bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of a LOV protein in apo-state and implications for construction of LOV-based optical tools
Authors: Arinkin Vladimir , Granzin Joachim , Röllen Katrin , Krauss Ulrich , Jaeger Karl-Erich , Willbold Dieter , Batra-Safferling Renu
Published: February 2017

Unique features of Light-Oxygen-Voltage (LOV) proteins like relatively small size (~12–19 kDa), inherent modularity, highly-tunable photocycle and oxygen-independent fluorescence have lately been exploited for the generation of optical tools. Structures of LOV domains reported so far contain a flavin chromophore per protein molecule. Here we report two new findings on the short LOV protein W619_1-LOV from Pseudomonas putida. First, the apo-state crystal structure of W619_1-LOV at 2.5 Å resolution reveals conformational rearrangements in the secondary structure elements lining the chromophore pocket including elongation of the Fα helix, shortening of the Eα-Fα loop and partial unfolding of the Eα helix. Second, the apo W619_1-LOV protein binds both natural and structurally modified flavin chromophores. Remarkably different photophysical and photochemical properties of W619_1-LOV bound to 7-methyl-8-chloro-riboflavin (8-Cl-RF) and lumichrome imply application of these variants as novel optical tools as they offer advantages such as no adduct state formation, and a broader choice of wavelengths for in vitro studies.
Modified unsupervised discriminant projection with an electronic nose for the rapid determination of Chinese mitten crab freshness
Authors: Zhu Peiyi , Du Jie , Xu Benlian , Lu Mingli
Published: February 2017

In this paper, a method to rapidly determine living Chinese mitten crab freshness using an electronic nose (E-nose) and a non-linear data processing technique was studied.
Centrifuge-free dispersive liquid–liquid microextraction based on the salting-out effect followed by high performance liquid chromatography for simple and sensitive determination of polycyclic aromatic hydrocarbons in water samples
Authors: Arghavani-Beydokhti Somayeh , Rajabi Maryam , Bazregar Mohammad , Asghari Alireza
Published: February 2017

A simple approach is described for the elimination of the centrifugation step in dispersive liquid–liquid microextraction (DLLME).
Influence of orientation mismatch on charge transport across grain boundaries in tri-isopropylsilylethynyl (TIPS) pentacene thin films
Authors: Steiner Florian , Poelking Carl , Niedzialek Dorota , Andrienko Denis , Nelson Jenny
Published: February 2017

We present a multi-scale model for charge transport across grain boundaries in molecular electronic materials that incorporates packing disorder, electrostatic and polarisation effects.
Origin of non-conservative circular dichroism of the CP29 antenna complex of photosystem II
Authors: Lindorfer Dominik , Müh Frank , Renger Thomas
Published: February 2017

Structure-based explanation of the non-conservative circular dichroism spectrum of the photosynthetic antenna complex CP29 of photosystem II.
Three promising applications of microbial electrochemistry for the water sector
Authors: Modin Oskar , Aulenta Federico
Published: February 2017

The potential applications of microbial electrochemistry are many; three promising ones are sensors, in situ bioremediation, and metal recovery.
A copper-catalyzed oxidative coupling reaction of arylboronic acids, amines and carbon dioxide using molecular oxygen as the oxidant
Authors: Xiong Wenfang , Qi Chaorong , Guo Tianzuo , Zhang Min , Chen Kai , Jiang Huanfeng
Published: February 2017

A Cu-catalyzed oxidative coupling reaction of arylboronic acids, amines and carbon dioxide is described, providing a route to O-aryl carbamates.
Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology
Authors: Rangel-Chavez Cynthia , Galan-Vasquez Edgardo , Martinez-Antonio Agustino
Published: February 2017

Consensus of the architecture and composition of the elements that form transcriptional units inE. coliand comparison with synthetic genetic circuits.
Anion-templated nanosized silver clusters protected by mixed thiolate and diphosphine
Authors: Li Xiao-Yu , Wang Zhi , Su Hai-Feng , Feng Sheng , Kurmoo Mohamedally , Tung Chen-Ho , Sun Di , Zheng Lan-Sun
Published: February 2017

Anion template effects were exemplified in six novel high-nuclearity silver clusters constructed using mixed S- and P-donor ligands.
Preparation of hyperstar polymers with encapsulated Au25(SR)18 clusters as recyclable catalysts for nitrophenol reduction
Authors: Hu Daqiao , Jin Shan , Shi Yi , Wang Xiaofeng , Graff Robert W. , Liu Wenqi , Zhu Manzhou , Gao Haifeng
Published: February 2017

A composite hyperstar polymer with encapsulated Au25(SR)18 clusters was successfully prepared and used as recyclable catalyst for 4-nitrophenol reduction.
Reaction-based indicator displacement assay (RIA) for the colorimetric and fluorometric detection of hydrogen peroxide
Authors: Sun Xiaolong , Odyniec Maria L. , Sedgwick Adam C. , Lacina Karel , Xu Suying , Qiang Taotao , Bull Steven D. , Marken Frank , James Tony D.
Published: February 2017

Reaction-based indicator displacement assay for the optical cycle-monitoring of hydrogen peroxide.
Investigation into 1,3-butadiene and other bulk chemicals' formation from bioethanol over Mg–Al catalysts
Authors: Gao Meixiang , Zhang Minhua , Li Yonghui
Published: February 2017

Mg–Al catalysts were adopted in the direct synthesis of 1,3-butadiene and other bulk chemicals from bioethanol.
Theoretical insight into effect of doping of transition metal M (M = Ni, Pd and Pt) on CO2reduction pathways on Cu(111) and understanding of origin of electrocatalytic activity
Authors: Ou Lihui , Long Wenqi , Huang Jianxing , Chen Yuandao , Jin Junling
Published: February 2017

The doped Pt can simultaneously reduce overpotential for CO formation and further reduction and most easily remove OH, thus suggesting the best electrocatalytic activity.
Layered birnessite-type MnO2 with surface pits for enhanced catalytic formaldehyde oxidation activity
Authors: Wang Jinlong , Zhang Gaoke , Zhang Pengyi
Published: February 2017

Layered birnessite-type MnO2 with surface pits facilitates enhanced catalytic formaldehyde oxidation activity.
Cation ordering and oxygen transport behaviour in Sr1−3x/2LaxTiO3perovskites
Authors: Fossati Paul C. M. , Grimes Robin W.
Published: February 2017

Effects of cation ordering on oxygen diffusion mechanisms in (Sr,La)TiO3perovskites is investigated using atomistic modelling techniques.
Phase pure Sn4P3 nanotops by solution-liquid-solid growth for anode application in sodium ion batteries
Authors: Lan Danni , Wang Wenhui , Shi Liang , Huang Yuan , Hu Liangbin , Li Quan
Published: February 2017

The TOC includes a TEM image of the Sn4P3 nanotops, the brief reaction mechanism, and the electrochemical performance.
Activatable ultrasmall gold nanorods for “off–on” fluorescence imaging-guided photothermal therapy
Authors: Zhao Feixiang , Li Xue , Li Jiang , Dou Yan , Wang Lingwei , Wu Menglin , Liu Yajuan , Chang Jin , Zhang Xuening
Published: February 2017

We developed activatable ultrasmall gold nanorods (AUGNRs) to realize “off–on” switched fluorescence imaging-guided efficient PTT.
Engineering strategies for chitin nanofibers
Authors: Zhang Xiaolin , Rolandi Marco
Published: February 2017

Chitin nanofibers are the fundamental building blocks of numerous structural natural materials. From top-down to bottom-up, here we review engineering strategies to produce chitin nanofibers for engineered materials and their applications.
The metabolic pathway of flonicamid in oranges using an orthogonal approach based on high-resolution mass spectrometry and nuclear magnetic resonance
Authors: López-Ruiz R. , Ruiz-Muelle A. B. , Romero-González R. , Fernández I. , Martínez Vidal J. L. , Frenich A. Garrido
Published: February 2017

An orthogonal approach has been used to perform a metabolic profiling study of flonicamid in orange fruits.
Quinaldine red as a fluorescent light-up probe for i-motif structures
Authors: Jiang Guimei , Xu Lijun , Wang Kewei , Chen Xing , Wang Jine , Cao Weiguo , Pei Renjun
Published: February 2017

We report a new fluorescent probe for i-motif structures. When binding to i-motifs, quinaldine red exhibits a remarkable increase in its fluorescence, which benefits i-motif-involved label-free systems.
A GO–Se nanocomposite as an antioxidant nanozyme for cytoprotection
Authors: Huang Yanyan , Liu Chaoqun , Pu Fang , Liu Zhen , Ren Jinsong , Qu Xiaogang
Published: February 2017

GO–Se nanocomposites are fabricated with excellent glutathione peroxidase (GPx)-like properties to protect cells against oxidative stress.
Palladium-catalyzed cascade metallo-ene/Suzuki coupling reaction of allenamides
Authors: Liang Hanbing , Yan Fachao , Dong Xu , Liu Qing , Wei Xiaobing , Liu Sheng , Dong Yunhui , Liu Hui
Published: February 2017

A new type of cascade metallo-ene/Suzuki coupling reaction of allenamides catalyzed by palladium is described.
A two-photon fluorescent probe for real-time monitoring of autophagy by ultrasensitive detection of the change in lysosomal polarity
Authors: Jiang Jiacheng , Tian Xiaohe , Xu Changzhi , Wang Shuxin , Feng Yan , Chen Man , Yu Haizhu , Zhu Manzhou , Meng Xiangming
Published: February 2017

The first two-photon probe, Lyso-OC, was proposed for use in monitoring cell autophagy by detection of the change in the lysosomal polarity during the membrane fusion process.
Insights into the unprecedented epoxidation mechanism of fumitremorgin B endoperoxidase (FtmOx1) from Aspergillus fumigatus by QM/MM calculations
Authors: Wang Xiya , Su Hao , Liu Yongjun
Published: February 2017

QM/MM calculations indicate that the quintet of the FeIVO complex firstly abstracts the hydrogen from Tyr228 to initiate the reaction, then the generated Tyr228 radical extracts the hydrogen from C21 to form the C21 radical, which binds the second dioxygen to complete the epoxidation.
Impacts of anions on the oxygen reduction reaction kinetics on platinum and palladium surfaces in alkaline solutions
Authors: Zhu Shangqian , Hu Xiaomeng , Shao Minhua
Published: February 2017

(Bi)sulfate and (bi)carbonate have distinct impacts on ORR, and citrate was self-dissociated on Pt and Pd.
The effect of substituents on triply bonded boronantimony molecules: a theoretical approach
Authors: Lu Jia-Syun , Yang Ming-Chung , Su Ming-Der
Published: February 2017

Theoretical calculations using the M06-2X, B3PW91 and B3LYP levels of theory demonstrate that the attached substituents (R) play a decisive role in determining the stability of triply bonded RBSbR molecules. Theoretical evidence shows that, from the kinetic viewpoint, only bulkier substituents have a significant stabilizing effect on the formation of the triply bonded RBSbR compounds.
Thermodynamic stability of driven open systems and control of phase separation by electro-autocatalysis
Authors: Bazant Martin Z.
Published: February 2017

Motivated by the possibility of electrochemical control of phase separation, a variational theory of thermodynamic stability is developed for driven reactive mixtures, based on a nonlinear generalization of the Cahn–Hilliard and Allen–Cahn equations. The Glansdorff–Prigogine stability criterion is extended for driving chemical work, based on variations of nonequilibrium Gibbs free energy. Linear stability is generally determined by the competition of chemical diffusion and driven autocatalysis. Novel features arise for electrochemical systems, related to controlled total current (galvanostatic operation), concentration-dependent exchange current (Butler–Volmer kinetics), and negative differential reaction resistance (Marcus kinetics). The theory shows how spinodal decomposition can be controlled by solo-autocatalytic charge transfer, with only a single faradaic reaction. Experimental evidence is presented for intercalation and electrodeposition in rechargeable batteries, and further applications are discussed in solid state ionics, electrovariable optics, electrochemical precipitation, and biological pattern formation.
Thermolysis and radiofluorination of diaryliodonium salts derived from anilines
Authors: Linstad Ethan J. , Vāvere Amy L. , Hu Bao , Kempinger Jayson J. , Snyder Scott E. , DiMagno Stephen G.
Published: February 2017

Mechanistic and theoretical studies reveal new reactions of Ar2I salts that can interfere with radiolabeling of these substrates.
Sequential partial ion exchange synthesis of composite Ni3S2/Co9S8/NiSe nanoarrays with a lavender-like hierarchical morphology
Authors: Huang Shaobo , Zhang Wangxi , Cui Shizhong , Chen Weihua , Mi Liwei
Published: February 2017

A hierarchical Ni@Ni3S2/Co9S8/NiSe composite through sequential partial ion exchange for supercapacitor design.
Catalytic reduction of NACs by nano Fe3O4/quinone composites in the presence of a novel marine exoelectrogenic bacterium under hypersaline conditions
Authors: Zhang Haikun , Hu Xiaoke
Published: February 2017

Bioremediation of N-substituted aromatic compounds (NACs) has attracted a substantial amount of interest due to its cost effectiveness and environmental friendliness.
Ti3BN monolayer: the MXene-like material predicted by first-principles calculations
Authors: Wang Dandan , Sun ZhongHui , Han DongXue , Liu Lei , Niu Li
Published: February 2017

An MXene-like Ti3BN monolayer whose electronic properties could be modulated has been predicted following the strategy of “atomic transmutation”.
High-level ab initio potential energy surface and dynamics of the F−+ CH3I SN2 and proton-transfer reactions
Authors: Olasz Balázs , Szabó István , Czakó Gábor
Published: February 2017

The first analyticalab initiopotential energy surface reveals the dynamics and different mechanisms of the F−+ CH3I reaction.
Advanced electroanalytical chemistry at nanoelectrodes
Authors: Ying Yi-Lun , Ding Zhifeng , Zhan Dongping , Long Yi-Tao
Published: February 2017

In this perspective, we discuss the challenges, advances and opportunities in electroanalytical chemistry at nanoelectrodes, including nanoelectrode fabrication, real-time characterizations, and high-performance electrochemical instrumentation.
3D yolk–shell NiGa2S4 microspheres confined with nanosheets for high performance supercapacitors
Authors: Liu Shude , Kim Kwang Ho , Yun Je Moon , Kundu Aniruddha , Sankar K. Vijaya , Patil Umakant M. , Ray Chaiti , Chan Jun Seong
Published: February 2017

Recent advances in the development of two-dimensional transition-metal chalcogenides (2D TMCs) have opened up new avenues for supercapacitor applications.
Direct Surgery of Previously Coiled Large Internal Carotid Ophthalmic Aneurysm for the Purpose of Optic Nerve Decompression
Authors: Kawabata Shuhei , Toyota Shingo , Kumagai Tetsuya , Goto Tetsu , Mori Kanji , Taki Takuyu
Published: February 2017

Background Progressive visual loss after coil embolization of a large internal carotid ophthalmic aneurysm has been widely reported. It is generally accepted that the primary strategy for this complication should be conservative, including steroid therapy; however, it is not well known as to what approach to take when the conservative therapy is not effective.

Case Presentation We report a case of a 55-year-old female presenting with progressive visual loss after the coiling of a ruptured large internal carotid ophthalmic aneurysm. As the conservative therapy had not been effective, we performed neck clipping of the aneurysm with optic canal unroofing, anterior clinoidectomy, and partial removal of the embolized coils for the purpose of optic nerve decompression. After the surgery, the visual symptom was improved markedly.

Conclusions It is suggested that direct surgery for the purpose of optic nerve decompression may be one of the options when conservative therapy is not effective for progressive visual disturbance after coil embolization.
Preferences and Utilities for Health States after Treatment of Olfactory Groove Meningioma: Endoscopic versus Open
Authors: Yao Christopher , Kahane Alyssa , Monteiro Eric , Gentili Fred , Zadeh Gelareh , de Almeida John
Published: February 2017

Objectives The purpose of this study is to report health utility scores for patients with olfactory groove meningiomas (OGM) treated with either the standard transcranial approach, or the expanded endonasal endoscopic approach.

Design The time trade-off technique was used to derive health utility scores.

Setting Healthy individuals without skull base tumors were surveyed.

Main Outcome Measures Participants reviewed and rated scenarios describing treatment (endoscopic, open, stereotactic radiation, watchful waiting), remission, recurrence, and complications associated with the management of OGMs.

Results There were 51 participants. The endoscopic approach was associated with higher utility scores compared with an open craniotomy approach (0.88 vs. 0.74; p < 0.001) and watchful waiting (0.88 vs.0.74; p = 0.002). If recurrence occurred, revision endoscopic resection continued to have a higher utility score compared with revision open craniotomy (0.68; p = 0.008). On multivariate analysis, older individuals were more likely to opt for watchful waiting (p = 0.001), whereas participants from higher income brackets were more likely to rate stereotactic radiosurgery with higher utility scores (p = 0.017).

Conclusion The endoscopic approach was associated with higher utility scores than craniotomy for primary and revision cases. The present utilities can be used for future cost-utility analyses.
A 15-Year-Old with Aphasia and Right Hemiparesis
Authors: Wadowski Benjamin , Chadha Tanya , Wen Andy
Published: February 2017

Takayasu arteritis (TA) is the third most common vasculitis in childhood, peaking in the second to third decades of life but affecting patients as young as 6 months of age. It often presents with nonspecific systemic symptoms, although at late stages, it may present with cardiac, renal, or focal neurologic sequelae of vascular compromise. In this case, we describe a 15-year-old patient who presented acutely with stroke. In the absence of more classic rheumatological symptoms and significant laboratory abnormalities on initial testing, the diagnosis of TA was only reached through extensive vascular imaging following consultation with multiple subspecialty teams. This case demonstrates the need to maintain a high index of suspicion for vasculitis in pediatric patients presenting with new onset stroke in the absence of known predisposing factors. Doing so may reduce the time to diagnosis, hasten treatment, and optimize outcomes.
The Temporalis Muscle Flap for Palate Reconstruction: Case Series and Review of the Literature
Authors: Brennan Tara , Tham Tristan , Costantino Peter
Published: February 2017

Introduction The temporalis myofascial (TM) is an important reconstructive flap in palate reconstruction. Past studies have shown the temporalis myofascial flap to be safe as well as effective. Free flap reconstruction of palate defects is also a popular method used by contemporary surgeons. We aim to reaffirm the temporalis myofascial flap as a viable alternative to free flaps for palate reconstruction.

Objective We report our results using the temporalis flap for palate reconstruction in one of the largest case series reported. Our literature review is the first to describe complication rates of palate reconstruction using the TM flap.

Methods Retrospective chart review and review of the literature.

Results Fifteen patients underwent palate reconstruction with the TM flap. There were no cases of facial nerve injury. Five (33%) of these patients underwent secondary cranioplasty to address temporal hollowing after the TM flap. Three out of fifteen (20%) had flap related complications. Fourteen (93%) of the palate defects were successfully reconstructed, with the remaining case pending a secondary procedure to close the defect. Ultimately, all of the flaps (100%) survived.

Conclusion The TM flap is a viable method of palate defect closure with a high defect closure rate and flap survival rate. TM flaps are versatile in repairing palate defects of all sizes, in all regions of the palate. Cosmetic deformity created from TM flap harvest may be addressed using cranioplasty implant placement, either primarily or during a second stage procedure.
A Multicenter Initiative for Critical Congenital Heart Disease Newborn Screening in Texas Neonatal Intensive Care Units
Authors: Guillory Charleta , Creel Liza , Livingtson Judith , McKee-Garrett Tiffany , Fortunov Regine , Gong Alice
Published: February 2017

Objective The objective of this study was to implement a strategy for critical congenital heart disease (CCHD) newborn screening in the neonatal intensive care unit (NICU).

Design A NICU-specific curriculum, screening algorithm, slide presentations, and templates of orders, policies, and procedures were developed into a toolkit for training NICU personnel. Screening was conducted on first and second screen pre- and postductal oxygen saturations (SpO2) on newborns admitted or transferred to the NICU.

Results We trained 347 NICU personnel in 13 Texas hospitals, representing rural, suburban, and metropolitan settings. Key hospital staff submitted deidentified, case-based screening data. Of 4,621 NICU admissions, 80% received a first screen. Second screening rates were substantially lower in all gestational age groups. Screening rates on first and second screens were lowest among infants born < 28 weeks. For the first screen, SpO2 was lowest among the youngest gestational ages. The false positive rate was 2.3%.

Conclusion CCHD screening in the NICU is challenging, given the complexities of the NICU population. A modified screening protocol that recognizes special circumstances of neonatal intensive care could facilitate a more efficient system.
Analysis and optimization of acoustic wave micro-resonators integrating piezoelectric zinc oxide layers
Authors: Mortada O. , Zahr A. H. , Orlianges J.-C. , Crunteanu A. , Chatras M. , Blondy P.
Published: February 2017

This paper reports on the design, simulation, fabrication, and test results of ZnO-based contour-mode micro-resonators integrating piezoelectric zinc oxide (ZnO) layers. The inter-digitated (IDT) type micro-resonators are fabricated on ZnO films and suspended top of 2 μm thick silicon membranes using silicon-on insulator technology. We analyze several possibilities of increasing the quality factor (Q) and the electromechanical coupling coefficient (kt2) of the devices by varying the numbers and lengths of the IDT electrodes and using different thicknesses of the ZnO layer. We designed and fabricated IDTs of different finger numbers (n = 25, 40, 50, and 80) and lengths (L = 100/130/170/200 μm) for three different thicknesses of ZnO films (200, 600, and 800 nm). The measured Q factor confirms that reducing the length and the number of IDT fingers enables us to reach better electrical performances at resonant frequencies around 700 MHz. The extracted results for an optimized micro-resonator device having an IDT length of 100 μm and 40 finger electrodes show a Q of 1180 and a kt2 of 7.4%. We demonstrate also that the reduction of the ZnO thickness from 800 nm to 200 nm increases the quality factor from 430 to 1600, respectively, around 700 MHz. Experimental data are in very good agreement with theoretical simulations of the fabricated devices
Nonlinear ultrasound imaging of nanoscale acoustic biomolecules
Authors: Maresca David , Lakshmanan Anupama , Lee-Gosselin Audrey , Melis Johan M. , Ni Yu-Li , Bourdeau Raymond W. , Kochmann Dennis M. , Shapiro Mikhail G.
Published: February 2017

Ultrasound imaging is widely used to probe the mechanical structure of tissues and visualize blood flow. However, the ability of ultrasound to observe specific molecular and cellular signals is limited. Recently, a unique class of gas-filled protein nanostructures called gas vesicles (GVs) was introduced as nanoscale (∼250 nm) contrast agents for ultrasound, accompanied by the possibilities of genetic engineering, imaging of targets outside the vasculature and monitoring of cellular signals such as gene expression. These possibilities would be aided by methods to discriminate GV-generated ultrasound signals from anatomical background. Here, we show that the nonlinear response of engineered GVs to acoustic pressure enables selective imaging of these nanostructures using a tailored amplitude modulation strategy. Finite element modeling predicted a strongly nonlinear mechanical deformation and acoustic response to ultrasound in engineered GVs. This response was confirmed with ultrasound measurements in the range of 10 to 25 MHz. An amplitude modulation pulse sequence based on this nonlinear response allows engineered GVs to be distinguished from linear scatterers and other GV types with a contrast ratio greater than 11.5 dB. We demonstrate the effectiveness of this nonlinear imaging strategy in vitro, in cellulo, and in vivo.
Mass-analyzed threshold ionization spectroscopy of lanthanum-hydrocarbon radicals formed by C—H bond activation of propene
Authors: Kumari Sudesh , Cao Wenjin , Hewage Dilrukshi , Silva Ruchira , Yang Dong-Sheng
Published: February 2017

La(C3H4) and La(C3H6) are observed from the reaction of laser-vaporized La atoms with propene by photoionization time-of-flight mass spectrometry and characterized by mass-analyzed threshold ionization spectroscopy. Two isomers of La(C3H4) are identified as methyl-lanthanacyclopropene [La(CHCCH3)] (Cs) and lanthanacyclobutene [La(CHCHCH2)] (C1); La(C3H6) is determined to be H—La(η3-allyl) (Cs), a C—H bond inserted species. All three metal-hydrocarbon radicals prefer a doublet ground state with a La 6s-based electron configuration. Ionization of the neutral doublet state of each of these radicals produces a singlet ion state by removing the La-based 6s electron. The threshold ionization allows accurate measurements of the adiabatic ionization energy of the neutral doublet state and metal-ligand and ligand-based vibrational frequencies of the neutral and ionic states. The formation of the three radicals is investigated by density functional theory computations. The inserted species is formed by La inserting into an allylic C—H bond and lanthanacyclopropene by concerted vinylic H2 elimination, whereas lanthanacyclobutene involves both allylic and vinylic dehydrogenations. The inserted species is identified as an intermediate for the formation of lanthanacyclobutene.
Waiting time distribution for electron transport in a molecular junction with electron-vibration interaction
Authors: Kosov Daniel S.
Published: February 2017

On the elementary level, electronic current consists of individual electron tunnelling events that are separated by random time intervals. The waiting time distribution is a probability to observe the electron transfer in the detector electrode at time t+τ given that an electron was detected in the same electrode at an earlier time t. We study waiting time distribution for quantum transport in a vibrating molecular junction. By treating the electron-vibration interaction exactly and molecule-electrode coupling perturbatively, we obtain the master equation and compute the distribution of waiting times for electron transport. The details of waiting time distributions are used to elucidate microscopic mechanism of electron transport and the role of electron-vibration interactions. We find that as nonequilibrium develops in the molecular junction, the skewness and dispersion of the waiting time distribution experience stepwise drops with the increase of the electric current. These steps are associated with the excitations of vibrational states by tunnelling electrons. In the strong electron-vibration coupling regime, the dispersion decrease dominates over all other changes in the waiting time distribution as the molecular junction departs far away from the equilibrium.
High temperature surface Brillouin scattering study of mechanical properties of boron-doped epitaxial polysilicon
Authors: Mathe B. A. , Comins JD , Every A. G. , Hobbs L. W.
Published: February 2017

A study of the mechanical properties of a boron-doped epitaxial polysilicon layer deposited on a Si (100) substrate specimen has been carried out by surface Brillouin scattering at high temperatures. This type of specimen is widely used in micro-electro-mechanical systems (MEMS). By accumulating spectra with the Rayleigh mode and the Lamb continuum the isotropic elastic constants C44 and C11 were obtained, from which the values of the bulk, shear and Young’s moduli and Poisson’s ratio for the layer were determined over a range of temperatures from 20 °C to 110 °C. By contrast, an examination of the literature on polycrystalline silicon shows that other methods each provide a limited range of the above properties and thus additional experiments and techniques were needed. The SBS method is applicable to other polycrystalline materials such as silicon carbide, silicon nitride, silicon germanium and amorphous diamond that have also been used for MEMS applications.
A single-phase axially-magnetized permanent-magnet oscillating machine for miniature aerospace power sources
Authors: Sui Yi , Zheng Ping , Cheng Luming , Wang Weinan , Liu Jiaqi
Published: February 2017

A single-phase axially-magnetized permanent-magnet (PM) oscillating machine which can be integrated with a free-piston Stirling engine to generate electric power, is investigated for miniature aerospace power sources. Machine structure, operating principle and detent force characteristic are elaborately studied. With the sinusoidal speed characteristic of the mover considered, the proposed machine is designed by 2D finite-element analysis (FEA), and some main structural parameters such as air gap diameter, dimensions of PMs, pole pitches of both stator and mover, and the pole-pitch combinations, etc., are optimized to improve both the power density and force capability. Compared with the three-phase PM linear machines, the proposed single-phase machine features less PM use, simple control and low controller cost. The power density of the proposed machine is higher than that of the three-phase radially-magnetized PM linear machine, but lower than the three-phase axially-magnetized PM linear machine.
Simulation studies of a novel electromagnetic actuation scheme for focusing magnetic micro/nano-carriers into a deep target region
Authors: Le Tuan-Anh , Zhang Xingming , Hoshiar Ali Kafash , Kim Myeong Ok , Yoon Jungwon
Published: February 2017

The ability to focus spherical particles (SPPs) to a deep tumor region remains one of the major challenges in magnetic drug targeting (MDT). A number of studies have attempted to overcome this problem using fast magnetic pulses and ferromagnetic rods. However, focusing of the SPPs in the deep body organs remains unsolved using existing schemes. In this paper, we propose a novel electro-magnetic actuation scheme for pushing and focusing SPPs. The simulation results demonstrate that the newly proposed actuation scheme can focus SPPs to a target surface region, inside of a block filled with an environment that has the characteristics of blood. We then investigated the effects of the proposed focusing scheme in realistic blood vessels with a maximum length of about 10–12 cm. The results show that SPPs of 500 nm can be concentrated onto a target tumor region with up to 97.9% efficiency. The proposed electromagnetic actuation scheme can maximize the efficiency of MDT, while minimizing the side effects of drugs in other tissues.
Effect of surface hybridization on RKKY coupling in ferromagnet/topological insulator/ferromagnet trilayer system
Authors: Ho Cong Son , Jalil Mansoor B. A.
Published: February 2017

We theoretically investigate the RKKY exchange coupling between two ferromagnets (FM) separated by a thin topological insulator film (TI). We find an unusual dependence of the RKKY exchange coupling Φex on the TI thickness (tTI). First, when tTI decreases, the coupling amplitude increases at first and reaches its maximum value at some critical thickness, below which the amplitude turns to diminish. This trend is attributed to the hybridization between surfaces of the TI film, which opens a gap below critical thickness and thus turns the surfaces into insulating state from semi-metal state. In insulating phase, diamagnetism induced by the gap-opening compensates paramagnetism of Dirac state, resulting in a diminishing magnetic susceptibility and RKKY coupling. For typical parameters, the critical thickness in Bi2Se3 thin film is estimated to be in the range of 3-5 nm.
Filoviruses and bats
Authors: Schuh Amy J , Amman Brian R , Towner Jonathan S
Published: February 2017

While Reston and Lloviu viruses have never been associated with human disease, the other filoviruses cause outbreaks of hemorrhagic fever characterised by person-to-person transmission and high case fatality ratios. Cumulative evidence suggests that bats are the most likely reservoir hosts of the filoviruses. Ecological investigations following Marburg virus disease outbreaks associated with entry into caves inhabited by Rousettus aegyptiacus bats led to the identification of this bat species as the natural reservoir host of the marburgviruses. Experimental infection of R. aegyptiacus with Marburg virus has provided insight into the natural history of filovirus infection in bats that may help guide the search for the reservoir hosts of the ebolaviruses.
Shakespearean Perspectives
Authors: Lucking David
Published: February 2017

David Lucking sees Shakespeare’s plays as negotiating tensions between a number of alternative, and sometimes mutually antagonistic perspectives. Some of these perspectives are associated with particular languages, cultures and texts, while others involve philosophical issues such as the nature of personal ontology and distinctions between reality and dream, being and nothingness. In elaborating his insights Lucking draws extensive comparisons with Lucretius’ De Rerum Natura, and between Sophocles’ Theban plays and King Lear, and he also pays close attention to A Midsummer Night’s Dream, Henry V, Julius Caesar, Hamlet, and Antony and Cleopatra. Re-assessing a wide range of earlier commentary, his nine essays confirm the lasting value of apposite contextualization in tandem with detailed close reading.
Noun-modifying constructions in Korean
Authors: Kim Shin-Sook , Sells Peter
Published: February 2017

We survey clausal noun-modification examples in Korean, initially setting out constructions into these types: argument and adjunct NMCCs, content noun NMCCs, and a group of other extended NMCCs. We show that the range of interpretations of NMCCs in Korean is not quite as broad as Japanese, but nevertheless we argue that the wide variety of interpretations in Korean motivates the claim that it has a GNMCC. We also argue, based on observed constraints on movement, that the Korean argument and adjunct NMCCs constitute an RC construction. We propose that there is no conflict in a language having both a syntactically identifiable RC construction as well as a GNMCC.
Noun-modifying clauses in Cantonese
Authors: Matthews Stephen , Yip Virginia
Published: February 2017

Whether relative clauses can be identified in Chinese is a recurrent question. We ask whether relative clauses are distinct from other noun-modifying clause constructions in Cantonese, one of many East Asian languages in which a noun can be preceded by a diverse range of modifying clauses. The relationship between head noun and modifying clause may be a grammatical one, with the head noun being understood as an argument or an adjunct of the modifying clause; or its interpretation may be dependent on semantic and pragmatic factors. We conclude that Cantonese has a General Noun-Modifying Clause Construction as proposed for Japanese (Matsumoto et al., this volume), with relative clauses forming a subset of modifying clauses in which a grammatical relation obtains.
The general noun-modifying clause construction in Tundra Nenets and its possible origin
Authors: Nikolaeva Irina
Published: February 2017

Tundra Nenets (Uralic) exhibits unambiguous relative clauses and sentential complements of nouns, but I show that it also has a previously unstudied but structurally distinct GNMCC. The GNMCC covers a diversity of functions although its usage is restricted in various ways. The paper suggests that it has a direct parallel in the non-sentential domain in terms of its syntactic behaviour, the morphosyntactic expression of the constructional ingredients and the basic semantics: it is modelled after the non-clausal compound-like structure employed for the very general purpose of modifying one noun by reference to another noun. Such modification-by-noun constructions served as a historical source of Tundra Nenets GNMCCs, which emerged when the modifying deverbal noun was reanalysed as heading a clausal domain.
Noun-modifying constructions and relativization in the central and western Caucasus
Authors: Nichols Johanna
Published: February 2017

Languages of the Nakh-Daghestanian family in the central and eastern Caucasus uniformly use gap strategies for relativization and GNMCC’s, despite different contact histories. Languages to the west and southwest (West Caucasian, Kartvelian) are very different, using relative pronouns and finite verbs. Despite long contact there is almost no accommodation of eastern and western types to each other. This sharp typological divide is a continuation of a larger Eurasian divide between western languages, which use finite relativization with relative pronouns, and eastern ones, which use participles and gaps. The stability of the divide in the Caucasus and its evident antiquity there are testimony to the non-Sprachbund status of the Caucasus.
Conclusion
Authors: Comrie Bernard , Sells Peter , Matsumoto Yoshiko
Published: February 2017

In this conclusion, we address three issues: a) the geographic extent of GNMCCs in Eurasia, including considerations of areal phenomena resulting from language contact; b) delimiting GNMCCs from other constructions, in particular those that in Japanese fall under GNMCCs; and c) structural properties that favor or disfavor GNMCCs.
The role of botanic gardens in the twenty-first century.
Authors: Krishnan S. , Novy A.
Published: February 2017

Botanic gardens and their functions and role in society have evolved over time. Originally established for study of medicinal plants in the mid-sixteenth century, they morphed into active sites for introduction, cultivation and dissemination of economically important crops during European expansion of colonies in Asia, America and Africa during the seventeenth-nineteenth centuries. During the second half of the twentieth century, importance was placed on the need for conservation and sustainable use of biodiversity. In the twenty-first century, botanic gardens are challenged to address issues that extend beyond the garden walls by placing social and environmental responsibility as key mission drivers.
Defamilisation measures and women's labour force participation – a comparative study of twelve countries
Authors: Chau Ruby C.M. , Yu Sam W.K. , Foster Liam , Lau Maggie K.W.
Published: February 2017

This paper examines the relevance of two interpretations of defamilisation (“freedom of the family” and “freedom of women from the family”) to the search for effective measures for strengthening women's participation in the paid labour market. Based on these two interpretations, two types of defamilisation measures (care-focused and women's economic) are identified. Two defamilisation indices are developed respectively covering twelve countries. The importance of the two types of defamilisation measures in assisting women to access employment are discussed from two angles. The input angle refers to the extent to which countries are committed to the provision of these defamilisation measures. The output angle is about the relationship between these defamilisation measures and the degree of women's participation in the paid labour market. Through conducting these analytical tasks, this paper also contributes to the examination of the relationship between types of welfare regimes and the provision of defamilisation measures.
27-Hydroxycholesterol impairs neuronal glucose uptake through an IRAP/GLUT4 system dysregulation
Authors: Ismail Muhammad-Al-Mustafa , Mateos Laura , Maioli Silvia , Merino-Serrais Paula , Ali Zeina , Lodeiro Maria , Westman Eric , Leitersdorf Eran , Gulyás Balázs , Olof-Wahlund Lars , Winblad Bengt , Savitcheva Irina , Björkhem Ingemar , Cedazo-Mínguez Angel
Published: February 2017

Hypercholesterolemia is associated with cognitively deteriorated states. Here, we show that excess 27-hydroxycholesterol (27-OH), a cholesterol metabolite passing from the circulation into the brain, reduced in vivo brain glucose uptake, GLUT4 expression, and spatial memory. Furthermore, patients exhibiting higher 27-OH levels had reduced 18F-fluorodeoxyglucose uptake. This interplay between 27-OH and glucose uptake revealed the engagement of the insulin-regulated aminopeptidase (IRAP). 27-OH increased the levels and activity of IRAP, countered the IRAP antagonist angiotensin IV (AngIV)–mediated glucose uptake, and enhanced the levels of the AngIV-degrading enzyme aminopeptidase N (AP-N). These effects were mediated by liver X receptors. Our results reveal a molecular link between cholesterol, brain glucose, and the brain renin-angiotensin system, all of which are affected in some neurodegenerative diseases. Thus, reducing 27-OH levels or inhibiting AP-N maybe a useful strategy in the prevention of the altered glucose metabolism and memory decline in these disorders.
Intersection of a correspondence with a graph of Frobenius
Authors: Varshavsky Yakov
Published: February 2017

The goal of this note is to give a short geometric proof of a theorem of Hrushovski asserting that an intersection of a correspondence with a graph of a sufficiently large power of Frobenius is non-empty.
Role of STARD4 in sterol transport between the endocytic recycling compartment and the plasma membrane
Authors: Iaea David B. , Mao Shu , Lund Frederik W. , Maxfield Frederick R.
Published: February 2017

Cholesterol is an essential constituent of membranes in mammalian cells. The plasma membrane and the endocytic recycling compartment (ERC) are both highly enriched in cholesterol. The abundance and distribution of cholesterol among organelles are tightly controlled by a combination of mechanisms involving vesicular and nonvesicular sterol transport processes. Using the fluorescent cholesterol analogue dehydroergosterol, we examined sterol transport between the plasma membrane and the ERC using fluorescence recovery after photobleaching and a novel sterol efflux assay. We found that sterol transport between these organelles in a U2OS cell line has a t1/2=12–15 min. Approximately 70% of sterol transport is ATP independent and therefore is nonvesicular. Increasing cellular cholesterol levels dramatically increases bidirectional transport rate constants, but decreases in cholesterol levels have only a modest effect. A soluble sterol transport protein, STARD4, accounts for ∼25% of total sterol transport and ∼33% of nonvesicular sterol transport between the plasma membrane and ERC. This study shows that nonvesicular sterol transport mechanisms and STARD4 in particular account for a large fraction of sterol transport between the plasma membrane and the ERC.
Partial Identification Methods for Evaluating Food Assistance Programs: A Case Study of the Causal Impact of SNAP on Food Insecurity
Authors: Gundersen Craig , Kreider Brent , Pepper John V.
Published: February 2017

We illustrate how partial identification methods can be used to provide credible inferences on the causal impacts of food assistance programs, focusing on the impact that the Supplemental Nutrition Assistance Program (SNAP, formerly known as the Food Stamp Program) has on food insecurity among households with children. Recent research applies these methods to address two key issues confounding identification: missing counterfactuals and nonrandomly misclassified treatment status. In this paper, we illustrate and extend the recent literature by using data from the Survey of Income and Program Participation (SIPP) to study the robustness of prior conclusions. The SIPP confers important advantages: the detailed information about income and eligibility allows us to apply a modified discontinuity design to sharpen inferences, and the panel nature allows us to reduce uncertainty about true participation status. We find that SNAP reduces the prevalence of food insecurity in households with children by at least six percentage points.
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis
Authors: Zhang Yun , Topham David J , Thakar Juilee , Qiu Xing
Published: February 2017

Motivation

Gene set enrichment analyses (GSEAs) are widely used in genomic research to identify underlying biological mechanisms (defined by the gene sets), such as Gene Ontology terms and molecular pathways. There are two caveats in the currently available methods: (i) they are typically designed for group comparisons or regression analyses, which do not utilize temporal information efficiently in time-series of transcriptomics measurements; and (ii) genes overlapping in multiple molecular pathways are considered multiple times in hypothesis testing.

Results

We propose an inferential framework for GSEA based on functional data analysis, which utilizes the temporal information based on functional principal component analysis, and disentangles the effects of overlapping genes by a functional extension of the elastic-net regression. Furthermore, the hypothesis testing for the gene sets is performed by an extension of Mann-Whitney U test which is based on weighted rank sums computed from correlated observations. By using both simulated datasets and a large-scale time-course gene expression data on human influenza infection, we demonstrate that our method has uniformly better receiver operating characteristic curves, and identifies more pathways relevant to immune-response to human influenza infection than the competing approaches.

Availability and Implementation

The methods are implemented in R package FUNNEL, freely and publicly available at: https://github.com/yunzhang813/FUNNEL-GSEA-R-Package.

Supplementary information

Supplementary data are available at Bioinformatics online.
Pseudoalignment for metagenomic read assignment
Authors: Schaeffer L , Pimentel H , Bray N , Melsted P , Pachter L
Published: February 2017

Motivation

Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains.

Results

We find that the recent idea of pseudoalignment introduced in the RNA-Seq context is highly applicable in the metagenomics setting. When coupled with the Expectation-Maximization (EM) algorithm, reads can be assigned far more accurately and quickly than is currently possible with state of the art software, making it possible and practical for the first time to analyze abundances of individual genomes in metagenomics projects.

Availability and Implementation

Pipeline and analysis code can be downloaded from http://github.com/pachterlab/metakallisto