogenous NTR in living cells, tissues and zebrafish.
Bioluminescent detection of tick-borne encephalitis virus in native ticks
Authors: Kudryavtsev A. N. , Burakova L. P. , Frank L. A.
Published: March 2017

Easy-to-use and fast bioluminescent immunoassay for tick-borne encephalitis virus in natural ticks based on the hybrid protein 14D5a-Rm7 was developed. The approach holds much promise with a view of practical applicability.
Pico-HPLC system integrating an equal inner diameter femtopipette into a 900 nm I.D. porous layer open tubular column
Authors: Li Ruonan , Shao Yunlong , Yu Yanmin , Wang Xiayan , Guo Guangsheng
Published: March 2017

A pico-HPLC method was developed using a bifunctional chromatographic column enabling femtoliter volume sampling and separation.
Surfactant-assisted synthesis of polythiophene/Ni0.5Zn0.5Fe2−xCexO4ferrite composites: study of structural, dielectric and magnetic properties for EMI-shielding applications
Authors: Dar M. Abdullah , Majid Kowsar , Hanief Najar Mohd. , Kotnala R. K. , Shah Jyoti , Dhawan S. K. , Farukh M.
Published: March 2017

This work reports the exploitation of nanocrystalline Ni0.5Zn0.5Fe2−xCexO4ferrite for EMI shielding application by designing quasi-spherical shaped polythiophene (PTH) compositesvia in situemulsion polymerization.
Correction: Band-gap tailoring and visible-light-driven photocatalytic performance of porous (GaN)1−x(ZnO)x solid solution
Authors: Wu Aimin , Li Jing , Liu Baodan , Yang Wenjin , Jiang Yanan , Liu Lusheng , Zhang Xinglai , Xiong Changmin , Jiang Xin
Published: March 2017

Correction for ‘Band-gap tailoring and visible-light-driven photocatalytic performance of porous (GaN)1−x(ZnO)x solid solution’ by Aimin Wu et al., Dalton Trans., 2017, 46, 2643–2652.
Impact of graphene oxide on the antibacterial activity of antibiotics against bacteria
Authors: Gao Yang , Wu Jianchun , Ren Xuemei , Tan Xiaoli , Hayat Tasawar , Alsaedi Ahmed , Cheng Cheng , Chen Changlun
Published: March 2017

Schematic diagram of the influence of GO on bacteria and antibiotics.
Electrochemical intramolecular dehydrogenative C–S bond formation for the synthesis of benzothiazoles
Authors: Wang Pan , Tang Shan , Lei Aiwen
Published: March 2017

An external oxidant-free intramolecular dehydrogenative C–S cross-coupling has been developed under undivided electrolytic conditions.
Independent responsive behaviour and communication in hydrogel objects
Authors: Jaggers Ross W. , Bon Stefan A. F.
Published: March 2017

We show the fabrication of autonomous soft hydrogel alginate-based objects, namely fibres and beads. They have an individually programmed time delay in their response to a shared environmental stimulus and the ability to communicate when in close proximity to one another.
Synthesis, optical properties and applications of light-emitting copper nanoclusters
Authors: Wang Zhenguang , Chen Bingkun , Rogach Andrey L.
Published: March 2017

Copper is an earth abundant, inexpensive metal readily available from commercial sources, which is increasingly coming into focus for light-emitting metal nanocluster research.
Reverse micelle-based water-soluble nanoparticles for simultaneous bioimaging and drug delivery
Authors: Chen Ying , Liu Yong , Yao Yongchao , Zhang Shiyong , Gu Zhongwei
Published: March 2017

With special confined water pools, reverse micelles (RMs) have shown potential for a wide range of applications.
Palladium-catalyzed highly regioselective hydroaminocarbonylation of aromatic alkenes to branched amides
Authors: Zhu Jinping , Gao Bao , Huang Hanmin
Published: March 2017

Pd(t-Bu3P)2 has been successfully identified as an efficient catalyst for the hydroaminocarbonylation of aromatic alkenes to branched amides under relatively mild reaction conditions.
Towards the biodegradation pathway of fosfomycin
Authors: Pallitsch K. , Schweifer A. , Roller A. , Hammerschmidt F.
Published: March 2017

A degradation intermediate, a pro-metabolite and an enzyme inhibitor have been synthesised to study the biodegradation of fosfomycin inR. huakuiiPMY1.
A wheat straw cellulose based semi-IPN hydrogel reactor for metal nanoparticles preparation and catalytic reduction of 4-nitrophenol
Authors: Ding Jianzi , Li Qian , Zhao Liwei , Li Xiaodi , Yue Qinyan , Gao Baoyu
Published: March 2017

A wheat straw cellulose-g-poly(acrylic acid)/poly(vinyl alcohol) semi-IPN hydrogel (WSC-g-PAA/PVA) was synthesized.
Thermo-responsive fluorescence of AIE-active poly(N-isopropylacrylamides) labeled with highly twisted bis(N,N-dialkylamino)arenes
Authors: Sasaki Shunsuke , Konishi Gen-ichi
Published: March 2017

A thermo-responsive fluorescent polymer materials were synthesized fromN-isopropylacrylamides with AIE-active 9,10-bis(N,N-dialkylamino)arene monomers.
Dichroic nonlinear absorption response of silver nanoprism arrays
Authors: Cesca Tiziana , García-Ramírez Emma Vianey , Sánchez-Esquivel Hectór , Michieli Niccolò , Kalinic Boris , Gómez-Cervantes Juan Manuel , Rangel-Rojo Raul , Reyes-Esqueda Jorge Alejandro , Mattei Giovanni
Published: March 2017

The dichroic nonlinear absorption of Ag nanoprism arrays is interpreted using FEM simulations of the polarization-dependent local electric field distribution.
Cation exchanged MOF-derived nitrogen-doped porous carbons for CO2capture and supercapacitor electrode materials
Authors: Pan Ying , Zhao Yuxin , Mu Shanjun , Wang Yu , Jiang Chunming , Liu Quanzhen , Fang Qianrong , Xue Ming , Qiu Shilun
Published: March 2017

N-Doped hierarchical porous carbons with enhanced microporosity were prepared byin situintroduction of active site K+into MOF precursors.
High permselectivity hyperbranched polyester/polyamide ultrathin films with nanoscale heterogeneity
Authors: Kong Xin , Qiu Ze-Lin , Lin Chun-Er , Song You-Zhi , Zhu Bao-Ku , Zhu Li-Ping , Wei Xiu-Zhen
Published: March 2017

Incorporating hyperbranched polyesters into a cross-linked polyamide matrix by interfacial polymerization to construct an ultrathin film with high permselectivity performance.
Low-temperature vapour phase polymerized polypyrrole nanobrushes for supercapacitors
Authors: Santino Luciano M. , Acharya Shinjita , D'Arcy Julio M.
Published: March 2017

A low temperature modified vapor phase polymerization affords high-aspect ratio nanofibers of polypyrrole, which conformally coat fibrous substrates.
Reduced bimolecular recombination in blade-coated, high-efficiency, small-molecule solar cells
Authors: Engmann Sebastian , Ro Hyun Wook , Herzing Andrew A. , DeLongchamp Dean M. , Snyder Chad R. , Richter Lee J. , Barito Adam , Gundlach David J.
Published: March 2017

We report the performance and morphology of blade-coated bulk heterojunction devices based on the small molecule donor p-DTS(FBTTh2)2 treated with a postdeposition solvent vapor annealing process that improves the device performance and significantly reduces bimolecular recombination.
Recent advances and challenges of metal–organic framework membranes for gas separation
Authors: Kang Zixi , Fan Lili , Sun Daofeng
Published: March 2017

In this review, we summarized the recent advances in improving the gas separation performance of MOF membranes and the issues faced with MOF membranes in terms of designation and growth for their practical applications.
Construction of blood compatible lysine-immobilized chitin/carbon nanotube microspheres and potential applications for blood purified therapy
Authors: Wu Shuangquan , Duan Bo , Zeng Xianpeng , Lu Ang , Xu Xiaojuan , Wang Yanfeng , Ye Qifa , Zhang Lina
Published: March 2017

Novel lysine-immobilized chitin/carbon nanotube microspheres are prepared with excellent bilirubin adsorption properties and good blood compatibility for blood purified therapy.
The physics and chemistry of silica-in-silicates nanocomposite hydrogels and their phycocompatibility
Authors: Ahmed Nada Ben , Ronsin Olivier , Mouton Ludovic , Sicard Clémence , Yéprémian Claude , Baumberger Tristan , Brayner Roberta , Coradin Thibaud
Published: March 2017

Understanding the formation and structure of silica-in-silicates nanocomposite hydrogels allows for the identification of optimal conditions for micro-algae encapsulation.
Exploring the role of molecular chirality in the photo-responsiveness of dipeptide-based gels
Authors: Chen Zhonghui , Lv Ziyu , Qing Guangyan , Sun Taolei
Published: March 2017

Chiral effect: upon UV light irradiation, the l-gel has a markedly faster gel–sol transition than the d-gel.
Maternal, Labor, Delivery, and Perinatal Outcomes Associated with Placental Abruption: A Systematic Review
Authors: Grantz Katherine , Shenassa Edmond , Downes Katheryne
Published: March 2017

Objective Risk factors for placental abruption have changed, but there has not been an updated systematic review investigating outcomes.

Methods We searched PubMed, EMBASE, Web of Science, SCOPUS, and CINAHL for publications from January 1, 2005 through December 31, 2016. We reviewed English-language publications reporting estimated incidence and/or risk factors for maternal, labor, delivery, and perinatal outcomes associated with abruption. We excluded case studies, conference abstracts, and studies that lacked a referent/comparison group or did not clearly characterize placental abruption.

Results A total of 123 studies were included. Abruption was associated with elevated risk of cesarean delivery, postpartum hemorrhage and transfusion, preterm birth, intrauterine growth restriction or low birth weight, perinatal mortality, and cerebral palsy. Additional maternal outcomes included relaparotomy, hysterectomy, sepsis, amniotic fluid embolism, venous thromboembolism, acute kidney injury, and maternal intensive care unit admission. Additional perinatal outcomes included acidosis, encephalopathy, severe respiratory disorders, necrotizing enterocolitis, acute kidney injury, need for resuscitation, chronic lung disease, infant death, and epilepsy.

Conclusion Few studies examined outcomes beyond the initial birth period, but there is evidence that both mother and child are at risk of additional adverse outcomes. There was also considerable variation in, or absence of, the reporting of abruption definitions.
Using a State Birth Registry as a Quality Improvement Tool
Authors: Kaplan Heather , Friar Kelly , Fuller Sandra , Ford Susan , White Beth , Besl John , Paulson John , Marcotte Michael , Krew Michael , Bailit Jennifer , Iams Jay , Lannon Carole
Published: March 2017

Background Birth registry data are universally collected, generating large administrative datasets. However, these data are typically not used for quality improvement (QI) initiatives in perinatal medicine because the quality and timeliness of the information is uncertain.

Objective We sought to identify and address causes of inaccuracy in recording birth registry information so that birth registry data could support statewide obstetrical quality initiatives in Ohio.

Study Design The Ohio Perinatal Quality Collaborative and the Ohio Department of Health Vital Statistics used QI techniques in 15 medium-sized maternity hospitals to identify and remove systemic sources of inaccuracy in birth registry data. The primary outcome was the rate of scheduled deliveries without medical indication between 370/7 and 386/7 weeks at participating hospitals from birth registry data.

Results Inaccurate birth registry data most commonly resulted from limited communication between clinical and medical record staff. The rate of scheduled births between 370/7 and 386/7 weeks' gestation without a documented medical indication as recorded in the birth registry declined by 35%.

Conclusion A QI initiative aimed at increasing the accuracy of birth registry information demonstrated the utility of these data for surveillance of perinatal outcomes and has led to ongoing efforts to support birth registrars in submitting accurate data.
Characterizing Literacy and Cognitive Function during Pregnancy and Postpartum
Authors: Kamel Leslie , Quader Zara , Rajan Priya , Taylor Shaneah , O'Conor Rachel , Wolf Michael , Simon Melissa , Yee Lynn
Published: March 2017

Objective The objective of this study was to characterize health literacy and cognitive function in a diverse cohort of pregnant women.

Methods Pregnant and postpartum women underwent in-depth assessments of health literacy/numeracy and the cognitive domains of verbal ability, working memory, long-term memory, processing speed, and inductive reasoning. Differences by demographic characteristics and gestational age were assessed using chi-square tests and multivariable logistic regression.

Results In this cohort of pregnant (N = 77) or postpartum (N = 24) women, 41.6% had limited health literacy/numeracy. Women were more likely to score in the lowest quartile for literacy and verbal ability if they were less educated, younger, nonwhite or had Medicaid. These factors were associated with low scores for long-term memory, processing speed, and inductive reasoning. Although there were no differences in literacy or cognitive function by parity or gestational age, postpartum women were more likely to score in the lowest quartile for processing speed (adjusted odds ratio [aOR]: 3.79, 95% confidence interval [CI]: 1.32–10.93) and inductive reasoning (aOR: 4.07, 95% CI: 1.21–13.70).

Conclusion Although postpartum status was associated with reduced inductive reasoning and processing speed, there were no differences in cognitive function across pregnancy.

Practice Implications Postpartum maternal learning may require enhanced support. In addition, cognitive skills and health literacy may be a mediator of perinatal outcomes inequities.
Comparison of the diagnostic ability of blue laser imaging magnification versus pit pattern analysis for colorectal polyps
Authors: Nakano Arihiro , Hirooka Yoshiki , Yamamura Takeshi , Watanabe Osamu , Nakamura Masanao , Funasaka Kohei , Ohno Eizaburo , Kawashima Hiroki , Miyahara Ryoji , Goto Hidemi
Published: March 2017

Background and study aims There have been few evaluations of the diagnostic ability of new narrow band light observation blue laser imaging (BLI). The present prospective study compared the diagnostic ability of BLI magnification and pit pattern analysis for colorectal polyps.

Patients and methods We collected lesions prospectively, and the analysis of images was made by two endoscopists, retrospectively. A total of 799 colorectal polyps were examined by BLI magnification and pit pattern analysis at Nagoya University Hospital. The Hiroshima narrow-band imaging classification was used for BLI. Differentiation of neoplastic from non-neoplastic lesions and diagnosis of deeply invasive submucosal cancer (dSM) were compared between BLI magnification and pit pattern analysis. Type C2 in the Hiroshima classification was evaluated separately, because application of this category as an index of the depth of cancer invasion was considered difficult.

Results We analyzed 748 colorectal polyps, excluding 51 polyps that were inflammatory polyps, sessile serrated adenoma/polyps, serrated adenomas, advanced colorectal cancers, or other lesions. The accuracy of differential diagnosis between neoplastic and non-neoplastic lesions was 98.4 % using BLI magnification and 98.7 % with pit pattern analysis. In addition, the diagnostic accuracy of BLI magnification and pit pattern analysis for dSM for cancer was 89.5 % and 92.1 %, respectively. When type C2 lesions were excluded, the diagnostic accuracy of BLI for dSM was 95.9 %. The 18 type C2 lesions comprised 1 adenoma, 9 intramucosal or slightly invasive submucosal cancers, and 8 dSM. Pit pattern analysis allowed accurate diagnosis of the depth of invasion in 13 lesions (72.2 %).

Conclusions Most colorectal polyps could be diagnosed accurately by BLI magnification without pit pattern analysis, but we should add pit pattern analysis for type C2 lesions in the Hiroshima classification.
On the characteristics of obliquely propagating electrostatic structures in non-Maxwellian plasmas in the presence of ion pressure anisotropy
Authors: Adnan Muhammad , Qamar Anisa , Mahmood Shahzad , Kourakis Ioannis
Published: March 2017

The dynamical characteristics of large amplitude ion-acoustic waves are investigated in a magnetized plasma comprising ions presenting space asymmetry in the equation of state and non-Maxwellian electrons. The anisotropic ion pressure is defined using the double adiabatic Chew-Golberger-Low theory. An excess in the superthermal component of the electron population is assumed, in agreement with long-tailed (energetic electron) distribution observations in space plasmas; this is modeled via a kappa-type distribution function. Large electrostatic excitations are assumed to propagate in a direction oblique to the external magnetic field. In the linear (small amplitude) regime, two electrostatic modes are shown to exist. The properties of arbitrary amplitude (nonlinear) obliquely propagating ion-acoustic solitary excitations are thus investigated via a pseudomechanical energy balance analogy, by adopting a Sagdeev potential approach. The combined effect of the ion pressure anisotropy and excess superthermal electrons is shown to alter the parameter region where solitary waves can exist. An excess in the suprathermal particles is thus shown to be associated with solitary waves, which are narrower, faster, and of larger amplitude. Ion pressure anisotropy, on the other hand, affects the amplitude of the solitary waves, which become weaker (in strength), wider (in spatial extension), and thus slower in comparison with the cold ion case.
Study of the beam profile and position instability of a post-accelerated pseudospark-sourced electron beam
Authors: Zhao J. , Yin H. , Zhang L. , Shu G. , He W. , Phelps A. D. R. , Cross A. W. , Pang L. , Zhang Q.
Published: March 2017

A pseudospark-sourced electron beam is a promising candidate for driving a THz millimeter wave radiation source. However, the physics governing the electron beam density profile and the beam center deviation from the axis of the structure, which may be caused by the randomness in the pseudospark discharge process, remains still unclear especially for the high energy component of the pseudospark-sourced electron beam, which is usually non-mono-energetic. It is essential to study the electron beam density profile and the beam center position distribution for optimizing the pseudospark discharge configuration. In this paper, images of some single-shot electron beam pulses have been captured using a 50 μm thickness stopping copper foil and a phosphor screen coated with a P47 scintillator to study the electron beam density profile and the beam center position distribution of the high energy component of the electron beam. The experiments have been carried out on two pseudospark discharge configurations with two different size hollow cathode cavities. The influence of the cathode aperture of each configuration has also been studied according to the beam images. Experimental results show that the beam profile of the high energy component has a Lorentzian distribution and is much smaller than the axial aperture size with the beam centers dispersing within a certain range around the axis of the discharge structure. The pseudospark-sourced electron beam with a larger hollow cathode cavity shows a smaller full width at half maximum radius and a more concentrated beam center distribution.
Multiple secondary islands formation in nonlinear evolution of double tearing mode simulations
Authors: Guo W. , Ma J. , Yu Z.
Published: March 2017

A new numerical code solving the conservative perturbed resistive magnetohydrodynamic (MHD) model is developed. Numerical tests of the ideal Kelvin-Helmholtz instability and the resistive double tearing mode (DTM) show its capability in solving linear and nonlinear MHD instabilities. The nonlinear DTM evolution in 2D geometry is numerically investigated with low guiding field Bz0, short half-distance y0 between the equilibrium current sheets, and small resistivity η. The interaction of islands on the two initial current sheets may generate an unstable flow driven current sheet with a high length-to-thickness aspect ratio (α), and multiple secondary islands can form. In general, the length-to-thickness aspect ratio α and the number of secondary islands increase with decreasing guide field Bz0, decreasing half-distance y0, and increasing Lundquist number of the flow driven current sheet  SL although the dependence may be non-monotonic. The reconnection rate dependence on SL,  Bz0, and y0 is also investigated.
Electronic structures of rutile (011)(2 × 1) surfaces: A many-body perturbation theory study
Authors: Liu Guokui , Chen Tingwei , Liu Xiaobiao , Jin Fan , Yuan Shiling , Ma Yuchen
Published: March 2017

Using the GW method within many-body perturbation theory, we investigate the electronic properties of the rutile (011) surfaces with different reconstruction patterns. We find that keeping the Ti:O ratio on the reconstructed surface to 1:2 enlarges the bandgap of the rutile (011) surface to ca. 4.0 eV. Increasing the content of O atoms in the surface can turn rutile into a semi-metal. For some surfaces, it is important to apply self-consistent GW calculation to get the correct charge distributions for the frontier orbitals, which are relevant to the photocatalytic behavior of TiO2.
1.55 μm room-temperature lasing from subwavelength quantum-dot microdisks directly grown on (001) Si
Authors: Shi Bei , Zhu Si , Li Qiang , Tang Chak Wah , Wan Yating , Hu Evelyn L. , Lau Kei May
Published: March 2017

Miniaturized laser sources can benefit a wide variety of applications ranging from on-chip optical communications and data processing, to biological sensing. There is a tremendous interest in integrating these lasers with rapidly advancing silicon photonics, aiming to provide the combined strength of the optoelectronic integrated circuits and existing large-volume, low-cost silicon-based manufacturing foundries. Using III-V quantum dots as the active medium has been proven to lower power consumption and improve device temperature stability. Here, we demonstrate room-temperature InAs/InAlGaAs quantum-dot subwavelength microdisk lasers epitaxially grown on (001) Si, with a lasing wavelength of 1563 nm, an ultralow-threshold of 2.73 μW, and lasing up to 60 °C under pulsed optical pumping. This result unambiguously offers a promising path towards large-scale integration of cost-effective and energy-efficient silicon-based long-wavelength lasers.
The contribution of turbulent plume dynamics to long-range spotting
Authors: Thurston William , Kepert Jeffrey D. , Tory Kevin J. , Fawcett Robert J. B.
Published: March 2017

Spotting can start fires up to tens of kilometres ahead of the primary fire front, causing rapid spread and placing immense pressure on suppression resources. Here, we investigate the dynamics of the buoyant plume generated by the fire and its ability to transport firebrands. We couple large-eddy simulations of bushfire plumes with a firebrand transport model to assess the effects of turbulent plume dynamics on firebrand trajectories. We show that plume dynamics have a marked effect on the maximum spotting distance and determine the amount of lateral and longitudinal spread in firebrand landing position. In-plume turbulence causes much of this spread and can increase the maximum spotting distance by a factor of more than 2 over that in a plume without turbulence in our experiments. The substantial impact of plume dynamics on the spotting process implies that fire spread models should include parametrisations of turbulent plume dynamics to improve their accuracy and physical realism.
Perceptual integration without conscious access
Authors: Fahrenfort Johannes J. , van Leeuwen Jonathan , Olivers Christian N. L. , Hogendoorn Hinze
Published: March 2017

Significance

Our brain constantly selects salient and/or goal-relevant objects from the visual environment, so that it can operate on neural representations of these objects, but what is the fate of objects that are not selected? Are these discarded so that the brain only has an impoverished nonperceptual representation of them, or does the brain construct perceptually rich representations, even when objects are not consciously accessed by our cognitive system? Here, we answer that question by manipulating the information that enters into awareness, while simultaneously measuring cortical activity using EEG. We show that objects that do not enter consciousness can nevertheless have a neural signature that is indistinguishable from perceptually rich representations that occur for objects that do enter into conscious awareness.
Progression of type 1 diabetes from the prediabetic stage is controlled by interferon-α signaling
Authors: Marro Brett S. , Ware Brian C. , Zak Jaroslav , de la Torre Juan Carlos , Rosen Hugh , Oldstone Michael B. A.
Published: March 2017

Significance

Type 1 diabetes (T1D) is an increasing medical health problem caused by autoimmune T cells killing insulin-producing β cells in the islets of Langerhans. When the majority of β cells are destroyed, unless exogenous insulin is administered, ketoacidosis and death follow. However, providing exogenous insulin does not prevent the resultant complications of stroke, heart disease, visual impairment, or faulty wound healing, indicating the need to preserve β cells in the prediabetic stage to insure endogenous insulin production. We show that blockage of IFN-α signaling prior to clinical T1D disease by antibody or a sphingosine-1 receptor agonist prevents autoaggressive T cells from entering the islets and killing β cells. The result is aborting T1D by acting at the prediabetic stage.
Spatial and Temporal Consumption Dynamics of Trout in Catch‐and‐Release Areas in Arkansas Tailwaters
Authors: Flinders Jon M. , Magoulick Daniel D.
Published: March 2017

Restrictive angling regulations in tailwater trout fisheries may be unsuccessful if food availability limits energy for fish to grow. We examined spatial and temporal variation in energy intake and growth in populations of Brown Trout Salmo trutta and Rainbow Trout Oncorhynchus mykiss within three catch‐and‐release (C‐R) areas in Arkansas tailwaters to evaluate food availability compared with consumption. Based on bioenergetic simulations, Rainbow Trout fed at submaintenance levels in both size‐classes (≤400 mm TL, >400 mm TL) throughout most seasons. A particular bottleneck in food availability occurred in the winter for Rainbow Trout when the daily ration was substantially below the minimum required for maintenance, despite reduced metabolic costs associated with lower water temperatures. Rainbow Trout growth rates followed a similar pattern to consumption with negative growth rates during the winter periods. All three size‐classes (<250 mm TL, 250–400 mm TL, >400 mm TL) of Brown Trout experienced high growth rates and limited temporal bottlenecks in food availability. We observed higher mean densities for Rainbow Trout (47–342 fish/ha) than for Brown Trout (3–84 fish/ha) in all C‐R areas. Lower densities of Brown Trout coupled with an ontogenetic shift towards piscivory may have allowed for higher growth rates and sufficient consumption rates to meet energetic demands. Brown Trout at current densities were more effective in maintaining adequate growth rates and larger sizes in C‐R areas than were Rainbow Trout. Bioenergetic simulations suggest that reducing stocking levels of Rainbow Trout in the tailwaters may be necessary in order to achieve increased catch rates of larger trout in the C‐R areas.

Received August 31, 2016; accepted January 9, 2017 Published online March 21, 2017
How far does neoliberalism go in Egypt? Gender, citizenship and the making of the ‘rural’ woman
Authors: Malak Karim , Salem Sara
Published: March 2017

This paper focuses on civil society in Egypt as a site in which the ‘Egyptian rural woman’ is made by looking at processes of microfinance which often ‘fail’ to realise their stated goals of ‘empowerment’, ‘poverty alleviation’ or ‘social mobility’. Using ethnographic material from a microfinance programme in the Egyptian governorate of al-Minya, such programmes are problematised beyond their stated goals. Instead, such initiatives put in place an infrastructure that links micro-borrowers to the market. Thus, what it means to be a ‘liberated’ woman in the Egyptian context is built on access, participation in and creation of ‘the market’.
Change deafness, dual-task performance, and domain-specific expertise
Authors: Neuhoff John G , Bochtler Katharina S
Published: March 2017

In a change deafness manipulation using radio broadcasts of sporting events, we show that change deafness to a switch in talker increases when listeners are asked to monitor both lexical and indexical information for change. We held semantic content constant and demonstrated a change deafness rate of 85% when participants listened to the home team broadcast of a hockey game that switched midway to the away team broadcast with a different announcer. In Study 2, participants were asked to monitor either the indexical characteristics ( listen for a change in announcer) or both the indexical and semantic components ( listen for a change in announcer or a goal scored). Monitoring both components led to significantly greater change deafness even though both groups were alerted to the possibility of a change in announcer. In Study 3, we changed both the indexical and the semantic components when the broadcast switched from a hockey game to a basketball game. We found a negative correlation between sports expertise and change deafness. The results are discussed in terms of the nature of perceptual representation and the influence of expertise and evolution on attention allocation.
Psycholinguistic norms for 320 fixed expressions (idioms and proverbs) in French
Authors: Bonin Patrick , Méot Alain , Boucheix Jean-Michel , Bugaiska Aurélia
Published: March 2017

We provide psycholinguistic norms for a new set of 160 French idiomatic expressions and 160 proverbs: knowledge, predictability, literality, compositionality, subjective and objective frequency, familiarity, age of acquisition (AoA) and length. Different analyses (reliability, descriptive statistics and correlations) performed on the norms are reported and discussed. The norms can be downloaded as Supplemental Material .
Macrophages: micromanagers of antagonistic signaling nanoclusters
Authors: Eggeling Christian , Davis Simon J.
Published: March 2017

How cells integrate antagonistic receptor signaling events is enigmatic. Using superresolution optical microscopy, Lopes et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201608094) demonstrate the nanometer-scale molecular reorganization of antagonistic signaling receptors in macrophages, after engagement by the receptors of activating and inhibitory ligands. They propose that large-scale rearrangements of this type underpin decision-making by these cells.
Iterates of generic polynomials and generic rational functions
Authors: Juul J.
Published: March 2017

In 1985, Odoni showed that in characteristic

0
0

the Galois group of the

n
n

-th iterate of the generic polynomial with degree

d
d

is as large as possible. That is, he showed that this Galois group is the

n
n

-th wreath power of the symmetric group

S
d

S_d

. We generalize this result to positive characteristic, as well as to the generic rational function. These results can be applied to prove certain density results in number theory, two of which are presented here. This work was partially completed by the late R.W.K. Odoni in an unpublished paper.
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
Authors: Yan Koon-Kiu , Yardımcı Galip Gürkan , Yan Chengfei , Noble William S , Gerstein Mark
Published: March 2017

Genome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of the genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit the 2D nature of Hi-C contact maps, matrix techniques like spectral analysis are particularly useful. Here, we present HiC-spector, a collection of matrix-related functions for analyzing Hi-C contact maps. In particular, we introduce a novel reproducibility metric for quantifying the similarity between contact maps based on spectral decomposition. The metric successfully separates contact maps mapped from Hi-C data coming from biological replicates, pseudo-replicates and different cell types.

Availability and Implementation

Source code in Julia and Python, and detailed documentation is available at https://github.com/gersteinlab/HiC-spector.

Supplementary information

Supplementary data are available at Bioinformatics online.
IcyTree: rapid browser-based visualization for phylogenetic trees and networks
Authors: Vaughan Timothy G
Published: March 2017

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible.

Availability and Implementation

IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License.
Deep mining heterogeneous networks of biomedical linked data to predict novel drug–target associations
Authors: Zong Nansu , Kim Hyeoneui , Ngo Victoria , Harismendy Olivier
Published: March 2017

Motivation

A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug–target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug–target prediction.

Results

We propose a similarity-based drug–target prediction method that enhances existing association discovery methods by using a topology-based similarity measure. DeepWalk, a deep learning method, is adopted in this study to calculate the similarities within Linked Tripartite Network (LTN), a heterogeneous network generated from biomedical linked datasets. This proposed method shows promising results for drug–target association prediction: 98.96% AUC ROC score with a 10-fold cross-validation and 99.25% AUC ROC score with a Monte Carlo cross-validation with LTN. By utilizing DeepWalk, we demonstrate that: (i) this method outperforms other existing topology-based similarity computation methods, (ii) the performance is better for tripartite than with bipartite networks and (iii) the measure of similarity using network topology outperforms the ones derived from chemical structure (drugs) or genomic sequence (targets). Our proposed methodology proves to be capable of providing a promising solution for drug–target prediction based on topological similarity with a heterogeneous network, and may be readily re-purposed and adapted in the existing of similarity-based methodologies.

Availability and Implementation

The proposed method has been developed in JAVA and it is available, along with the data at the following URL: https://github.com/zongnansu1982/drug-target-prediction.

Supplementary information

Supplementary data are available at Bioinformatics online.
SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials
Authors: Fiore-Gartland Andrew , Kullman Nicholas , deCamp Allan C , Clenaghan Graham , Yang Wayne , Magaret Craig A , Edlefsen Paul T , Gilbert Peter B
Published: March 2017

Analysis of HIV-1 virions from participants infected in a randomized controlled preventive HIV-1 vaccine efficacy trial can help elucidate mechanisms of partial protection. By comparing the genetic sequence of viruses from vaccine and placebo recipients to the sequence of the vaccine itself, a technique called ‘sieve analysis’, one can identify functional specificities of vaccine-induced immune responses. We have created an interactive web-based visualization and data access tool for exploring the results of sieve analyses performed on four major preventive HIV-1 vaccine efficacy trials: (i) the HIV Vaccine Trial Network (HVTN) 502/Step trial, (ii) the RV144/Thai trial, (iii) the HVTN 503/Phambili trial and (iv) the HVTN 505 trial. The tool acts simultaneously as a platform for rapid reinterpretation of sieve effects and as a portal for organizing and sharing the viral sequence data. Access to these valuable datasets also enables the development of novel methodology for future sieve analyses.

Availability and Implementation

Visualization: http://sieve.fredhutch.org/viz. Source code: https://github.com/nkullman/SIEVE. Data API: http://sieve.fredhutch.org/data.
A novel but frequent variant in LPA KIV-2 is associated with a pronounced Lp(a) and cardiovascular risk reduction
Authors: Coassin Stefan , Erhart Gertraud , Weissensteiner Hansi , Eca Guimarães de Araújo Mariana , Lamina Claudia , Schönherr Sebastian , Forer Lukas , Haun Margot , Losso Jamie Lee , Köttgen Anna , Schmidt Konrad , Utermann Gerd , Peters Annette , Gieger Christian , Strauch Konstantin , Finkenstedt Armin , Bale Reto , Zoller Heinz , Paulweber Bernhard , Eckardt Kai-Uwe , Hüttenhofer Alexander , Huber Lukas A. , Kronenberg Florian
Published: March 2017

Aims

Lp(a) concentrations represent a major cardiovascular risk factor and are almost entirely controlled by one single locus (LPA). However, many genetic factors in LPA governing the enormous variance of Lp(a) levels are still unknown. Since up to 70% of the LPA coding sequence are located in a difficult to access hypervariable copy number variation named KIV-2, we hypothesized that it may contain novel functional variants with pronounced effects on Lp(a) concentrations. We performed a large scale mutation analysis in the KIV-2 using an extreme phenotype approach.

Methods and Results

We compiled an discovery set of 123 samples showing discordance between LPA isoform phenotype and Lp(a) concentrations and controls. Using ultra-deep sequencing, we identified a splice site variant (G4925A) in preferential association with the smaller LPA isoforms. Follow-up in a European general population (n = 2892) revealed an exceptionally high carrier frequency of 22.1% in the general population. The variant explains 20.6% of the Lp(a) variance in carriers of low molecular weight (LMW) apo(a) isoforms (P = 5.75e-38) and reduces Lp(a) concentrations by 31.3 mg/dL. Accordingly the odds ratio for cardiovascular disease was reduced from 1.39 [95% confidence interval (CI): 1.17–1.66, P = 1.89e-04] for wildtype LMW individuals to 1.19 [95%CI: 0.92; 1.56, P = 0.19] in LMW individuals who were additionally positive for G4925A. Functional studies point towards a reduction of splicing efficiency by this novel variant.

Conclusion

A highly frequent but until now undetected variant in the LPA KIV-2 region is strongly associated with reduced Lp(a) concentrations and reduced cardiovascular risk in LMW individuals.
Flawless diamond separation in simultaneous source acquisition by seismic apparition
Authors: Andersson Fredrik , Robertsson Johan O.A. , van Manen Dirk-Jan , Wittsten Jens , Eggenberger Kurt , Amundsen Lasse
Published: March 2017

In this paper we prove that the recently introduced method of signal apparition optimally separates signals from interfering sources recorded during simultaneous source seismic data acquisition. By utilizing a periodic sequence of source signatures along one source line, that wavefield becomes separately partially visible in the spectral domain where it can be isolated from interfering signals, processed, and subtracted from the original recordings, thereby separating the wavefields from each other. Whereas other methods for simultaneous source separation can recover data in a triangle-shaped region in the spectral domain, signal apparition allows for the exact separation of data in a diamond-shaped region that is twice as large thereby enabling superior reconstruction of separated wavefields throughout the entire data bandwidth.
Suppressed star formation by a merging cluster system
Authors: Mansheim A. S. , Lemaux B. C. , Tomczak A. R. , Lubin L. M. , Rumbaugh N. , Wu P.-F. , Gal R. R. , Shen L. , Dawson W. A. , Squires G. K.
Published: March 2017

We examine the effects of an impending cluster merger on galaxies in the large-scale structure (LSS) RX J0910 at z =1.105. Using multiwavelength data, including 102 spectral members drawn from the Observations of Redshift Evolution in Large Scale Environments (ORELSE) survey and precise photometric redshifts, we calculate star formation rates and map the specific star formation rate density of the LSS galaxies. These analyses along with an investigation of the colour–magnitude properties of LSS galaxies indicate lower levels of star formation activity in the region between the merging clusters relative to the outskirts of the system. We suggest that gravitational tidal forces due to the potential of the merging haloes may be the physical mechanism responsible for the observed suppression of star formation in galaxies caught between the merging clusters.