bluuebunny/crossref_metadata_2025 huggingface dataset:
Responsory prosae and the post-Christmas ‘Choir Solemnities’ at Salisbury Cathedral
Authors: MAHRT WILLIAM PETER
Published: March 2016

The Christmas octave in the Sarum rite included the singing of prosae on Christmas Day and on the three days following Christmas – the feasts of St Stephen, St John the Evangelist and the Holy Innocents. After the Vespers preceding each of these three days, a procession was made to an appropriate altar in the church, during which a responsory was sung with its prosa and wordless melismas after each prosa verse, with two responsory prosae based upon the melody from Christmas. These processions featured, in turn, the deacons, the priests and the choirboys, vested in silken copes and carrying lighted candles, going to the altar of St Stephen, of St Peter and All Apostles, and of Trinity and All Saints (the Lady Chapel). Rubrics indicate their special character, especially for St Stephen, described as solemnitas diaconorum, but also for all three, described as being for the sake of deacons, priests and choirboys in turn. Processions to altars in Salisbury Cathedral were strictly limited to one each year; these processions took up those three altars, which then had no further processions on their proper days. The processions had been established during the initial building-phases of the cathedral, when only these three altars existed. This exceptional series of processions emphasised the distinct importance of the Christmas octave and honoured the hierarchy of the choir, who served the liturgy throughout the year.
Do low-carbon-emission diets lead to higher nutritional quality and positive health outcomes? A systematic review of the literature
Authors: Payne Charlotte LR , Scarborough Peter , Cobiac Linda
Published: March 2016

Objective

To evaluate what is known about the relative health impacts, in terms of nutrient intake and health outcomes, of diets with reduced greenhouse gas emissions (GHGE).

Design

We systematically reviewed the results of published studies that link GHGE of dietary patterns to nutritional content or associated consequences for health.

Setting

We included studies published in English in peer-reviewed journals that included data on actual and modelled diets and enabled a matched comparison of GHGE with nutrient composition and/or health outcomes.

Subjects

Studies included used data from subjects from the general population, who had taken part in dietary surveys or prospective cohort studies.

Results

We identified sixteen eligible studies, with data on 100 dietary patterns. We present the results as dietary links between GHGE reduction and impact on nutrients to limit (n 151), micronutrient content (n 158) and health outcomes (n 25). The results were highly heterogeneous. Across all measures of ‘healthiness’, 64 % (n 214) of dietary links show that reduced GHGE from diets were associated with worse health indicators. However, some trends emerged. In particular, reduced saturated fat and salt are often associated with reduced GHGE in diets that are low in animal products (57/84). Yet these diets are also often high in sugar (38/55) and low in essential micronutrients (129/158).

Conclusions

Dietary scenarios that have lower GHGE compared with average consumption patterns may not result in improvements in nutritional quality or health outcomes. Dietary recommendations for reduced GHGE must also address sugar consumption and micronutrient intake.
Protecting the past for the future: How does law protect tangible and intangible cultural heritage in armed conflict?
Authors: Johannot-Gradis Christiane
Published: March 2016

In war, individuals are vulnerable not only physically but also in terms of their cultural identity, and the obliteration of cultural heritage often becomes a central issue. This is particularly the case in armed conflicts with an ethnic, cultural or religious character. In some regions, cultural heritage consists more of monuments and objects; it is a “tangible” heritage, mostly protected by the law of armed conflict. Elsewhere, where structures are impermanent, cultural heritage is mainly expressed through orality, gestures, rituals, music and other forms of expression that individuals create using various media and instruments. Such heritage is mainly “intangible”. This essay aims to show that cultural heritage is both tangible and intangible, and that the law which protects such heritage is not limited to the law of armed conflict. Cultural heritage also benefits from the protection of other applicable instruments, such as human rights treaties and the UNESCO cultural heritage conventions.
Rapid evolution of microbe-mediated protection against pathogens in a worm host
Authors: King Kayla C , Brockhurst Michael A , Vasieva Olga , Paterson Steve , Betts Alex , Ford Suzanne A , Frost Crystal L , Horsburgh Malcolm J , Haldenby Sam , Hurst Gregory D D
Published: March 2016

Microbes can defend their host against virulent infections, but direct evidence for the adaptive origin of microbe-mediated protection is lacking. Using experimental evolution of a novel, tripartite interaction, we demonstrate that mildly pathogenic bacteria (Enterococcus faecalis) living in worms (Caenorhabditis elegans) rapidly evolved to defend their animal hosts against infection by a more virulent pathogen (Staphylococcus aureus), crossing the parasitism–mutualism continuum. Host protection evolved in all six, independently selected populations in response to within-host bacterial interactions and without direct selection for host health. Microbe-mediated protection was also effective against a broad spectrum of pathogenic S. aureus isolates. Genomic analysis implied that the mechanistic basis for E. faecalis-mediated protection was through increased production of antimicrobial superoxide, which was confirmed by biochemical assays. Our results indicate that microbes living within a host may make the evolutionary transition to mutualism in response to pathogen attack, and that microbiome evolution warrants consideration as a driver of infection outcome.
Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments
Authors: Thiam Hawa-Racine , Vargas Pablo , Carpi Nicolas , Crespo Carolina Lage , Raab Matthew , Terriac Emmanuel , King Megan C. , Jacobelli Jordan , Alberts Arthur S. , Stradal Theresia , Lennon-Dumenil Ana-Maria , Piel Matthieu
Published: March 2016

Cell migration has two opposite faces: although necessary for physiological processes such as immune responses, it can also have detrimental effects by enabling metastatic cells to invade new organs. In vivo, migration occurs in complex environments and often requires a high cellular deformability, a property limited by the cell nucleus. Here we show that dendritic cells, the sentinels of the immune system, possess a mechanism to pass through micrometric constrictions. This mechanism is based on a rapid Arp2/3-dependent actin nucleation around the nucleus that disrupts the nuclear lamina, the main structure limiting nuclear deformability. The cells’ requirement for Arp2/3 to pass through constrictions can be relieved when nuclear stiffness is decreased by suppressing lamin A/C expression. We propose a new role for Arp2/3 in three-dimensional cell migration, allowing fast-moving cells such as leukocytes to rapidly and efficiently migrate through narrow gaps, a process probably important for their function.
Inducing amnesia through systemic suppression
Authors: Hulbert Justin C. , Henson Richard N. , Anderson Michael C.
Published: March 2016

Hippocampal damage profoundly disrupts the ability to store new memories of life events. Amnesic windows might also occur in healthy people due to disturbed hippocampal function arising during mental processes that systemically reduce hippocampal activity. Intentionally suppressing memory retrieval (retrieval stopping) reduces hippocampal activity via control mechanisms mediated by the lateral prefrontal cortex. Here we show that when people suppress retrieval given a reminder of an unwanted memory, they are considerably more likely to forget unrelated experiences from periods surrounding suppression. This amnesic shadow follows a dose-response function, becomes more pronounced after practice suppressing retrieval, exhibits characteristics indicating disturbed hippocampal function, and is predicted by reduced hippocampal activity. These findings indicate that stopping retrieval engages a suppression mechanism that broadly compromises hippocampal processes and that hippocampal stabilization processes can be interrupted strategically. Cognitively triggered amnesia constitutes an unrecognized forgetting process that may account for otherwise unexplained memory lapses following trauma.
An entangled-LED-driven quantum relay over 1 km
Authors: Varnava Christiana , Stevenson R Mark , Nilsson Jonas , Skiba-Szymanska Joanna , Dzurňák Branislav , Lucamarini Marco , Penty Richard V , Farrer Ian , Ritchie David A , Shields Andrew J
Published: March 2016

Quantum cryptography allows confidential information to be communicated between two parties, with secrecy guaranteed by the laws of nature alone. However, upholding guaranteed secrecy over networks poses a further challenge, as classical receive-and-resend routing nodes can only be used conditional of trust by the communicating parties, which arguably diminishes the value of the underlying quantum cryptography. Quantum relays offer a potential solution by teleporting qubits from a sender to a receiver, without demanding additional trust from end users. Here we demonstrate the operation of a quantum relay over 1 km of optical fibre, which teleports a sequence of photonic quantum bits to a receiver by utilising entangled photons emitted by a semiconductor light-emitting diode. The average relay fidelity of the link is 0.90±0.03, exceeding the classical bound of 0.75 for the set of states used, and sufficiently high to allow error correction. The fundamentally low multiphoton emission statistics and the integration potential of the source present an appealing platform for future quantum networks.
Surface wave excitations and backflow effect over dense polymer brushes
Authors: Biagi Sofia , Rovigatti Lorenzo , Sciortino Francesco , Misbah Chaouqi
Published: March 2016

Polymer brushes are being increasingly used to tailor surface physicochemistry for diverse applications such as wetting, adhesion of biological objects, implantable devices and much more. Here we perform Dissipative Particle Dynamics simulations to study the behaviour of dense polymer brushes under flow in a slit-pore channel. We discover that the system displays flow inversion at the brush interface for several disconnected ranges of the imposed flow. We associate such phenomenon to collective polymer dynamics: a wave propagating on the brush surface. The relation between the wavelength, the amplitude and the propagation speed of the flow-generated wave is consistent with the solution of the Stokes equations when an imposed traveling wave is assumed as the boundary condition (the famous Taylor’s swimmer).
NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis
Authors: Tervaniemi Mari H. , Katayama Shintaro , Skoog Tiina , Siitonen H. Annika , Vuola Jyrki , Nuutila Kristo , Sormunen Raija , Johnsson Anna , Linnarsson Sten , Suomela Sari , Kankuri Esko , Kere Juha , Elomaa Outi
Published: March 2016

Psoriatic skin differs distinctly from normal skin by its thickened epidermis. Most gene expression comparisons utilize full-thickness biopsies, with substantial amount of dermis. We assayed the transcriptomes of normal, lesional and non-lesional psoriatic epidermis, sampled as split-thickness skin grafts, with 5′-end RNA sequencing. We found that psoriatic epidermis contains more mRNA per total RNA than controls and took this into account in the bioinformatic analysis. The approach highlighted innate immunity-related pathways in psoriasis, including NOD-like receptor (NLR) signaling and inflammasome activation. We demonstrated that the NLR signaling genes NOD2, PYCARD, CARD6 and IFI16 are upregulated in psoriatic epidermis and strengthened these findings by protein expression. Interestingly, PYCARD, the key component of the inflammasome, showed an altered expression pattern in the lesional epidermis. The profiling of non-lesional skin highlighted PSORS4 and mitochondrially encoded transcripts, suggesting that their gene expression is altered already before the development of lesions. Our data suggest that all components needed for the active inflammasome are present in the keratinocytes of psoriatic skin. The characterization of inflammasome pathways provides further opportunities for therapy. Complementing previous transcriptome studies, our approach gives deeper insight into the gene regulation in psoriatic epidermis.
A Dual-Colour Architecture for Pump-Probe Spectroscopy of Ultrafast Magnetization Dynamics in the Sub-10-femtosecond Range
Authors: Gonçalves C. S. , Silva A. S. , Navas D. , Miranda M. , Silva F. , Crespo H. , Schmool D. S.
Published: March 2016

Current time-resolution-limited dynamic measurements clearly show the need for improved techniques to access processes on the sub-10-femtosecond timescale. To access this regime, we have designed and constructed a state-of-the-art time-resolved magneto-optic Kerr effect apparatus, based on a new dual-color scheme, for the measurement of ultrafast demagnetization and precessional dynamics in magnetic materials. This system can operate well below the current temporal ranges reported in the literature, which typically lie in the region of around 50 fs and above. We have used a dual-colour scheme, based on ultra broadband hollow-core fibre and chirped mirror pulse compression techniques, to obtain unprecedented sub-8-fs pump and probe pulse durations at the sample plane. To demonstrate the capabilities of this system for ultrafast demagnetization and precessional dynamics studies, we have performed measurements in a ferrimagnetic GdFeCo thin film. Our study has shown that the magnetization shows a sudden drop within the first picosecond after the pump pulse, a fast recovery (remagnetization) within a few picoseconds, followed by a clear oscillation or precession during a slower magnetization recovery. Moreover, we have experimentally confirmed for the first time that a sub-10-fs pulse is able to efficiently excite a magnetic system such as GdFeCo.
Proinflammatory isoforms of IL-32 as novel and robust biomarkers for control failure in HIV-infected slow progressors
Authors: El-Far Mohamed , Kouassi Pascale , Sylla Mohamed , Zhang Yuwei , Fouda Ahmed , Fabre Thomas , Goulet Jean-Philippe , van Grevenynghe Julien , Lee Terry , Singer Joel , Harris Marianne , Baril Jean-Guy , Trottier Benoit , Ancuta Petronela , Routy Jean-Pierre , Bernard Nicole , Tremblay Cécile L. ,   Investigators of the Canadian HIV+ Slow Progressor Cohort, Angel Jonathan , Conway Brian , Côté Pierre , Gill John , Johnston Lynn , Kovacs Colin , Loutfy Mona , Logue Kenneth , Piché Alain , Rachlis Anita , Rouleau Danielle , Thompson Bill , Thomas Réjean , Trottier Sylvie , Walmsley Sharon , Wobeser Wendy
Published: March 2016

HIV-infected slow progressors (SP) represent a heterogeneous group of subjects who spontaneously control HIV infection without treatment for several years while showing moderate signs of disease progression. Under conditions that remain poorly understood, a subgroup of these subjects experience failure of spontaneous immunological and virological control. Here we determined the frequency of SP subjects who showed loss of HIV control within our Canadian Cohort of HIV+ Slow Progressors and identified the proinflammatory cytokine IL-32 as a robust biomarker for control failure. Plasmatic levels of the proinflammatory isoforms of IL-32 (mainly β and γ) at earlier clinic visits positively correlated with the decline of CD4 T-cell counts, increased viral load, lower CD4/CD8 ratio and levels of inflammatory markers (sCD14 and IL-6) at later clinic visits. We present here a proof-of-concept for the use of IL-32 as a predictive biomarker for disease progression in SP subjects and identify IL-32 as a potential therapeutic target.
Primary brain calcification in patients undergoing treatment with the biphosphanate alendronate
Authors: Oliveira J. R. M , Oliveira M. F
Published: March 2016

Brain calcification might be associated with various metabolic, infectious or vascular conditions. Clinically, brain calcification can include symptons such as migraine, parkinsonism, psychosis or dementia. The term Primary Brain Calcification was recently used for those patients without an obvious cause (formerly idiopathic) while Primary Familial Brain Calcifications was left for the cases with autosomal dominant inheritance. Recent studies found mutations in four genes (SLC20A2, PDGFRB, PDGFB and XPR1). However, these gene represent only 60% of all familial cases suggesting other genes remain to be elucidated. Studies evaluating treatments for such a devastating disease are scattered, usually appearing as single case reports. In the present study, we describe a case series of 7 patients treated with Alendronate, a widely prescribed biphosphanate. We observed good tolerance and evidence of improvements and stability by some patients. No side effects were reported and no specific symptoms related to medication. Younger patients and one individual continuing a prescription (prior to study commencement) appeared to respond more positively with some referred improvements in symptoms. Biphosphanates may represent an excellent prospect for the treatment of brain calcifications due to their being well tolerated and easily available. Conversely, prospective and controlled studies should promptly address weaknesses found in the present analysis.
On Sequence Learning Models: Open-loop Control Not Strictly Guided by Hick’s Law
Authors: Pavão Rodrigo , Savietto Joice P. , Sato João R. , Xavier Gilberto F. , Helene André F.
Published: March 2016

According to the Hick’s law, reaction times increase linearly with the uncertainty of target stimuli. We tested the generality of this law by measuring reaction times in a human sequence learning protocol involving serial target locations which differed in transition probability and global entropy. Our results showed that sigmoid functions better describe the relationship between reaction times and uncertainty when compared to linear functions. Sequence predictability was estimated by distinct statistical predictors: conditional probability, conditional entropy, joint probability and joint entropy measures. Conditional predictors relate to closed-loop control models describing that performance is guided by on-line access to past sequence structure to predict next location. Differently, joint predictors relate to open-loop control models assuming global access of sequence structure, requiring no constant monitoring. We tested which of these predictors better describe performance on the sequence learning protocol. Results suggest that joint predictors are more accurate than conditional predictors to track performance. In conclusion, sequence learning is better described as an open-loop process which is not precisely predicted by Hick’s law.
Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses
Authors: Liu Bingqiang , Zhou Chuan , Li Guojun , Zhang Hanyuan , Zeng Erliang , Liu Qi , Ma Qin
Published: March 2016

Regulons are the basic units of the response system in a bacterial cell and each consists of a set of transcriptionally co-regulated operons. Regulon elucidation is the basis for studying the bacterial global transcriptional regulation network. In this study, we designed a novel co-regulation score between a pair of operons based on accurate operon identification and cis regulatory motif analyses, which can capture their co-regulation relationship much better than other scores. Taking full advantage of this discovery, we developed a new computational framework and built a novel graph model for regulon prediction. This model integrates the motif comparison and clustering and makes the regulon prediction problem substantially more solvable and accurate. To evaluate our prediction, a regulon coverage score was designed based on the documented regulons and their overlap with our prediction; and a modified Fisher Exact test was implemented to measure how well our predictions match the co-expressed modules derived from E. coli microarray gene-expression datasets collected under 466 conditions. The results indicate that our program consistently performed better than others in terms of the prediction accuracy. This suggests that our algorithms substantially improve the state-of-the-art, leading to a computational capability to reliably predict regulons for any bacteria.
Phonon-assisted nonlinear optical processes in ultrashort-pulse pumped optical parametric amplifiers
Authors: Isaienko Oleksandr , Robel István
Published: March 2016

Optically active phonon modes in ferroelectrics such as potassium titanyl phosphate (KTP) and potassium titanyl arsenate (KTA) in the ~7–20 THz range play an important role in applications of these materials in Raman lasing and terahertz wave generation. Previous studies with picosecond pulse excitation demonstrated that the interaction of pump pulses with phonons can lead to efficient stimulated Raman scattering (SRS) accompanying optical parametric oscillation or amplification processes (OPO/OPA) and to efficient polariton-phonon scattering. In this work, we investigate the behavior of infrared OPAs employing KTP or KTA crystals when pumped with ~800-nm ultrashort pulses of duration comparable to the oscillation period of the optical phonons. We demonstrate that under conditions of coherent impulsive Raman excitation of the phonons, when the effective χ(2) nonlinearity cannot be considered instantaneous, the parametrically amplified waves (most notably, signal) undergo significant spectral modulations leading to an overall redshift of the OPA output. The pump intensity dependence of the redshifted OPA output, the temporal evolution of the parametric gain, as well as the pump spectral modulations suggest the presence of coupling between the nonlinear optical polarizations PNL of the impulsively excited phonons and those of parametrically amplified waves.
Frequency and amplitude modulation of ultra-compact terahertz quantum cascade lasers using an integrated avalanche diode oscillator
Authors: Castellano Fabrizio , Li Lianhe , Linfield Edmund H. , Davies A. Giles , Vitiello Miriam S.
Published: March 2016

Mode-locked comb sources operating at optical frequencies underpin applications ranging from spectroscopy and ultrafast physics, through to absolute frequency measurements and atomic clocks. Extending their operation into the terahertz frequency range would greatly benefit from the availability of compact semiconductor-based sources. However, the development of any compact mode-locked THz laser, which itself is inherently a frequency comb, has yet to be achieved without the use of an external stimulus. High-power, electrically pumped quantum cascade lasers (QCLs) have recently emerged as a promising solution, owing to their octave spanning bandwidths, the ability to achieve group-velocity dispersion compensation and the possibility of obtaining active mode-locking. Here, we propose an unprecedented compact architecture to induce both frequency and amplitude self-modulation in a THz QCL. By engineering a microwave avalanche oscillator into the laser cavity, which provides a 10 GHz self-modulation of the bias current and output power, we demonstrate multimode laser emission centered around 3 THz, with distinct multiple sidebands. The resulting microwave amplitude and frequency self-modulation of THz QCLs opens up intriguing perspectives, for engineering integrated self-mode-locked THz lasers, with impact in fields such as nano- and ultrafast photonics and optical metrology.
Accurate Determination of Conformational Transitions in Oligomeric Membrane Proteins
Authors: Sanz-Hernández Máximo , Vostrikov Vitaly V. , Veglia Gianluigi , De Simone Alfonso
Published: March 2016

The structural dynamics governing collective motions in oligomeric membrane proteins play key roles in vital biomolecular processes at cellular membranes. In this study, we present a structural refinement approach that combines solid-state NMR experiments and molecular simulations to accurately describe concerted conformational transitions identifying the overall structural, dynamical, and topological states of oligomeric membrane proteins. The accuracy of the structural ensembles generated with this method is shown to reach the statistical error limit, and is further demonstrated by correctly reproducing orthogonal NMR data. We demonstrate the accuracy of this approach by characterising the pentameric state of phospholamban, a key player in the regulation of calcium uptake in the sarcoplasmic reticulum, and by probing its dynamical activation upon phosphorylation. Our results underline the importance of using an ensemble approach to characterise the conformational transitions that are often responsible for the biological function of oligomeric membrane protein states.
Growth inhibition and apoptosis in cancer cells induced by polyphenolic compounds of Acacia hydaspica: Involvement of multiple signal transduction pathways
Authors: Afsar Tayyaba , Trembley Janeen H. , Salomon Christine E. , Razak Suhail , Khan Muhammad Rashid , Ahmed Khalil
Published: March 2016

Acacia hydaspica R. Parker is known for its medicinal uses in multiple ailments. In this study, we performed bioassay-guided fractionation of cytotoxic compounds from A. hydaspica and investigated their effects on growth and signaling activity in prostate and breast cancer cell lines. Four active polyphenolic compounds were identified as 7-O-galloyl catechin (GC), catechin (C), methyl gallate (MG), and catechin-3-O-gallate (CG). The four compounds inhibited prostate cancer PC-3 cell growth in a dose-dependent manner, whereas CG and MG inhibited breast cancer MDA-MB-231 cell growth. All tested compounds inhibited cell survival and colony growth in both cell lines, and there was evidence of chromatin condensation, cell shrinkage and apoptotic bodies. Further, acridine orange, ethidium bromide, propidium iodide and DAPI staining demonstrated that cell death occurred partly via apoptosis in both PC-3 and MDA-MB-231 cells. In PC-3 cells treatment repressed the expression of anti-apoptotic molecules Bcl-2, Bcl-xL and survivin, coupled with down-regulation of signaling pathways AKT, NFκB, ERK1/2 and JAK/STAT. In MDA-MB-231 cells, treatment induced reduction of CK2α, Bcl-xL, survivin and xIAP protein expression along with suppression of NFκB, JAK/STAT and PI3K pathways. Our findings suggest that certain polyphenolic compounds derived from A. hydaspica may be promising chemopreventive/therapeutic candidates against cancer.
Crystal Field Splitting is Limiting the Stability and Strength of Ultra-incompressible Orthorhombic Transition Metal Tetraborides
Authors: Zhang R. F. , Wen X. D. , Legut D. , Fu Z. H. , Veprek S. , Zurek E. , Mao H. K.
Published: March 2016

The lattice stability and mechanical strengths of the supposedly superhard transition metal tetraborides (TmB4, Tm = Cr, Mn and Fe) evoked recently much attention from the scientific community due to the potential applications of these materials, as well as because of general scientific interests. In the present study, we show that the surprising stabilization of these compounds from a high symmetry to a low symmetry structure is accomplished by an in-plane rotation of the boron network, which maximizes the in-plane hybridization by crystal field splitting between d orbitals of Tm and p orbitals of B. Studies of mechanical and electronic properties of TmB4suggest that these tetraborides cannot be intrinsically superhard. The mechanical instability is facilitated by a unique in-plane or out-of-plane weakening of the three-dimensional covalent bond network of boron along different shear deformation paths. These results shed a novel view on the origin of the stability and strength of orthorhombic TmB4, highlighting the importance of combinational analysis of a variety of parameters related to plastic deformation of the crystalline materials when attempting to design new ultra-incompressible, and potentially strong and hard solids.
Genomic identification of WRKY transcription factors in carrot (Daucus carota) and analysis of evolution and homologous groups for plants
Authors: Li Meng-Yao , Xu Zhi-Sheng , Tian Chang , Huang Ying , Wang Feng , Xiong Ai-Sheng
Published: March 2016

WRKY transcription factors belong to one of the largest transcription factor families. These factors possess functions in plant growth and development, signal transduction and stress response. Here, we identified 95 DcWRKY genes in carrot based on the carrot genomic and transcriptomic data and divided them into three groups. Phylogenetic analysis of WRKY proteins from carrot and Arabidopsis divided these proteins into seven subgroups. To elucidate the evolution and distribution of WRKY transcription factors in different species, we constructed a schematic of the phylogenetic tree and compared the WRKY family factors among 22 species, which including plants, slime mold and protozoan. An in-depth study was performed to clarify the homologous factor groups of nine divergent taxa in lower and higher plants. Based on the orthologous factors between carrot and Arabidopsis, 38 DcWRKY proteins were calculated to interact with other proteins in the carrot genome. Yeast two-hybrid assay showed that DcWRKY20 can interact with DcMAPK1 and DcMAPK4. The expression patterns of the selected DcWRKY genes based on transcriptome data and qRT-PCR suggested that those selected DcWRKY genes are involved in root development, biotic and abiotic stress response. This comprehensive analysis provides a basis for investigating the evolution and function of WRKY genes.
Therapeutic and prophylactic activity of itraconazole against human rhinovirus infection in a murine model
Authors: Shim Aeri , Song Jae-Hyoung , Kwon Bo-Eun , Lee Jeong-Jun , Ahn Jae-Hee , Kim Yeon-Jeong , Rhee Ki-Jong , Chang Sun-Young , Cha Younggil , Lee Yong-Soo , Kweon Mi-Na , Park Kwi Sung , Kim Dong-Eun , Cho Sungchan , Cho Hyun-Jong , Ko Hyun-Jeong
Published: March 2016

Human rhinovirus (HRV) is the most common viral infectious agent in humans and is the predominant cause of the common cold. There is a need for appropriate vaccines or therapeutic agents to treat HRV infection. In this study, we investigated whether itraconazole (ICZ) can protect cells from HRV-induced cytotoxicity. Replication of HRV1B was reduced by ICZ treatment in the lungs of HRV1B- as compared to vehicle-treated mice. The numbers of immune cells, including granulocytes and monocytes, were reduced in bronchoalveolar lavage fluid (BALF) by ICZ administration after HRV1B infection, corresponding to decreased pro-inflammatory cytokine and chemokine levels in BALF. A histological analysis of lung tissue showed that ICZ suppressed inflammation caused by HRV1B infection. Interestingly, pretreatment of mice with ICZ in the form of a nasal spray had potent prophylactic antiviral activity. Cholesterol accumulation in the plasma membrane was observed upon HRV infection; ICZ blocked cholesterol trafficking to the plasma membrane, as well as resulted in its accumulation in subcellular compartments near the nucleus. These findings suggest that ICZ is a potential antiviral agent for the treatment of HRV infection, which can be adopted preventatively as well as therapeutically.
Minicircle DNA Provides Enhanced and Prolonged Transgene Expression Following Airway Gene Transfer
Authors: Munye Mustafa M. , Tagalakis Aristides D. , Barnes Josephine L. , Brown Rachel E. , McAnulty Robin J. , Howe Steven J. , Hart Stephen L.
Published: March 2016

Gene therapy for cystic fibrosis using non-viral, plasmid-based formulations has been the subject of intensive research for over two decades but a clinically viable product has yet to materialise in large part due to inefficient transgene expression. Minicircle DNA give enhanced and more persistent transgene expression compared to plasmid DNA in a number of organ systems but has not been assessed in the lung. In this study we compared minicircle DNA with plasmid DNA in transfections of airway epithelial cells. In vitro, luciferase gene expression from minicircles was 5–10-fold higher than with plasmid DNA. In eGFP transfections in vitro both the mean fluorescence intensity and percentage of cells transfected was 2–4-fold higher with minicircle DNA. Administration of equimolar amounts of DNA to mouse lungs resulted in a reduced inflammatory response and more persistent transgene expression, with luciferase activity persisting for 2 weeks from minicircle DNA compared to plasmid formulations. Transfection of equal mass amounts of DNA in mouse lungs resulted in a 6-fold increase in transgene expression in addition to more persistent transgene expression. Our findings have clear implications for gene therapy of airway disorders where plasmid DNA transfections have so far proven inefficient in clinical trials.
Continuous time Bayesian networks identify Prdm1 as a negative regulator of TH17 cell differentiation in humans
Authors: Acerbi Enzo , Viganò Elena , Poidinger Michael , Mortellaro Alessandra , Zelante Teresa , Stella Fabio
Published: March 2016

T helper 17 (TH17) cells represent a pivotal adaptive cell subset involved in multiple immune disorders in mammalian species. Deciphering the molecular interactions regulating TH17 cell differentiation is particularly critical for novel drug target discovery designed to control maladaptive inflammatory conditions. Using continuous time Bayesian networks over a time-course gene expression dataset, we inferred the global regulatory network controlling TH17 differentiation. From the network, we identified the Prdm1 gene encoding the B lymphocyte-induced maturation protein 1 as a crucial negative regulator of human TH17 cell differentiation. The results have been validated by perturbing Prdm1 expression on freshly isolated CD4+ naïve T cells: reduction of Prdm1 expression leads to augmentation of IL-17 release. These data unravel a possible novel target to control TH17 polarization in inflammatory disorders. Furthermore, this study represents the first in vitro validation of continuous time Bayesian networks as gene network reconstruction method and as hypothesis generation tool for wet-lab biological experiments.
Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats
Authors: Han Hongxing , Xiao Hailong , Zhang Kai , Lu Zhenmei
Published: March 2016

The impact of 4-epi-oxytetracycline (4-EOTC), one of the main oxytetracycline (OTC) metabolites, on the gut microbiota and physiological metabolism of Wistar rats was analyzed to explore the dynamic alterations apparent after repeated oral exposure (0.5, 5.0 or 50.0 mg/kg bw) for 15 days as shown by 16S rRNA pyrosequencing and UPLC-Q-TOF/MS analysis. Both principal component analysis and cluster analysis showed consistently altered patterns with distinct differences in the treated groups versus the control groups. 4-EOTC treatment at 5.0 or 50.0 mg/kg increased the relative abundance of the Actinobacteria, specifically Bifidobacteriaceae and improved the synthesis of lysophosphatidylcholine (LysoPC), as shown by the lipid biomarkers LysoPC(16:0), LysoPC(18:3), LysoPC(20:3) and LysoPC(20:4). The metabolomic analysis of urine samples also identified four other decreased metabolites: diacylglycerol, sphingomyelin, triacylglycerol and phosphatidylglycerol. Notably, the significant changes observed in these biomarkers demonstrated the ongoing disorder induced by 4-EOTC. Blood and urine analysis revealed that residual 4-EOTC accumulated in the rats, even two weeks after oral 4-EOTC administration, ceased. Thus, through thorough analysis, it can be concluded that the alteration of the gut microbiota and disorders in blood metabolomics are correlated with 4-EOTC treatment.
Design of a hydrophobic tripeptide that self-assembles into amphiphilic superstructures forming a hydrogel biomaterial
Authors: Vargiu A. V. , Iglesias D. , Styan K. E. , Waddington L. J. , Easton C. D. , Marchesan S.
Published: March 2016

We report the rational design of a heterochiral hydrophobic tripeptide self-assembling into amphiphilic d-superstructures that yield a self-supportive hydrogel at physiological pH.
Aerosol-assisted synthesis of mesoporous aluminosilicate microspheres: the effect of the aluminum precursor
Authors: Fiorilli Sonia , Cauda Valentina , Pontiroli Lucia , Vitale-Brovarone Chiara , Onida Barbara
Published: March 2016

Spray-dried mesoporous aluminosilicates, with spherical morphology, high surface area and accessible porosity, have been synthesized under mild acidic aqueous conditions by using different aluminum precursors.
An adhesive elastomeric supramolecular polyurethane healable at body temperature
Authors: Feula Antonio , Tang Xuegang , Giannakopoulos Ioannis , Chippindale Ann M. , Hamley Ian W. , Greco Francesca , Paul Buckley C. , Siviour Clive R. , Hayes Wayne
Published: March 2016

We report a non-cytotoxic supramolecular polyurethane network whose mechanical properties can be recovered efficiently (>99%) at body temperature.
A new approach to rapid determination of 18 bioactive constituents in Alpinia oxyphylla using UPLC-MS/MS with positive–negative conversion multiple reaction monitor (+/−MRM) technology
Authors: Hou Lei , Zuo Lihua , Sun Zhi , Sun Zhiyong , Zhu Zhenfeng , Kang Jian , Gao Li , Zhang Xiaojian , Huang Wenhua
Published: March 2016

A new approach was developed for the simultaneous separation and determination of 18 active components (including one new component) in Fructus Alpinia oxyphylla by UPLC-MS/MS with +/−MRM technology.
Rotation mixing-assisted liquid–liquid microextraction: a new microextraction approach for the determination of priority phenols in water samples
Authors: Çabuk Hasan , Ata Şevket
Published: March 2016

In this study, a new sample pretreatment method termed as rotation mixing-assisted liquid–liquid microextraction combined with liquid chromatography with ultraviolet detection was developed for the determination of selected priority phenols in water samples.
Design and development of an amperometric immunosensor based on screen-printed electrodes
Authors: Mistry Kalyan Kumar , Layek Keya , Chell Tarak Nath , Chaudhuri Chirasree Roy , Saha Hiranmay
Published: March 2016

An amperometric immunosensor has been developed from laboratory fabricated screen-printed electrodes for the detection of bovine serum albumin antigen.
Fast sequential determination of manganese and chromium in vegetable oil and biodiesel samples by high-resolution continuum source graphite furnace atomic absorption spectrometry
Authors: Almeida Jorge S. , Brandão Geovani C. , dos Santos Gabriel L. , Teixeira Leonardo S. G.
Published: March 2016

HR-CS GF AAS was used for the sequential determination of Mn and Cr in vegetable oil and biodiesel samples.
An irregular-shaped homogeneous refractive index model for interpretation of the surface plasmon resonance response from living cell attachment
Authors: Deng Shijie , Yu Xinglong , Wang Peng
Published: March 2016

A simple but quantitative mathematical formalism was developed for interpretation of the SPR response from living cell attachment.
Enhanced photocatalytic activity of TiO2–Cu/C with regulation and matching of energy levels by carbon and copper for photoreduction of CO2 into CH4
Authors: Yan Yabin , Yu Yanlong , Cao Chi , Huang Shaolong , Yang Yajun , Yang Xiaodan , Cao Yaan
Published: March 2016

A novel copper and carbon co-modified TiO2 photocatalyst (TiO2–Cu/C) was prepared using a simple sol–gel method.
A study of the impact of co-adsorbents on DSSC electron transfer processes: anti-π-stacking vs. shield effect
Authors: Cisneros R. , Beley M. , Lapicque F.
Published: March 2016

In this study we report a detailed exploration of the use of two different co-adsorbents – namely bis-methoxyphenylphosphinic acid (BMPP) and chenodeoxycholic acid (CDCA) – known to increase photoconversion efficiency (PCE) of DSSCs sensitized with N719.
Force exerted by a nanoscale capillary water bridge between two planar substrates
Authors: Valenzuela Gerson E. , Saavedra Jorge H. , Rozas Roberto E. , Toledo Pedro G.
Published: March 2016

Molecular dynamics simulation of a nanoscale capillary water bridge between two planar substrates is used to determine the resulting force between the substrates without arbitrariness regarding geometry and location of the free surface of the bridge.
An abnormal N-heterocyclic carbene based nickel complex for catalytic reduction of nitroarenes
Authors: Vijaykumar Gonela , Mandal Swadhin K.
Published: March 2016

The NiCl2(aNHC)2complex has been used as an efficient catalyst for the reduction of nitroarenes with hydrosilanes to give aromatic amines in good to excellent yields.
A DFT study to unravel the ligand exchange kinetics and thermodynamics of OsVIIIoxo/hydroxido/aqua complexes in aqueous matrices
Authors: van Niekerk Daniel M. E. , Gerber Wilhelmus J. , Koch Klaus R.
Published: March 2016

The OsVIIIoxo/hydroxido complexes abundant in mild to relatively concentrated basic aqueous solutions are OsVIIIO4, [OsVIIIO4(OH)]−and twocis-[OsVIIIO4(OH)2]2−species.
Perovskite type oxide-supported Ni catalysts for the production of 2,5-dimethylfuran from biomass-derived 5-hydroxymethylfurfural
Authors: Chen Meng-Yuan , Chen Chu-Bai , Zada Bakht , Fu Yao
Published: March 2016

Hydrogenolysis of biomass-derived 5-hydroxymethylfurfural to 2,5-dimethylfuran was performed over perovskite type oxide-supported Ni catalysts. A yield of 98.3% of 2,5-dimethylfuran was obtained.
Multi-color luminescence properties and energy transfer behaviour in host-sensitized CaWO4:Tb3+,Eu3+phosphors
Authors: Zhang Yang , Gong Weitao , Yu Jingjie , Cheng Zhiyuan , Ning Guiling
Published: March 2016

A series of host-sensitized and color-tunable CaWO4:Tb3+,Eu3+phosphors have been successfully synthesizedviathe high-temperature solid-state reaction route and their photoluminescence properties and energy transfer mechanism have been carefully investigated.
An ultrasensitive sandwich-type electrochemical immunosensor based on functionalized mesoporous carbon for IgG detection
Authors: Yang Yuying , Liu Qing , Liu Yan , Li Zhaohui , Li Yueyun , Wang Ping , Zhang Daopeng , Zhao Zengdian , Liu Yuying , Dong Yunhui
Published: March 2016

Immunoglobulin (IgG) plays an important role in the accurate diagnosis of some diseases.
Tunable and highly efficient light-harvesting antenna systems based on 1,7-perylene-3,4,9,10-tetracarboxylic acid derivatives
Authors: Dubey Rajeev K. , Inan Damla , Sengupta Sanchita , Sudhölter Ernst J. R. , Grozema Ferdinand C. , Jager Wolter F.
Published: March 2016

Efficient harvesting of solar energy, without interference from electron transfer, is reported for a series of bichromophoric light-harvesting antenna molecules.
In situ growth of NiCo2S4@Ni3V2O8 on Ni foam as a binder-free electrode for asymmetric supercapacitors
Authors: Niu Lengyuan , Wang Yidan , Ruan Fengping , Shen Cheng , Shan Shen , Xu Man , Sun Zhenkun , Li Can , Liu Xinjuan , Gong Yinyan
Published: March 2016

A NiCo2S4@Ni3V2O8//AC asymmetric supercapacitor was successfully fabricated and it can deliver both high energy density and high power density.
Development of compartment for studies on the growth of protein crystals in space
Authors: Yamazaki T. , Tsukamoto K. , Yoshizaki I. , Fukuyama S. , Miura H. , Shimaoka T. , Maki T. , Oshi K. , Kimura Y.
Published: March 2016

To clarify the growth mechanism of a protein crystal, it is essential to measure its growth rate with respect to the supersaturation. We developed a compartment (growth cell) for measuring the growth rate (<0.1 nm s−1) of the face of a protein crystal at a controlled supersaturation by interferometry over a period of half a year in space. The growth cell mainly consists of quartz glass, in which the growth solution and a seed crystal are enclosed by capillaries, the screw sample holder, and a helical insert. To avoid the destruction of the cell and the evaporation of the water from the solution inside the cell, we selected the materials for these components with care. The equipment was successfully used to examine the growth of a lysozyme crystal at a controlled supersaturation in space, where convection is negligible because of the microgravity environment, thereby advancing our understanding of the mechanism of protein crystal growth from solution. The technique used to develop the growth cell is useful not only for space experiments but also for kinetic studies of materials with very slow growth and dissolution rates (<10−3 nm s−1).
Perspective: NanoMine: A material genome approach for polymer nanocomposites analysis and design
Authors: Zhao He , Li Xiaolin , Zhang Yichi , Schadler Linda S. , Chen Wei , Brinson L. Catherine
Published: March 2016

Polymer nanocomposites are a designer class of materials where nanoscale particles, functional chemistry, and polymer resin combine to provide materials with unprecedented combinations of physical properties. In this paper, we introduce NanoMine, a data-driven web-based platform for analysis and design of polymer nanocomposite systems under the material genome concept. This open data resource strives to curate experimental and computational data on nanocomposite processing, structure, and properties, as well as to provide analysis and modeling tools that leverage curated data for material property prediction and design. With a continuously expanding dataset and toolkit, NanoMine encourages community feedback and input to construct a sustainable infrastructure that benefits nanocomposite material research and development.
Conservation triage or injurious neglect in endangered species recovery
Authors: Gerber Leah R.
Published: March 2016

Significance

Although government funding available for species protection and recovery is one of the best predictors of successful recovery, government spending is both insufficient and highly disproportionate among groups of species. Here I demonstrate that expenditures for recovery in excess of the recommended recovery budget would not necessarily translate into better conservation outcomes. More importantly, elimination of the budget surplus for “costly yet futile” recovery plans can provide sufficient funding to offset funding deficits for more than 180 species. Using a return on investment analysis, I show that triage by budget compression provides better funding for a larger sample of species, and that a larger sample of adequately funded recovery plans should produce better outcomes even if by chance.
Multiple First Names in the Netherlands (1760–2014)
Authors: Bloothooft Gerrit , Onland David
Published: March 2016

Although in Europe the custom to choose more than one name for a child first arose in the early Renaissance in Italy, its popularity reached the Netherlands only in the eighteenth century. On the basis of a high-coverage sample of the birth and name information for 26 million individuals from 1760 until 2014, the preference for multiple first names in the Netherlands has been studied, both annually and geographically. With the exception of recent years, religion has played a dominant role in name choices, including the number of names. Protestants only started to adopt double names in the nineteenth century, while Catholics increasingly chose three names, many including Maria (but only during a period of 50 years in the mid-twentieth century for boys). A tax proposal in 1915 on the number of names not only demonstrates the effect of financial cost on naming, but also the consistency of parents’ name choices concerning their children. Whereas during previous centuries the changes were gradual, preferences varied rapidly over the last 50 years.