bluuebunny/crossref_metadata_2025 huggingface dataset:
Matrix metalloproteinase‐11 as a marker of metastasis and predictor of poor survival in urothelial carcinomas
Authors: Li Wei‐Ming , Wei Yu‐Ching , Huang Chun‐Nung , Ke Hung‐Lung , Li Ching‐Chia , Yeh Hsin‐Chih , Chang Lin‐Li , Huang Chun‐Hsiung , Li Chien‐Feng , Wu Wen‐Jeng
Published: February 2016

Background and Objectives

Urothelial carcinomas (UC) of urinary bladder (UB) and upper urinary tract (UT) are heterogeneous diseases with high morbidity and mortality. We looked for genes with metalloendopeptidase activity in a published UBUC transcriptomic database (GSE31684):MMP‐11 was the most significant, showing stepwise up‐regulation. We analyzed MMP‐11 expression and association with clinicopathologic factors and survival in our well‐characterized cohort of UCs.

Methods

We determined MMP‐11 expression in 295 UBUCs and 340 UTUCs with immunohistochemistry, evaluated by H‐score. In a retrospective study, MMP‐11 expression was correlated with clinicopathologic features and with disease‐specific survival (DSS) and metastasis‐free survival (MeFS). The statistical significance was evaluated with univariate and multivariate analyses.

Results

High MMP‐11 expression was significantly associated with advanced pT status, nodal metastasis, high histological grade, vascular and perineural invasion, and frequent mitoses. In multivariate Cox regression analyses, which adjusted for standard clinicopathologic characteristics, MMP‐11 expression was independently associated with cancer‐specific mortality (hazard ratio [HR] in UTUC:3.027, P = 0.005; in UBUC: 2.631, P = 0.010) and with metastasis development (HR in UTUC:2.261, P = 0.018; in UBUC:1.801, P = 0.026).

Conclusions

MMP‐11 overexpression is associated with aggressive tumor phenotype and unfavorable clinical outcome in UTUC and UBUC, suggesting it may serve as a novel prognostic and therapeutic target. J. Surg. Oncol. 2016;113:700–707. © 2016 Wiley Periodicals, Inc.
Ultra‐high performance liquid chromatography with linear ion trap‐Orbitrap hybrid mass spectrometry combined with a systematic strategy based on fragment ions for the rapid separation and characterization of components in Stellera chamaejasme extracts
Authors: Wang Zhixin , Qu Yang , Wang Li , Zhang Xiaozhe , Xiao Hongbin
Published: February 2016

Stellera chamaejasme, a famous toxic herb, has been used in traditional Chinese medicine to treat various diseases. For decades, increasing attention in modern pharmacological studies has been drawn to S. chamaejasme because of its potential anti‐tumor, anti‐virus, and anti‐fungus activities. However, due to the intrinsic complexity of chemical constitutes, hardly any investigations formed an overall recognition for the chemical profiles of this herb. In this study, a rapid and sensitive ultra‐high performance liquid chromatography coupled with linear ion trap‐Orbitrap mass spectrometry method was developed to characterize the chemical components of S. chamaejasme extracts. Based on optimized ultra‐high performance liquid chromatography and mass spectrometry conditions and systematic fragment ions‐based strategy, a total of 47 components including flavones, diterpenes, coumarins, and lignans were simultaneously detected and identified or tentatively identified for the first time. The MSn fragmentation patterns of all the characterized compounds in positive or negative electrospray ionization modes were also explored and summarized. These results provided essential data for further pharmacological research on S. chamaejasme. Moreover, the method was demonstrated to be an efficient tool for rapid qualitative analysis of secondary metabolites from natural resources.
Identification and functional analysis of a bacteriocin, pyocin S6, with ribonuclease activity from a Pseudomonas aeruginosa cystic fibrosis clinical isolate
Authors: Dingemans Jozef , Ghequire Maarten G. K. , Craggs Michael , De Mot René , Cornelis Pierre
Published: February 2016

S‐type pyocins are bacteriocins produced by Pseudomonas aeruginosa isolates to antagonize or kill other strains of the same species. They have a modular organization comprising a receptor‐binding domain recognizing a surface constituent of the target bacterium, a domain for translocation through the periplasm, and a killing or toxic domain with DNase, tRNase, or pore‐forming activity. Pyocins S2, S3, S4, and S5 recognize TonB‐dependent ferri‐siderophore receptors in the outer membrane. We here describe a new nuclease bacteriocin, pyocin S6, encoded in the genome of a P. aeruginosa cystic fibrosis (CF) clinical isolate, CF_PA39. Similarly to pyocins S1 and S2, the S6 toxin–immunity gene tandem was recruited to the genomic region encoding exotoxin A. The pyocin S6 receptor‐binding and translocation domains are identical to those of pyocin S1, whereas the killing domain is similar to the 16S ribonuclease domain of Escherichia coli colicin E3. The cytotoxic activity was abolished in pyocin S6 forms with a mutation in the colicin E3‐equivalent catalytic motif. The CF_PA39 S6 immunity gene displays a higher expression level than the gene encoding the killing protein, the latter being only detected when bacteria are grown under iron‐limiting conditions. In the S1‐pyocinogenic strain P. aeruginosa ATCC 25324 and pyocin S2 producer P. aeruginosa PAO1, a remnant of the pyocin S6 killing domain and an intact S6‐type immunity gene are located downstream of their respective pyocin operons. Strain PAO1 is insensitive for pyocin S6, and its S6‐type immunity gene provides protection against pyocin S6 activity. Purified pyocin S6 inhibits one‐fifth of 110 P. aeruginosa CF clinical isolates tested, showing clearer inhibition zones when the target cells are grown under iron limitation. In this panel, about half of the CF clinical isolates were found to host the S6 genes. The pyocin S6 locus is also present in the genome of some non‐CF clinical isolates.
Validation of conversion between mini–mental state examination and montreal cognitive assessment
Authors: Lawton Michael , Kasten Meike , May Margaret T. , Mollenhauer Brit , Schaumburg Martina , Liepelt‐Scarfone Inga , Maetzler Walter , Vollstedt Eva‐Juliane , Hu Michele T.M. , Berg Daniela , Ben‐Shlomo Yoav
Published: February 2016

Introduction

Harmonizing data across cohorts is important for validating findings or combining data in meta‐analyses. We replicate and validate a previous conversion of MoCA to MMSE in PD.

Methods

We used five studies with 1,161 PD individuals and 2,091 observations measured with both the MoCA and MMSE. We compared a previously published conversion table using equipercentile equating with log‐linear smoothing to our internally derived scores.

Results

Both conversions found good agreement within and across the studies when comparing true and converted MMSE (mean difference: 0.05; standard deviation: 1.84; median difference: 0; interquartile range: –1 to 1, using internal conversion).

Conclusions

These results show that one can get a reliable and valid conversion between two commonly used measures of cognition in PD studies. These approaches need to be applied to other scales and domains to enable large‐scale collaborative analyses across multiple PD cohorts. © 2016 International Parkinson and Movement Disorder Society
FDM and FEM solutions to linear dynamics of porous media: stabilised, monolithic and fractional schemes
Authors: Zhang Yunpeng , Pedroso Dorival M. , Li Ling
Published: February 2016

A number of methods have been developed for solving the dynamics of saturated porous media. However, most solutions are based on the finite element method, and only a few employ finite differences (FDM). One problem with the FDM is the difficulty in fulfilling the inf‐sup (Ladyženskaja‐Babuška‐Brezzi) condition. This paper explores solutions with the FDM, including the development of new schemes aiming at stabilised formulations. The efficiency, accuracy and stability of several FDM and finite element method algorithms are thoroughly investigated as well. A combination of primary variables from the theory of porous media is considered, including the so‐called up and uvp formulations. Six numerical schemes are produced and quantitatively studied. Simulations of 1D and 2D wave propagation problems are performed in order to reveal the advantages and drawbacks of all schemes. Copyright © 2016 John Wiley & Sons, Ltd.
THE CONTRIBUTION OF SCHOOL COUNSELORS’ SELF‐EFFICACY TO THEIR PROGRAMMATIC SERVICE DELIVERY
Authors: Mullen Patrick R. , Lambie Glenn W.
Published: February 2016

Self‐efficacy pertains to individuals’ belief about their capability to accomplish a task; consequently, school counselors’ positive self‐efficacy is a theoretically based prerequisite for their facilitation of school‐based interventions. In addition, school counselor‐led interventions and comprehensive, developmental guidance programs benefit students’ personal social, academic, and career development. Therefore, this investigation examined the contribution of practicing school counselors’ (N = 693) self‐efficacy in relation to the frequency of their programmatic service delivery. The findings indicate that participants’ self‐efficacy scores contributed to the frequency of their programmatic service delivery (48% of the variance explained). Implications for school counselors, supervisors, and educational researchers are discussed.
Depression and pain: the need for a new screening tool
Authors: Cocksedge Karen , Shankar Rohit , Simon Chantal
Published: February 2016

There is a strong association between pain and depression, and the presence of pain negatively affects the recognition and treatment of depression. Here, Dr Cocksedge and colleagues' explore the neurobiology behind this relationship and propose a new screening tool to assess patients with either condition for the coexistence of the other, with the potential for significantly better diagnosis, referral and hence treatment.
Formation of icosahedral nanowires
Authors: Fujita Naoya , Kurokawa Shu , Sakai Akira
Published: February 2016

An icosahedral nanowire (INW) is a one‐dimensional structure where a single atom and a five‐membered ring are alternating to form a stacking. The segment of this stacking forms an icosahedron and constitutes the unit cell of an INW. In molecular dynamics (MD) simulations of stretching of metal nanowires (NWs), INWs are frequently formed at their deformation necks. Previous simulations found that the formation of INWs is more favored for thin NWs than thick NWs. To closely investigate this size dependence of INW formation, we have carried out stretching simulations of Mg NWs and examined the creation of icosahedral arrangement of atoms at their deformation necks. Our results show that thin NWs tend to produce slender necks, the atoms of which first become disordered and then rearrange themselves into an icosahedral arrangement. Thick nanowires rarely form such slender necks and this accounts for their low yield of INWs. We have also investigated a continuous and bond‐conserving process that converts the HCP arrangement of atoms into an icosahedral one. We found that the nearest‐neighbor bonds are not conserved and only a small fraction of nearest‐neighbor atoms in an icosahedral unit cell are initially nearest neighbors.
Improved removal of volatile organic compounds for laser‐based spectroscopy of water isotopes
Authors: Chang Elliot , Wolf Adam , Gerlein‐Safdi Cynthia , Caylor Kelly K.
Published: February 2016

Rationale

Volatile organic compounds (VOCs) such as methanol and ethanol in water extracted from plants cause spectral interference in isotope ratio infrared spectroscopy (IRIS). This contamination degrades the accuracy of measurements, limiting the use of IRIS. In response, this study presents a new decontamination method of VOCs for enhanced IRIS measurements.

Methods

The isotopic compositions of water from laboratory‐made and field‐collected plant samples pre‐ and post‐treatment were analyzed using IRIS. Traditional treatment methods of activated charcoal and commercial pre‐combustion systems (MCM) were compared with our new treatment method that implements solid‐phase extraction (SPE). The absolute concentrations of contaminants pre‐ and post‐treatment were determined using 1H and 13C nuclear magnetic resonance to assess the effectiveness of the different treatments.

Results

SPE removes an average of 86.7% and 78.8% ethanol and methanol, respectively, significantly reducing spectral interference. SPE reduces errors to within instrumental noise for both ethanol and methanol at concentrations found in nature (<3.0% and 0.08%, respectively). Activated charcoal minimally affected alcohol concentrations. MCM significantly worsened ethanol‐contaminated water isotope measurements by producing primary alcohol oxidation products such as formic acid, another compound that interferes with IRIS absorption.

Conclusions

SPE is an effective, low‐cost method for eliminating errors in ethanol‐contaminated samples. For samples where methanol is prevalent, combining SPE and MCM is more effective than the use of SPE alone. Hence, SPE treatment alone or in conjunction with MCM is recommended as an effective pre‐analysis purification method for water extracted from plants. Copyright © 2016 John Wiley & Sons, Ltd.
EPOinduces changes in synaptic transmission and plasticity in the dentate gyrus of rats
Authors: Almaguer‐Melian William , Mercerón‐Martínez Daymara , Delgado‐Ocaña Susana , Pavón‐Fuentes Nancy , Ledón Nuris , Bergado Jorge A.
Published: February 2016

Erythropoietin has shown wide physiological effects on the central nervous system in animal models of disease, and in healthy animals. We have recently shown that systemic EPO administration 15 min, but not 5 h, after daily training in a water maze is able to induce the recovery of spatial memory in fimbria‐fornix chronic‐lesioned animals, suggesting that acute EPO triggers mechanisms which can modulate the active neural plasticity mechanism involved in spatial memory acquisition in lesioned animals. Additionally, this EPO effect is accompanied by the up‐regulation of plasticity‐related early genes. More remarkably, this time‐dependent effects on learning recovery could signify that EPO in nerve system modulate specific living‐cellular processes. In the present article, we focus on the question if EPO could modulate the induction of long‐term synaptic plasticity like LTP and LTD, which presumably could support our previous published data. Our results show that acute EPO peripheral administration 15 min before the induction of synaptic plasticity is able to increase the magnitude of the LTP (more prominent in PSA than fEPSP‐Slope) to facilitate the induction of LTD, and to protect LTP from depotentiation. These findings showing that EPO modulates in vivo synaptic plasticity sustain the assumption that EPO can act not only as a neuroprotective substance, but is also able to modulate transient neural plasticity mechanisms and therefore to promote the recovery of nerve function after an established chronic brain lesion. According to these results, EPO could be use as a molecular tool for neurorestaurative treatments.Synapse 70:240–252, 2016. © 2016 Wiley Periodicals, Inc.
Active-Transient Liquid Phase (A-TLP) Bonding of Pure Aluminum Matrix Composite Reinforced with Short Alumina Fiber Using Al-12Si-xTi Foils as Active Interlayer
Authors: Zhang Guifeng , Su Wei , Suzumura Akio
Published: February 2016

To optimize both the interlayer composition design route and pressure for joining aluminum matrix composite reinforced with short alumina fiber (as-cast 30 vol pct Al2O3sf/Al), traditional transient liquid phase (TLP) bonding using Al-12Si and Cu interlayer and active-TLP (A-TLP) bonding using an active Ti-containing interlayer (Al-12Si-xTi, x = 0.1, 0.5, and 1 wt pct) under the same condition [883 K (610 °C) × 30 minutes × 1 or 0.015 MPa in flowing argon] were compared in terms of interfacial wettability, bond seam microstructure, shear strength, and fracture path. It was found that not only the Ti content but also the pressure are critical factors affecting interfacial wettability and bond seam microstructure. The improvement in wettability by adding Ti as an active element were confirmed by reduction of expulsion of liquid interlayer, elimination of interfacial gap, higher shear strength and favorable fracture path (partially through bond seam and the composite). Because of the incubation period for wetting, reducing the pressure after melting of the interlayer could further increase joint shear strength by thickening the remaining bond seam of solid-solution matrix and decreasing fraction of the in situ newly formed Al-Si-Ti IMC phase (short bar shape) within the bond seam. The maximum shear strength of 88.6 MPa (99 pct of the as-cast composite) was obtained by adding trace Ti content (0.5 Ti wt pct) addition and using low pressure (0.015 MPa). The results showed that suitable combination of Ti content and pressure pattern is required for improving both wettability and bond seam microstructure.
Cognitive autonomy among adolescents with and without hearing loss: Associations with perceived social support
Authors: Michael Rinat , Attias Joseph
Published: February 2016

Cognitive autonomy is a skill which may help adolescents prepare for important decisions in adulthood. The current study examined the associations between cognitive autonomy and perceived social support among adolescents with and without hearing loss. Participants were 177 students: 55 were deaf and hard of hearing (dhh) and 122 were hearing. They completed the Cognitive Autonomy and Self‐Evaluation Inventory, the Multidimensional Scale of Perceived Social Support, and a demographic questionnaire. Significant positive correlations were found between some of the cognitive autonomy variables and some of the perceived social support variables. However, among the dhh group, they were fewer and weaker. Family support was found to be a significant predictor of three out of the five cognitive autonomy variables. In addition, significant differences were found between the dhh and hearing participants in some of the cognitive autonomy variables, but not in perceived social support. Implications for theory and practice are discussed.
Subtle Cognitive Dysfunction in Resolving High Altitude Cerebral Edema Revealed by a Clock Drawing Test
Authors: Quigley Ian , Zafren Ken
Published: February 2016

High altitude cerebral edema (HACE) is a life-threatening condition that can affect people who ascend to altitudes above 2500 m. Altered mental status and the presence of ataxia distinguishes HACE from acute mountain sickness (AMS). We describe a patient with subtle cognitive dysfunction, likely due to HACE that had not fully resolved. When he initially presented, the patient appeared to have normal mental status and was not ataxic. The diagnosis of HACE was missed initially but was made when further history became available. Cognitive dysfunction was then diagnosed based on abnormal performance of a clock drawing test. A formal mental status examination, using a clock drawing test, may be helpful in assessing whether a patient at high altitude with apparently normal mental status and with normal gait has HACE.
The Settlement Date of Iceland Revisited: Evaluation of 14C Dates from Sites of Early Settlers in Iceland by Bayesian Statistics
Authors: Sveinbjörnsdóttir Árný E , Ramsey Christopher Bronk , Heinemeier Jan
Published: February 2016

The settlement time of Iceland has been debated for years as radiocarbon dates of bulk wood samples have been interpreted to set a timing 150–200 yr earlier than indicated by tephrochronology (later than AD 871±2) and the Sagas (AD 874). This early date is also in conflict with the dating results on extensive series of short-lived material such as grain and domestic animal and human bone remains of early settlers. The old-wood effect for the charcoal and bulk wood samples has been suggested to explain this controversy. This study uses a Bayesian model, implemented in the OxCal program, to show that the charcoal data combined with short-lived material (grain/bone) suggest ages anywhere in the interval AD 854–922 (95.4% probability), indicating that the available 14C data cannot be taken as compelling evidence that there was a settlement any earlier than AD 922. The Bayesian model shows that the observed exponential distribution of the excess age of the bulk wood samples is exactly as expected if there was an old-wood effect evident in the samples.
Sialendoscopy-assisted transfacial surgery for the removal of an iatrogenic foreign body in Stensen's duct: a stone and broken wire basket
Authors: Capaccio P , Gaffuri M , Torretta S , Pignataro L
Published: February 2016

Background:

A foreign body is a rare cause of parotid gland obstructive sialadenitis; intra-oral penetration via Stensen's duct is unusual. The relatively recent introduction of interventional sialendoscopy to treat obstructive sialadenitis has allowed surgeons to adopt a gland-sparing approach by means of miniaturised endoscopes and instruments. However, unusual anatomy or pathological conditions can give rise to a risk of intraductal rupture that may lead to a subsequent iatrogenic foreign body.

Case report:

This paper describes the case of a patient with a 4 mm stone engaged by a broken wire basket stuck in a secondary branch of Stensen's duct.

Results:

The iatrogenic foreign body was successfully retrieved by means of sialendoscopy-assisted transfacial surgery.

Conclusion:

This is the first reported case of an intraductal rupture of a miniaturised device during interventional sialendoscopy successfully resolved by means of combined endoscopy and external surgery. This proved to be an effective method of rescuing a foreign body stuck in Stensen's duct.
CPDO WITH FINITE TERMINATION: MAXIMAL RETURN UNDER CASH-IN AND CASH-OUT CONDITIONS
Authors: YANG X. , LIANG J. , WU Y.
Published: February 2016

The maximal return and optimal leverage of a constant proportion debt obligation with finite termination and two boundaries are analysed by numerically solving Hamilton–Jacobi–Bellman equations. We discuss the probabilities of the asset value reaching the upper or lower bound under the optimal control and the optimal control problem with a time-varying boundary. Furthermore, we also analyse the relationship between the optimal return, the optimal policy and different parameters.
Competitive federalism, government's dual role and the power to tax
Authors: VANBERG VIKTOR J.
Published: February 2016

Theories of competitive federalism generally focus onexitas the principal mechanism for making governments responsive to the interests of those who are subject to their powers. This paper draws attention to the fact that democratic governments act in two distinguishable roles, as ‘territorial enterprises’ and as ‘club enterprises’. Asterritorial enterprisesthey define and enforce the rules and terms that apply to everybody, whether citizen or alien, who resides and/or operates within their jurisdictional boundaries. Asclub enterprises, they define and enforce the rules and terms ofmembershipin the respective polity. The focus of this paper is on the implications of the fact that ‘exit’ means something different when one looks at governments’ role as territorial enterprises (exit = leaving the territory) in contrast to their role as club enterprises (exit = giving up one's membership status/citizenship).
Financial property rights under colonialism: some counterfactual possibilities
Authors: CHATTERJEE ABHISHEK
Published: February 2016

This article seeks to explain the lack of the development of contemporaneously ‘modern’ money and credit markets in the 18th to 19th century economy of India. Borrowing from the literature on property rights, it demonstrates that the emergence of ‘modern’, and state-connected money markets was the result of a certain kind of power relationship between rulers and financial capital holders where the two were forced to mutually cooperate; financial systems represented the institutionalization of this mutual cooperation. Specific kinds of ‘colonialism’ represent just one special case of a relationship where the latter did not obtain. The article thus proposes a mechanism though which the spread of European capital could have retarded financial market formation in now-developing areas with otherwise considerable concentration of ‘native’ mercantile capital.
Millimeter wave antenna with frequency selective surface (FSS) for 79 GHz automotive radar applications
Authors: Aqlan Basem , Vettikalladi Hamsakutty , Alkanhal Majeed A.S.
Published: February 2016

In this paper a high gain aperture-coupled membrane antenna with a frequency selective surface (FSS) on a superstrate layer has been investigated. The base membrane antenna consists of a microstrip patch on the top of Roger RT-5580 substrate, supported by FR4 and is excited through an aperture fed by substrate-integrated waveguide (SIW). The CST Microwave Studio simulation results show that the proposed membrane structure has an impedance bandwidth (BW) of 8.85% from 75.97 to 82.96 GHz with a gain of 6.29 dBi at 79 GHz. To improve the gain, a superstrate layer is loaded above the membrane antenna, which increases the gain by 9.11 dB at 79 GHz. Furthermore by using FSS under superstrate layer, the gain is again increased by 2.5 dB. The total antenna structure provides a gain of 17.9 dBi at 79 GHz by keeping the same BW. The measured results are provided for the input matching (S11) only, the simulated results for the antenna gain and radiation patterns are obtained with the use of CST and are validated by using HFSS. The measured S11BW of the total antenna is from 75.57 to 84.18 GHz (10.89%), which is in agreement with the simulated results.
Neurospectral computation for the resonant characteristics of microstrip patch antenna printed on uniaxially anisotropic substrates
Authors: Barkat Lamia , Bedra Sami , Fortaki Tarek , Bedra Randa
Published: February 2016

Modeling and design of rectangular microstrip patch printed on isotropic or anisotropic substrate are accomplished in this paper. The use of spectral domain method in conjunction with artificial neural networks (ANNs) to compute the resonant characteristics of rectangular microstrip patch printed on isotropic or anisotropic substrates. The moment method implemented in the spectral domain offers good accurateness, but its computational cost is high owing to the evaluation of the slowly decaying integrals and the iterative nature of the solution process. The paper introduces the electromagnetic knowledge combined with ANN in the analysis of rectangular microstrip antenna on uniaxially anisotropic substrate to reduce the complexity of the spectral domain method and to minimize the CPU time necessary to obtain the numerical results. The numerical comparison between neurospectral and conventional moment methods shows significant improvements in time convergence and computational cost. Hence, the use of neurospectral approach presented here as a promising fast technique in the design of microstrip antennas.
High sensitivity SOA-PIN/TIA photoreceiver for 40 Gb/s applications and beyond
Authors: Angelini Philippe , Blache Fabrice , Caillaud Christophe , Goix Michel , Jorge Filipe , Mekhazni Karim , Dupuy Jean-Yves , Achouche Mohand
Published: February 2016

This paper reports a differential photoreceiver module designed for short reach applications such as access network and data center interconnect. It consists of a monolithically integrated semi-conductor optical amplifier with a PIN photodiode and a linear transimpedance amplifier (TIA) mounted on the same carrier. A matching circuit is placed between the PIN and the TIA in order to increase the cut-off frequency. The module shows a −3 dB bandwidth of 43 GHz, a single-ended conversion gain of 10 000 V/W for an optical input power of −25 dBm and a sensitivity at 40 Gb/s non-return-to-zero operation of −22.5 dBm for a bit error rate of 10−9.
Modeling the Future of Dissolved Organic Carbon in Boreal Forests
Authors: Stanley Sarah
Published: February 2016

Climate change and forest harvesting will increase the concentration and flow of dissolved organic carbon in boreal streams.
2017 AGU Fall Meeting Heads to New Orleans, 2018 to Washington, D. C.
Authors: Weiss Peter
Published: February 2016

The American Geophysical Union opts to relocate its 26,000-plus-attendee meeting from San Francisco for 2 years to avoid detrimental impacts from extensive construction at the convention center.
Linking the T cell receptor to the single cell transcriptome in antigen‐specific human T cells
Authors: Eltahla Auda A , Rizzetto Simone , Pirozyan Mehdi R , Betz‐Stablein Brigid D , Venturi Vanessa , Kedzierska Katherine , Lloyd Andrew R , Bull Rowena A , Luciani Fabio
Published: February 2016

Heterogeneity of T cells is a hallmark of a successful adaptive immune response, harnessing the vast diversity of antigen‐specific T cells into a coordinated evolution of effector and memory outcomes. The T cell receptor (TCR) repertoire is highly diverse to account for the highly heterogeneous antigenic world. During the response to a virus multiple individual clones of antigen specific CD8+ (Ag‐specific) T cells can be identified against a single epitope and multiple epitopes are recognised. Advances in single‐cell technologies have provided the potential to study Ag‐specific T cell heterogeneity at both surface phenotype and transcriptome levels, thereby allowing investigation of the diversity within the same apparent sub‐population. We propose a new method (VDJPuzzle) to reconstruct the native TCRαβ from single cell RNA‐seq data of Ag‐specific T cells and then to link these with the gene expression profile of individual cells. We applied this method using rare Ag‐specific T cells isolated from peripheral blood of a subject who cleared hepatitis C virus infection. We successfully reconstructed productive TCRαβ in 56 of a total of 63 cells (89%), with double α and double β in 18, and 7% respectively, and double TCRαβ in 2 cells. The method was validated via standard single cell PCR sequencing of the TCR. We demonstrate that single‐cell transcriptome analysis can successfully distinguish Ag‐specific T cell populations sorted directly from resting memory cells in peripheral blood and sorted after ex vivo stimulation. This approach allows a detailed analysis of the TCR diversity and its relationship with the transcriptional profile of different clones.
Achromatic vector vortex beams from a glass cone
Authors: Radwell N. , Hawley R. D. , Götte J. B. , Franke-Arnold S.
Published: February 2016

The reflection of light is governed by the laws first described by Augustin-Jean Fresnel: on internal reflection, light acquires a phase shift, which depends on its polarization direction with respect to the plane of incidence. For a conical reflector, the cylindrical symmetry is echoed in an angular variation of this phase shift, allowing us to create light modes with phase and polarization singularities. Here we observe the phase and polarization profiles of light that is back reflected from a solid glass cone and, in the case of circular input light, discover that not only does the beam contain orbital angular momentum but can trivially be converted to a radially polarized beam. Importantly, the Fresnel coefficients are reasonably stable across the visible spectrum, which we demonstrate by measuring white light polarization profiles. This discovery provides a highly cost-effective technique for the generation of broadband orbital angular momentum and radially polarized beams.
Atomically isolated nickel species anchored on graphitized carbon for efficient hydrogen evolution electrocatalysis
Authors: Fan Lili , Liu Peng Fei , Yan Xuecheng , Gu Lin , Yang Zhen Zhong , Yang Hua Gui , Qiu Shilun , Yao Xiangdong
Published: February 2016

Hydrogen production through electrochemical process is at the heart of key renewable energy technologies including water splitting and hydrogen fuel cells. Despite tremendous efforts, exploring cheap, efficient and durable electrocatalysts for hydrogen evolution still remains as a great challenge. Here we synthesize a nickel–carbon-based catalyst, from carbonization of metal-organic frameworks, to replace currently best-known platinum-based materials for electrocatalytic hydrogen evolution. This nickel-carbon-based catalyst can be activated to obtain isolated nickel atoms on the graphitic carbon support when applying electrochemical potential, exhibiting highly efficient hydrogen evolution performance with high exchange current density of 1.2 mA cm−2 and impressive durability. This work may enable new opportunities for designing and tuning properties of electrocatalysts at atomic scale for large-scale water electrolysis.
Giant conductivity switching of LaAlO3/SrTiO3 heterointerfaces governed by surface protonation
Authors: Brown Keith A. , He Shu , Eichelsdoerfer Daniel J. , Huang Mengchen , Levy Ishan , Lee Hyungwoo , Ryu Sangwoo , Irvin Patrick , Mendez-Arroyo Jose , Eom Chang-Beom , Mirkin Chad A. , Levy Jeremy
Published: February 2016

Complex-oxide interfaces host a diversity of phenomena not present in traditional semiconductor heterostructures. Despite intense interest, many basic questions remain about the mechanisms that give rise to interfacial conductivity and the role of surface chemistry in dictating these properties. Here we demonstrate a fully reversible >4 order of magnitude conductance change at LaAlO3/SrTiO3 (LAO/STO) interfaces, regulated by LAO surface protonation. Nominally conductive interfaces are rendered insulating by solvent immersion, which deprotonates the hydroxylated LAO surface; interface conductivity is restored by exposure to light, which induces reprotonation via photocatalytic oxidation of adsorbed water. The proposed mechanisms are supported by a coordinated series of electrical measurements, optical/solvent exposures, and X-ray photoelectron spectroscopy. This intimate connection between LAO surface chemistry and LAO/STO interface physics bears far-reaching implications for reconfigurable oxide nanoelectronics and raises the possibility of novel applications in which electronic properties of these materials can be locally tuned using synthetic chemistry.
Correction: Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human
Authors: Ramilowski Jordan A. , Goldberg Tatyana , Harshbarger Jayson , Kloppmann Edda , Lizio Marina , Satagopam Venkata P. , Itoh Masayoshi , Kawaji Hideya , Carninci Piero , Rost Burkhard , Forrest Alistair R. R.
Published: February 2016

Nature Communications 6: Article number: 7866 (2015); Published: 22 July 2015; Updated: 10 February 2016. The original version of this Article contained an error in the spelling of the author Edda Kloppmann, which was incorrectly given as Edda Kloppman. This has now been corrected in both the PDF and HTML versions of the Article.
The diagnostic accuracy of the MTBDRplus and MTBDRsl assays for drug-resistant TB detection when performed on sputum and culture isolates
Authors: Tomasicchio Michele , Theron Grant , Pietersen Elize , Streicher Elizabeth , Stanley-Josephs Danielle , van Helden Paul , Warren Rob , Dheda Keertan
Published: February 2016

Although molecular tests for drug-resistant TB perform well on culture isolates, their accuracy using clinical samples, particularly from TB and HIV-endemic settings, requires clarification. The MTBDRplus and MTBDRsl line probe assays were evaluated in 181 sputum samples and 270 isolates from patients with culture-confirmed drug-sensitive-TB, MDR-TB, or XDR-TB. Phenotypic culture-based testing was the reference standard. Using sputum, the sensitivities for resistance was 97.7%, 95.4%, 58.9%, 61.6% for rifampicin, isoniazid, ofloxacin and amikacin, respectively, whereas the specificities were 91.8%, 89%, 100% and 100%, respectively. MTBDRsl sensitivity differed in smear-positive vs. smear-negative samples (79.2% vs. 20%, p < 0.0001 for ofloxacin; 72.9% vs. 37%, p = 0.0023 for amikacin) but not by HIV status. If used sequentially, MTBDRplus and MTBDRsl could rule-in XDR-TB in 78.5% (22/28) and 10.5% (2/19) of smear-positive and smear-negative samples, respectively. On culture isolates, the sensitivity for resistance to rifampicin, isoniazid, ofloxacin and amikacin was 95.1%, 96.1%, 72.3% and 76.6%, respectively, whereas the specificities exceeded 96%. Using a sequential testing approach, rapid sputum-based diagnosis of fluoroquinolone or aminoglycoside-resistant TB is feasible only in smear-positive samples, where rule-in value is good. Further investigation is required in samples that test susceptible in order to rule-out second-line drug resistance.
Rapid mixing of viscous liquids by electrical coiling
Authors: Kong Tiantian , Li Jingmei , Liu Zhou , Zhou Zhuolong , Ng Peter Hon Yu , Wang Liqiu , Shum Ho Cheung
Published: February 2016

The control for the processing of precursor liquids determines whether the properties and functions of the final material product can be engineered. An inherent challenge of processing viscous liquids arises from their large resistance to deform. Here, we report on the discovery of an electric approach that can significantly contribute to address this challenge. The applied electric force can induce a straight viscous jet to coil and the resulting coiling characteristics are governed by the electric stress. We demonstrate the promising use of electrical coiling in the rapid and efficient mixing of viscous liquids. Remarkably, the degree of mixing can be precisely adjusted by tuning the applied electric stress. Our approach of controlling the coiling electrically has important implications on applications such as dispensing and printing of resins, printing patterned surfaces and scaffolds, processing of food and generating non-woven fabrics.
A herbal formula comprising Rosae Multiflorae Fructus and Lonicerae Japonicae Flos, attenuates collagen-induced arthritis and inhibits TLR4 signalling in rats
Authors: Cheng Brian Chi Yan , Yu Hua , Guo Hui , Su Tao , Fu Xiu-Qiong , Li Ting , Cao Hui-Hui , Tse Anfernee Kai-Wing , Wu Zheng-Zhi , Kwan Hiu-Yee , Yu Zhi-Ling
Published: February 2016

RL, a traditional remedy for Rheumatoid arthritis (RA), comprises two edible herbs, Rosae Multiflorae Fructus and Lonicerae Japonicae Flos. We have reported that RL could inhibit the production of inflammatory mediators in immune cells. Here we investigated the effects and the mechanism of action of RL in collagen-induced arthritis (CIA) rats. RL significantly increased food intake and weight gain of CIA rats without any observable adverse effect; ameliorated joint erythema and swelling; inhibited immune cell infiltration, bone erosion and osteophyte formation in joints; reduced joint protein expression levels of TLR4, phospho-TAK1, phospho-NF-κB p65, phospho-c-Jun and phospho-IRF3; lowered levels of inflammatory factors (TNF-α, IL-6, IL-1β, IL-17A and MCP-1 in sera and TNF-α, IL-6, IL-1β and IL-17A in joints); elevated serum IL-10 level; reinvigorated activities of antioxidant SOD, CAT and GSH-Px in the liver and serum; reduced Th17 cell proportions in splenocytes; inhibited splenocyte proliferation and activation; and lowered serum IgG level. In conclusion, RL at nontoxic doses inhibited TLR4 signaling and potently improved clinical conditions of CIA rats. These findings provide further pharmacological justifications for the traditional use of RL in RA management.
φXANES: In vivo imaging of metal-protein coordination environments
Authors: James Simon A. , Hare Dominic J. , Jenkins Nicole L. , de Jonge Martin D. , Bush Ashley I. , McColl Gawain
Published: February 2016

We have developed an X-ray absorption near edge structure spectroscopy method using fluorescence detection for visualizing in vivo coordination environments of metals in biological specimens. This approach, which we term fluorescence imaging XANES (φXANES), allows us to spatially depict metal-protein associations in a native, hydrated state whilst avoiding intrinsic chemical damage from radiation. This method was validated using iron-challenged Caenorhabditis elegans to observe marked alterations in redox environment.
Variation in susceptibility of African Plasmodium falciparum malaria parasites to TEP1 mediated killing in Anopheles gambiae mosquitoes
Authors: Eldering Maarten , Morlais Isabelle , van Gemert Geert-Jan , van de Vegte-Bolmer Marga , Graumans Wouter , Siebelink-Stoter Rianne , Vos Martijn , Abate Luc , Roeffen Will , Bousema Teun , Levashina Elena A. , Sauerwein Robert W.
Published: February 2016

Anopheles gambiae s.s. mosquitoes are efficient vectors for Plasmodium falciparum, although variation exists in their susceptibility to infection. This variation depends partly on the thioester-containing protein 1 (TEP1) and TEP depletion results in significantly elevated numbers of oocysts in susceptible and resistant mosquitoes. Polymorphism in the Plasmodium gene coding for the surface protein Pfs47 modulates resistance of some parasite laboratory strains to TEP1-mediated killing. Here, we examined resistance of P. falciparum isolates of African origin (NF54, NF165 and NF166) to TEP1-mediated killing in a susceptible Ngousso and a refractory L3–5 strain of A. gambiae. All parasite clones successfully developed in susceptible mosquitoes with limited evidence for an impact of TEP1 on transmission efficiency. In contrast, NF166 and NF165 oocyst densities were strongly reduced in refractory mosquitoes and TEP1 silencing significantly increased oocyst densities. Our results reveal differences between African P. falciparum strains in their capacity to evade TEP1-mediated killing in resistant mosquitoes. There was no significant correlation between Pfs47 genotype and resistance of a given P. falciparum isolate for TEP1 killing. These data suggest that polymorphisms in this locus are not the sole mediators of immune evasion of African malaria parasites.
Reprogramming of Seed Metabolism Facilitates Pre-harvest Sprouting Resistance of Wheat
Authors: Liu Caixiang , Ding Feng , Hao Fuhua , Yu Men , Lei Hehua , Wu Xiangyu , Zhao Zhengxi , Guo Hongxiang , Yin Jun , Wang Yulan , Tang Huiru
Published: February 2016

Pre-harvest sprouting (PHS) is a worldwide problem for wheat production and transgene antisense-thioredoxin-s (anti-trx-s) facilitates outstanding resistance. To understand the molecular details of PHS resistance, we analyzed the metabonomes of the transgenic and wild-type (control) wheat seeds at various stages using NMR and GC-FID/MS. 60 metabolites were dominant in these seeds including sugars, organic acids, amino acids, choline metabolites and fatty acids. At day-20 post-anthesis, only malate level in transgenic wheat differed significantly from that in controls whereas at day-30 post-anthesis, levels of amino acids and sucrose were significantly different between these two groups. For mature seeds, most metabolites in glycolysis, TCA cycle, choline metabolism, biosynthesis of proteins, nucleotides and fatty acids had significantly lower levels in transgenic seeds than in controls. After 30-days post-harvest ripening, most metabolites in transgenic seeds had higher levels than in controls including amino acids, sugars, organic acids, fatty acids, choline metabolites and NAD+. These indicated that anti-trx-s lowered overall metabolic activities of mature seeds eliminating pre-harvest sprouting potential. Post-harvest ripening reactivated the metabolic activities of transgenic seeds to restore their germination vigor. These findings provided essential molecular phenomic information for PHS resistance of anti-trx-s and a credible strategy for future developing PHS resistant crops.
Paediatric obstructive sleep apnoea syndrome (OSAS) is associated with tonsil colonisation by Streptococcus pyogenes
Authors: Viciani Elisa , Montagnani Francesca , Tavarini Simona , Tordini Giacinta , Maccari Silvia , Morandi Matteo , Faenzi Elisa , Biagini Cesare , Romano Antonio , Salerni Lorenzo , Finco Oretta , Lazzi Stefano , Ruggiero Paolo , De Luca Andrea , Barocchi Michèle A. , Manetti Andrea G. O.
Published: February 2016

The involvement of pathogenic bacteria in obstructive sleep apnoea syndrome (OSAS) has yet to be elucidated. We investigated the possible role of group A streptococcus (GAS) in OSAS pathogenesis. In 40 tonsillectomized patients affected by OSAS and 80 healthy controls, significant (p < 0.0001) association of GAS with paediatric OSAS was found. Supernatant from streptolysin O (SLO)-producing GAS induced production of cysteinyl leukotrienes (CysLTs) in tonsil mononuclear cells (TMCs). CysLTs-treated TMCs showed significant (p < 0.05) proliferation of CD4+ T, CD19+ and CD19+CD27+CD38+ B lymphocytes. We discovered a SLO-dependent activation of CysLTs production through a pathway involving TOLL-like receptor 4 (TLR4), TIR-domain-containing adapter-inducing interferon-β (TRIF), Myeloid differentiation primary response gene 88 (MyD88), and p38 MAP Kinase. In conclusion, we hypothesise that GAS may contribute to paediatric tonsillar hyperplasia through CysLTs production induced by SLO, and this might explain its association with OSAS.
Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest
Authors: Xu Wumei , Liu Lu , He Tianhua , Cao Min , Sha Liqing , Hu Yuehua , Li Qiaoming , Li Jie
Published: February 2016

A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community.
Field-programmable beam reconfiguring based on digitally-controlled coding metasurface
Authors: Wan Xiang , Qi Mei Qing , Chen Tian Yi , Cui Tie Jun
Published: February 2016

Digital phase shifters have been applied in traditional phased array antennas to realize beam steering. However, the phase shifter deals with the phase of the induced current; hence, it has to be in the path of each element of the antenna array, making the phased array antennas very expensive. Metamaterials and/or metasurfaces enable the direct modulation of electromagnetic waves by designing subwavelength structures, which opens a new way to control the beam scanning. Here, we present a direct digital mechanism to control the scattered electromagnetic waves using coding metasurface, in which each unit cell loads a pin diode to produce binary coding states of “1” and “0”. Through data lines, the instant communications are established between the coding metasurface and the internal memory of field-programmable gate arrays (FPGA). Thus, we realize the digital modulation of electromagnetic waves, from which we present the field-programmable reflective antenna with good measurement performance. The proposed mechanism and functional device have great application potential in new-concept radar and communication systems.