bluuebunny/crossref_metadata_2025 huggingface dataset:
Strain relaxation in semipolar (202¯1) InGaN grown by plasma assisted molecular beam epitaxy
Authors: Sawicka M. , Kryśko M. , Muziol G. , Turski H. , Siekacz M. , Wolny P. , Smalc-Koziorowska J. , Skierbiszewski C.
Published: May 2016

Strain relaxation in semipolar (202¯1) InGaN layers grown by plasma assisted molecular beam epitaxy (PAMBE) was investigated with high-resolution X-ray diffraction (XRD) reciprocal space mapping, cathodoluminescence (CL), fluorescent light microscopy (FLM), and atomic force microscopy. We find that XRD detects lattice relaxation much later than its actual onset occurs. Other techniques used in this study allowed to detect local footprints of plastic relaxation before it was evidenced by XRD: at the initial stages of strain relaxation, we observed changes in layer morphology, i.e., formation of short trench line segments on the surface along the ⟨112¯0⟩ direction as well as dark lines in CL and FLM. The misfit dislocations formation and glide were observed in two slip systems: initially in basal slip system ⟨112¯0⟩{0001} and for larger amount of strain in non-basal, prismatic slip system ⟨112¯0⟩{11¯00}. Experimentally determined critical thickness for InGaN layers grown by PAMBE on semipolar (202¯1) bulk GaN substrates agrees well with literature data obtained with metalorganic vapor phase epitaxy and follows the Matthews-Blakeslee model prediction. We discuss the impact of substrate structural properties on the strain relaxation onset and mechanisms. We also describe the layer morphology and surface roughness evolution related to the increasing In content and strain relaxation of the semipolar (202¯1) InGaN layers.
Characterization of the dominating bulk recombination in bulk-heterojunction blends using photoinduced absorption
Authors: Sandén S. , Wilson N. M. , Sandberg O. J. , Österbacka R.
Published: May 2016

In this work we show how to clarify the dominating bulk recombination in organic solar cells by using photoinduced absorption. We show how to use the intensity and frequency dependence of the in-phase and quadrature signals to obtain the effective reaction order. For trap-assisted recombination, we can show using a multiple trapping and retrapping model with an exponential tail-state distribution that a temperature dependent reaction order is obtained which allows for determination of the characteristic energy of the exponential distribution of trap-states. In the model system pBTTT:PC60BM, we show that trap-assisted recombination is the dominating bulk recombination in 1:1 blends with a characteristic energy of the exponential trap distribution Ech=44±5 meV. The 1:4 blend, on the other hand, shows temperature independent behavior in good agreement with a dominating 2D Langevin bulk recombination.
Nanoporosity-induced superhydrophobicity and large antireflection in InSb
Authors: Datta Debi Prasad , Som Tapobrata
Published: May 2016

A porous nanostructure evolves in InSb due to keV ion implantation which leads to superhydrophobic and large antireflective property, indicating a single-step facile fabrication to introduce both functionalities. In particular, it is observed that the contact angle of a water droplet on the nanoporous InSb surface exceeds 150°, revealing the transition to a superhydrophobic surface. Correlation between the contact angle and the porous nanostructures is qualitatively understood in light of the Cassie-Baxter model. It is found that a decrease in the fraction of solid surface wetted by the water droplet and a corresponding increase in the air-water interface fraction lead to the enhancement in the hydrophobicity. We further observe that the large broadband antireflection (in the range of 200–800 nm) is also correlated to the nanoporous structure, arising out of a large reduction in the refractive index due to its increasing porosity. Such a surface with the combination of superhydrophobicity and large antireflection can be very useful for applications of InSb nanostructures in electronic, photonic devices, or infrared detectors.
Anomalously large electro-optic Pockels effect at the air-water interface with an electric field applied parallel to the interface
Authors: Suzuki Yuto , Osawa Kengo , Yukita Shunpei , Kobayashi Takayoshi , Tokunaga Eiji
Published: May 2016

The optical Pockels effect was observed at the air-water interface by electromodulation spectroscopy. When an AC electric field of frequency f was applied parallel to a water surface between Pt electrodes, the field induced a change in the transmitted light intensity synchronized at 1f proportional to the field strength. The 1f signals dominated over 2f signals by one order of magnitude and the signal disappeared when the electrodes were completely immersed under the water surface, strongly suggesting that the observed phenomena were due to the Pockels effect at the air-water interface. The Pockels coefficient was estimated to be |r|= 1.4 × 105 pm/V, which is much larger than that at the solid-water interface. However, this is unusual because the parallel electric field does not induce the break in inversion symmetry required for the appearance of the Pockels effect. The electrowetting effect was experimentally ruled out as a mechanism for the Pockels effect, and this made the existence of a field perpendicular to the surface, although extremely weak, the most likely explanation.
Exploration of vertical scaling limit in carbon nanotube transistors
Authors: Qiu Chenguang , Zhang Zhiyong , Yang Yingjun , Xiao Mengmeng , Ding Li , Peng Lian-Mao
Published: May 2016

Top-gated carbon nanotube field-effect transistors (CNT FETs) were fabricated by using ultra-thin (4.5 nm or thinner) atomic-layer-deposition grown HfO2 as gate insulator, and shown to exhibit high gate efficiency, i.e., all examined (totally 76) devices present very low room temperature subthreshold swing with an averaged value of 64 mV/Dec, without observable carrier mobility degradation. The gate leakage of the CNT FET under fixed gate voltage is dependent not only on the thickness of HfO2 insulator, but also on the diameter of the CNT. The vertical scaling limit of CNT FETs is determined by gate leakage standard in ultra large scale integrated circuits. HfO2 film with effective oxide thickness of 1.2 nm can provide both excellent gate electrostatic controllability and small gate leakage for sub-5 nm FETs based on CNT with small diameter.
Thermal gradient induced flexoelectric effects in bulk Ba0.67Sr0.33TiO3
Authors: Kim Taeyang , Huang Wenbin , Huang Shujin , Jiang Xiaoning
Published: May 2016

Flexoelectric effect, denoting electric field gradient induced mechanical strain or mechanical strain gradient induced electric polarization, is a universal phenomenon in all dielectrics. Although research on the topic of flexoelectricity under stress fields and electric fields has advanced significantly, information regarding the phenomenon under thermal fields is rather limited. In this letter, the flexoelectricity field of Ba0.67Sr0.33TiO3 (BST) was investigated by generating temperature gradients along the lengths of samples with symmetric geometry. An electric field gradient induced by a thermal gradient was analyzed based on the temperature-dependent dielectric property of BST. The strain was then experimentally verified due to the electric field gradient. Experimental results suggest converse flexoelectric effect of BST samples with symmetric geometry in a thermal field. This result was not only consistent with the theoretical prediction, but it also followed the scaling effect of flexoelectricity.
Periodic domain patterning by electron beam of proton exchanged waveguides in lithium niobate
Authors: Chezganov D. S. , Vlasov E. O. , Neradovskiy M. M. , Gimadeeva L. V. , Neradovskaya E. A. , Chuvakova M. A. , Tronche H. , Doutre F. , Baldi P. , De Micheli M. P. , Shur V. Ya.
Published: May 2016

Formation of domain structure by electron beam irradiation in congruent lithium niobate covered by surface dielectric layer with planar and channel waveguides produced by Soft Proton Exchange (SPE) process has been studied. Formation of domains with arbitrary shapes as a result of discrete switching has been revealed. The fact was attributed to ineffective screening of depolarization field in the crystals with a surface layer modified by SPE process. The dependences of the domain sizes on the dose and the distance between irradiated areas have been revealed. Finally, we have demonstrated that electron beam irradiation of lithium niobate crystals with surface resist layer can produce high quality periodical domain patterns after channel waveguide fabrication. Second harmonic generation with normalized nonlinear conversion efficiency up to 48%/(W cm2) has been achieved in such waveguides.
Diffuse-interface modeling of three-phase interactions
Authors: Park Jang Min , Anderson Patrick D.
Published: May 2016

In this work, a numerical model is developed to study the three-phase interactions which take place when two immiscible drops suspended in a third immiscible liquid are brought together. The diffuse-interface model coupled with the hydrodynamic equations is solved by a standard finite element method. Partial and complete engulfing between two immiscible drops is studied, and the effects of several parameters are discussed. In the partial-engulfing case, two stages of wetting and pulling are identified, which qualitatively agrees with the experiment. In the complete-engulfing case, three stages of wetting and/or penetration, pulling, and spreading are identified.
Highly sensitive terahertz dielectric sensor for small-volume liquid samples
Authors: Soltani A. , Neshasteh H. , Mataji-Kojouri A. , Born N. , Castro-Camus E. , Shahabadi M. , Koch M.
Published: May 2016

We present a resonator-based sensor for the measurement of the refractive index of dielectric liquid samples. The proposed sensor operates on the basis of an electromagnetic resonance between a thin metallic grating and a reflecting ground plane. The fluid whose refractive index is to be measured fills the region between the metallic grating and the ground plane and causes a considerable shift in the resonance frequency (>500 GHz/RIU). The sensor has a relatively simple structure; therefore, it can be manufactured economically on industrial scales.
Strong electroluminescence from direct band and defects in Ge n+/p shallow junctions at room temperature
Authors: Lin Guangyang , Wang Chen , Li Cheng , Chen Chaowen , Huang Zhiwei , Huang Wei , Chen Songyan , Lai Hongkai , Jin Chunyan , Sun Jiaming
Published: May 2016

Strong room temperature electroluminescence with two emission peaks at around 0.786 eV and 0.747 eV from Ge n+/p shallow junctions was reported. The peak at around 0.786 eV comes from direct band luminescence (DBL) in n + Ge regions, while the peak fixing at 0.747 eV is resulted from defects induced by ion implantation. Heavy n-type doping in Ge renders realization of strong defect-related luminescence (DRL) feasible. The peak intensity ratio of DRL/DBL decreases with increase of injection current since more electrons are filled in Γ valley. Above all, the Ge n+/p shallow junction is fully compatible with the source and drain in Ge metal-oxide-semiconductor field effect transistors.
Effect of 3D fractal dimension on contact area and asperity interactions in elastoplastic contact
Authors: Jourani Abdeljalil
Published: May 2016

Few models are devoted to investigate the effect of 3D fractal dimension Ds on contact area and asperity interactions. These models used statistical approaches or two-dimensional deterministic simulations without considering the asperity interactions and elastic–plastic transition regime. In this study, a complete 3D deterministic model is adopted to simulate the contact between fractal surfaces which are generated using a modified two-variable Weierstrass–Mandelbrot function. This model incorporates the asperity interactions and considers the different deformation modes of surface asperities which range from entirely elastic through elastic-plastic to entirely plastic contact. The simulations reveal that the elastoplastic model is more appropriate to calculate the contact area ratio and pressure field. It is also shown that the influence of the asperity interactions cannot be neglected, especially at lower fractal dimension Ds and higher load.
Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification
Authors: Rutherford Susan , Wilson Peter G. , Rossetto Maurizio , Bonser Stephen P.
Published: May 2016

Eucalyptus is a genus that occurs in a range of habitats in Australia, Papua New Guinea, Timor, Sulawesi and the Philippines, with several species being used as sources of timber and fibre. However, despite its ecological and commercial significance, understanding its evolutionary history remains a challenge. The focus of the present study is the green ashes (subgenus Eucalyptus section Eucalyptus). Although previous studies, based primarily on morphology, suggest that the green ashes form a monophyletic group, there has been disagreement concerning the divergence of taxa. The present study aims to estimate the phylogeny of the green ashes and closely related eucalypts (37 taxa from over 50 locations in south-eastern Australia), using genome-wide analyses based on Diversity Arrays Technology (DArT). Results of analyses were similar in topology and consistent with previous phylogenies based on sequence data. Many of the relationships supported those proposed by earlier workers. However, other relationships, particularly of taxa within the Sydney region and Blue Mountains, were not consistent with previous classifications. These findings raise important questions concerning how we define species and discern relationships in Eucalyptus and may have implications for other plant species, particularly those with a complex evolutionary history where hybridisation and recombination have occurred.
Cos-Seq for high-throughput identification of drug target and resistance mechanisms in the protozoan parasite
Leishmania
Authors: Gazanion Élodie , Fernández-Prada Christopher , Papadopoulou Barbara , Leprohon Philippe , Ouellette Marc
Published: May 2016

Significance

Gain-of-function screens using overexpression genomic libraries are powerful tools for discovering drug target/resistance genes, but several limitations make this technique less amenable to high-throughput screening. Using cosmid-based functional screening coupled to next-generation sequencing, an approach that we term Cosmid Sequencing (or “Cos-Seq”), we followed the dynamics of cosmid enrichment during drug pressure in
Leishmania
, the parasite responsible for leishmaniasis, a neglected tropical disease. This improved and sensitive method has led to the identification and functional characterization of an unprecedented number of drug target/resistance genes against all drugs currently used to treat leishmaniasis.
Collybolide is a novel biased agonist of κ-opioid receptors with potent antipruritic activity
Authors: Gupta Achla , Gomes Ivone , Bobeck Erin N. , Fakira Amanda K. , Massaro Nicholas P. , Sharma Indrajeet , Cavé Adrien , Hamm Heidi E. , Parello Joseph , Devi Lakshmi A.
Published: May 2016

Significance

In recent years, the κ-opioid receptor (κOR) has become an attractive therapeutic target for the treatment of a number of disorders including depression, visceral pain, and drug addiction. A search for natural products with novel scaffolds targeting κOR has been intensive. Here, we report the discovery of a natural product (Colly) from the fungus
Collybia maculata
as a novel scaffold that contains a furyl-δ-lactone core structure similar to that of Salvinorin A, another natural product isolated from the mint
Salvia divinorum.
We show that Colly functions as a κOR agonist with antinociceptive and antipruritic activity. Interestingly, Colly exhibits biased agonistic activity, suggesting that it could be used as a backbone for the generation of novel therapeutics targeting κOR with reduced side effects.
ROR1 is essential for proper innervation of auditory hair cells and hearing in humans and mice
Authors: Diaz-Horta Oscar , Abad Clemer , Sennaroglu Levent , Foster Joseph , DeSmidt Alexandra , Bademci Guney , Tokgoz-Yilmaz Suna , Duman Duygu , Cengiz F. Basak , Grati M’hamed , Fitoz Suat , Liu Xue Z. , Farooq Amjad , Imtiaz Faiqa , Currall Benjamin B. , Morton Cynthia Casson , Nishita Michiru , Minami Yasuhiro , Lu Zhongmin , Walz Katherina , Tekin Mustafa
Published: May 2016

Significance

The inner ear is a vertebrate organ of delicate and complex architecture that translates sound into electrical signals deciphered by the brain. This study utilizes a genetic approach to associate a mutation of
ROR1
(receptor tyrosine kinase-like orphan receptor 1) with inner ear anomalies and deafness in humans. Characterization of
Ror1
mutant mice reveals fasciculation deficiencies of spiral ganglion axons and disruption of sensory hair cell synapses and peripheral innervations. The molecular basis of this phenotype involves alterations of the NF-κB pathway. Thus, we present
ROR1
as a previously unrecognized gene that is essential for the development of the inner ear and hearing in humans and mice.
Hedgehog signaling enables nutrition-responsive inhibition of an alternative morph in a polyphenic beetle
Authors: Kijimoto Teiya , Moczek Armin P.
Published: May 2016

Significance

Complex, nongradual responses to environmental conditions are commonplace in nature and perhaps most extreme in polyphenic insects where continuous variation in nutrition experienced in early development gives rise to discrete alternative castes or morphs. This research shows that the hedgehog (Hh) pathway has acquired a novel and highly unusual role in the nutrition-dependent regulation of polyphenic development of a beetle. Experimental repression of Hh signaling returns a highly discontinuous response to nutrition to its presumed ancestral, gradual state. Our results suggest that recruitment of the Hh signaling pathway may have been a key step in the evolution of trait thresholds and the corresponding origin of alternative phenotypes and complex allometries.
Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design
Authors: Tian Xiao-Jun , Zhang Hang , Sannerud Jens , Xing Jianhua
Published: May 2016

Significance

For sensitive smell detection, each mammalian olfactory sensory neurons need to express stochastically only one allele of 1 out of possibly more than 1,000 types of olfactory receptors. The mechanism for this monoallelic expression remains as one of the biggest unresolved questions for decades. Using mathematical modeling and computer simulations, we identified a three-layer regulation mechanism the olfactory system adopts to achieve single allelic expression and several other biological requirements such as maximizing the overall diversity of expressed olfactory receptors. The revealed mechanism provides insight for formulating biological processes as multiple-objective optimization problems.
Enhancement of β-catenin activity by BIG1 plus BIG2 via Arf activation and cAMP signals
Authors: Li Chun-Chun , Le Kang , Kato Jiro , Moss Joel , Vaughan Martha
Published: May 2016

Significance

Transcriptional coactivator β-catenin promotes cell proliferation in development and tumorigenesis, via actions enhanced by PKA-catalyzed phosphorylation of its C-terminal region S675. Specific phosphorylation near the N terminus triggers ubiquitination and proteasomal degradation. Depletion of HeLa cell brefeldin A-inhibited guanine nucleotide-exchange factors (BIG)1 and/or BIG2 impaired β-catenin S675 phosphorylation and its transcriptional effects, as well as ADP-ribosylation factor activation-enhanced phospholipase D activity and vesicular trafficking, both required for restoration of transcriptional activation by appropriate BIG protein overexpression in depleted cells. We propose that interaction of β-catenin–bound BIG1 with BIG2 and its associated PKA complex, simultaneously or sequentially, are required for phosphorylation of S675, with nuclear entry of activated β-catenin followed by its acceleration of T-cell factor/lymphoid enhancer factor family gene transcription.
NLRC5/MHC class I transactivator is a target for immune evasion in cancer
Authors: Yoshihama Sayuri , Roszik Jason , Downs Isaac , Meissner Torsten B. , Vijayan Saptha , Chapuy Bjoern , Sidiq Tabasum , Shipp Margaret A. , Lizee Gregory A. , Kobayashi Koichi S.
Published: May 2016

Significance

Tumor antigen presentation to CD8+T cells by MHC class I molecules is crucial for immune responses against cancers, whereas the loss of MHC class I is a common immune evasion strategy used by cancers. However, the molecular mechanisms leading to MHC class I deficiency have remained poorly defined. We demonstrate here that MHC class I transactivator (CITA)/NOD-like receptor (NLR) family, caspase recruitment (CARD) domain containing 5 (NLRC5) is a major target for cancer immune evasion. Reduced expression of MHC class I and related genes in cancer is frequently associated with genetic and epigenetic changes inNLRC5. The reducedNLRC5expression is linked to impaired CD8+T-cell activation and poor patient prognosis. These data indicate that CITA/NLRC5 is a novel prognostic marker and potential therapeutic target of cancers.
Silk-based blood stabilization for diagnostics
Authors: Kluge Jonathan A. , Li Adrian B. , Kahn Brooke T. , Michaud Dominique S. , Omenetto Fiorenzo G. , Kaplan David L.
Published: May 2016

Significance

Both research and clinical care often require blood to be collected away from the laboratory setting. Remote collection presents a logistical and financial challenge, as it requires continuous access to portable cold storage. Although there has been a thrust to develop means to bypass the cold chain, available technologies such as dried spots, remain ineffective. Specifically, these methods fail to stabilize labile protein biomarkers against thermal damage. Herein we describe an alternative silk matrix encapsulation technique that overcomes these limitations and can be deployed using a simple air-drying approach. Potential clinical and research applications of this technology are far-reaching, and could ultimately decrease hospital burdens, improve patient compliance to monitoring, and open up new testing options for currently underserved populations.
Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection
Authors: Vvedenskaya Irina O. , Vahedian-Movahed Hanif , Zhang Yuanchao , Taylor Deanne M. , Ebright Richard H. , Nickels Bryce E.
Published: May 2016

Significance

For all cellular RNA polymerases, the position of the transcription start site (TSS) relative to core promoter elements is variable. Furthermore, environmental conditions and regulatory factors that affect TSS selection have profound effects on levels of gene expression. Thus, identifying determinants of TSS selection is important for understanding gene expression control. Here we identify a previously undocumented determinant for TSS selection by
Escherichia coli
RNA polymerase. We show that sequence-specific protein–DNA interactions between RNA polymerase core enzyme and a sequence element in unwound promoter DNA, the core recognition element, modulate TSS selection.
Enhancing protein stability with extended disulfide bonds
Authors: Liu Tao , Wang Yan , Luo Xiaozhou , Li Jack , Reed Sean A. , Xiao Han , Young Travis S. , Schultz Peter G.
Published: May 2016

Significance

This work describes a facile system for incorporating noncanonical amino acids containing long side-chain thiols using an expanded genetic code. These amino acids begin to overcome the distance and geometric constraints of the cysteine disulfide and can pair with cysteines to cross-link more remote sites in proteins. To demonstrate this notion, we constructed a library of random β-lactamase mutants containing these noncanonical amino acids and grew them at nonpermissive temperatures. We identified a mutant enzyme that is cross-linked by one such extended disulfide bond that has significantly enhanced thermal stability. This study suggests that an expanded set of amino acid building blocks can provide novel solutions to evolutionary challenges.
Prevalent presence of periodic actin–spectrin-based membrane skeleton in a broad range of neuronal cell types and animal species
Authors: He Jiang , Zhou Ruobo , Wu Zhuhao , Carrasco Monica A. , Kurshan Peri T. , Farley Jonathan E. , Simon David J. , Wang Guiping , Han Boran , Hao Junjie , Heller Evan , Freeman Marc R. , Shen Kang , Maniatis Tom , Tessier-Lavigne Marc , Zhuang Xiaowei
Published: May 2016

Significance

Actin, spectrin, and associated molecules form a submembrane periodic skeleton structure in neurons. In this study, we demonstrate that this membrane-associated periodic skeleton (MPS) is present in a broad range of neuronal cell types cultured from the central and peripheral nervous systems of rodents. The MPS structure is preferentially formed in axons compared with dendrites and is differentially regulated at the pre- and postsynaptic sites of neurons. Our data also suggest that MPS is conserved across a wide range of invertebrate and vertebrate animal species.
Analysis of reaction schemes using maximum rates of constituent steps
Authors: Motagamwala Ali Hussain , Dumesic James A.
Published: May 2016

Significance

The design of active and selective catalysts is essential for a wide range of industrial applications and societal issues. A fundamental approach is to identify the key elementary steps and to elucidate the predicted reaction kinetics for potential reaction mechanisms. We present a methodology to analyze analytically the performance of catalytic reaction schemes by calculation of the maximum rates of the constituent steps. This proposed methodology can be used to identify the important transition states and adsorbed species, such that more detailed calculations can be carried out for these species, whereas more approximate methods can be used for the remaining species, thereby substantially reducing the computational time required to elucidate how catalyst performance is controlled by the fundamental surface chemistry.
Histone deacetylase inhibition enhances antimicrobial peptide but not inflammatory cytokine expression upon bacterial challenge
Authors: Fischer Natalie , Sechet Emmanuel , Friedman Robin , Amiot Aurélien , Sobhani Iradj , Nigro Giulia , Sansonetti Philippe J. , Sperandio Brice
Published: May 2016

Significance

Antimicrobial peptides exert antimicrobial, antifungal, antiviral, and antiprotozoan activity. They are expressed at high concentrations at the intestinal mucosal surface, where they play a crucial role in intestinal homeostasis. Therefore, approaches aiming to boost expression of antimicrobial peptides represent a future therapeutic strategy to treat infections and dysbiosis-driven diseases in humans at a time of increasing incidence of antibiotic resistance.
SIM.EM-K3 Key comparison of 10 mH inductance standards at 1 kHz
Authors: Moreno J A , Côté M , Koffman A , Castro B I , Vasconcellos R de Barros e , Kyriazis G , Cazabat M , Izquierdo D , Faverio C , Slomovitz D
Published: May 2016

A key comparison of 10 mH inductance standards at 1 kHz has been carried out with the participation of seven National Metrology Institutes of the Inter-American Metrology System, within the frame of the International Committee for Weights and Measures Mutual Recognition Arrangement (MRA), which was piloted by CENAM, Mexico. Three previously characterized commercial inductors, contained in individual enclosures with controlled temperature were used as traveling standards. This document presents the results and technical details of the comparison.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
EURAMET.M.P-S9: comparison in the negative gauge pressure range −950 to 0 hPa
Authors: Saxholm S , Otal P , AltintaS A , Bermanec L G , Durgut Y , Hanrahan R , Kocas I , Lefkopoulos A , Pražák D , Sandu I , Åetina J , Spohr I , Steindl D , Tammik K , Testa N
Published: May 2016

A comparison in the negative gauge pressure range was arranged in the period 2011 - 2012. A total of 14 laboratories participated in this comparison: BEV (Austria), CMI (Czech Republic), DANIAmet-FORCE (Denmark), EIM (Greece), HMI/FSB-LPM (Croatia), INM (Romania), IPQ (Portugal), LNE (France), MCCAA (Malta), METROSERT (Estonia), MIKES (Finland), MIRS/IMT/LMT (Slovenia), NSAI (Ireland) and UME (Turkey). The project was divided into two loops: Loop1, piloted by MIKES, and Loop2, piloted by LNE. The results of the two loops are reported separately: Loop1 results are presented in this paper.

The transfer standard was Beamex MC5 no. 25516865 with internal pressure module INT1C, resolution 0.01 hPa. The nominal pressure range of the INT1C is −1000 hPa to +1000 hPa. The nominal pressure points for the comparison were 0 hPa, −200 hPa, −400 hPa, −600 hPa, −800 hPa and −950 hPa.

The reference values and their uncertainties as well as the difference uncertainty between the laboratory results and the reference values were determined from the measurement data by Monte Carlo simulations. Stability uncertainty of the transfer standard was included in the final difference uncertainty. Degrees of equivalences and mutual equivalences between the laboratories were calculated.

Each laboratory reported results for all twelve measurement points, which means that there were 168 reported values in total. Some 163 of the 168 values (97 %) agree with the reference values within the expanded uncertainties, with a coverage factor k = 2. Among the laboratories, four different methods were used to determine negative gauge pressure.

It is concluded that special attention must be paid to the measurements and methods when measuring negative gauge pressures. There might be a need for a technical guide or a workshop that provides information about details and practices related to the measurements of negative gauge pressure, as well as differences between the different methods.

The comparison is registered as EURAMET project no. 1170 and as a supplementary comparison EURAMET.M.P-S9 in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Determination of the magnetic susceptibility and the magentic polarization of weights by means of the susceptometer method
Authors: Quiroga A , Bermudez A , Kornblit F , Garcia F , Fang H , Caceres J , Peña L M , Ramos O , Viaggio A , Santo C
Published: May 2016

This report summarizes the results of a SIM comparison of magentic properties by means of the susceptometer method. It was carried out by seven SIM laboraories and BIPM. Five standards have been circulated: two OIML weights class E2, two of them with nominal value 1 kg and two of them with nominal value 2 g, and a steel disk. Most of the results were consistent with each other. This final report shows the degree of equivalence achieved by the participants

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Evaluation of hybrid and non-hybrid methods for
de novo
assembly of nanopore reads
Authors: Sović Ivan , Križanović Krešimir , Skala Karolj , Šikić Mile
Published: May 2016

Motivation : Recent emergence of nanopore sequencing technology set a challenge for established assembly methods. In this work, we assessed how existing hybrid and non-hybrid de novo assembly methods perform on long and error prone nanopore reads.

Results : We benchmarked five non-hybrid (in terms of both error correction and scaffolding) assembly pipelines as well as two hybrid assemblers which use third generation sequencing data to scaffold Illumina assemblies. Tests were performed on several publicly available MinION and Illumina datasets of Escherichia coli K-12, using several sequencing coverages of nanopore data (20×, 30×, 40× and 50×). We attempted to assess the assembly quality at each of these coverages, in order to estimate the requirements for closed bacterial genome assembly. For the purpose of the benchmark, an extensible genome assembly benchmarking framework was developed. Results show that hybrid methods are highly dependent on the quality of NGS data, but much less on the quality and coverage of nanopore data and perform relatively well on lower nanopore coverages. All non-hybrid methods correctly assemble the E. coli genome when coverage is above 40×, even the non-hybrid method tailored for Pacific Biosciences reads. While it requires higher coverage compared to a method designed particularly for nanopore reads, its running time is significantly lower.

Availability and Implementation:  https://github.com/kkrizanovic/NanoMark

Contact:  mile.sikic@fer.hr

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Missing Tooth: A Curious Case of Postobstructive Pneumonia
Authors: Holmes Ian , Gajurel Kiran , Montoya Jose
Published: May 2016

Foreign body aspirations that are not recognized at the time of aspiration can lead to insidious symptoms that can present a diagnostic challenge. We report the case of a 70-year-old man presenting with postobstructive pneumonia 2 months after aspirating his own tooth during a meal. He had been mistakenly diagnosed with asthma and treated with bronchodilators before a computed tomography scan of the thorax revealed the impacted tooth in his left bronchus. We review the clinical features and microbiology of postobstructive pneumonia and discuss the rationale of its treatment.
Bacterial strategies of resistance to antimicrobial peptides
Authors: Joo Hwang-Soo , Fu Chih-Iung , Otto Michael
Published: May 2016

Antimicrobial peptides (AMPs) are a key component of the host's innate immune system, targeting invasive and colonizing bacteria. For successful survival and colonization of the host, bacteria have a series of mechanisms to interfere with AMP activity, and AMP resistance is intimately connected with the virulence potential of bacterial pathogens. In particular, because AMPs are considered as potential novel antimicrobial drugs, it is vital to understand bacterial AMP resistance mechanisms. This review gives a comparative overview of Gram-positive and Gram-negative bacterial strategies of resistance to various AMPs, such as repulsion or sequestration by bacterial surface structures, alteration of membrane charge or fluidity, degradation and removal by efflux pumps.

This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
Antimicrobial peptides and cell processes tracking endosymbiont dynamics
Authors: Masson Florent , Zaidman-Rémy Anna , Heddi Abdelaziz
Published: May 2016

Many insects sustain long-term relationships with intracellular symbiotic bacteria that provide them with essential nutrients. Such endosymbiotic relationships likely emerged from ancestral infections of the host by free-living bacteria, the genomes of which experience drastic gene losses and rearrangements during the host–symbiont coevolution. While it is well documented that endosymbiont genome shrinkage results in the loss of bacterial virulence genes, whether and how the host immune system evolves towards the tolerance and control of bacterial partners remains elusive. Remarkably, many insects rely on a ‘compartmentalization strategy’ that consists in secluding endosymbionts within specialized host cells, the bacteriocytes, thus preventing direct symbiont contact with the host systemic immune system. In this review, we compile recent advances in the understanding of the bacteriocyte immune and cellular regulators involved in endosymbiont maintenance and control. We focus on the cereal weevils
Sitophilus
spp., in which bacteriocytes form bacteriome organs that strikingly evolve in structure and number according to insect development and physiological needs. We discuss how weevils track endosymbiont dynamics through at least two mechanisms: (i) a bacteriome local antimicrobial peptide synthesis that regulates endosymbiont cell cytokinesis and helps to maintain a homeostatic state within bacteriocytes and (ii) some cellular processes such as apoptosis and autophagy which adjust endosymbiont load to the host developmental requirements, hence ensuring a fine-tuned integration of symbiosis costs and benefits.

This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
Antimicrobial peptides in marine invertebrate health and disease
Authors: Destoumieux-Garzón Delphine , Rosa Rafael Diego , Schmitt Paulina , Barreto Cairé , Vidal-Dupiol Jeremie , Mitta Guillaume , Gueguen Yannick , Bachère Evelyne
Published: May 2016

Aquaculture contributes more than one-third of the animal protein from marine sources worldwide. A significant proportion of aquaculture products are derived from marine protostomes that are commonly referred to as ‘marine invertebrates’. Among them, penaeid shrimp (Ecdysozosoa, Arthropoda) and bivalve molluscs (Lophotrochozoa, Mollusca) are economically important. Mass rearing of arthropods and molluscs causes problems with pathogens in aquatic ecosystems that are exploited by humans. Remarkably, species of corals (Cnidaria) living in non-exploited ecosystems also suffer from devastating infectious diseases that display intriguing similarities with those affecting farmed animals. Infectious diseases affecting wild and farmed animals that are present in marine environments are predicted to increase in the future. This paper summarizes the role of the main pathogens and their interaction with host immunity, with a specific focus on antimicrobial peptides (AMPs) and pathogen resistance against AMPs. We provide a detailed review of penaeid shrimp AMPs and their role at the interface between the host and its resident/pathogenic microbiota. We also briefly describe the relevance of marine invertebrate AMPs in an applied context.

This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
Towards a paradigm shift in innate immunity—seminal work by Hans G. Boman and co-workers
Authors: Faye Ingrid , Lindberg Bo G.
Published: May 2016

Four decades ago, immunological research was dominated by the field of lymphoid biology. It was commonly accepted that multicellular eukaryotes defend themselves through phagocytosis. The lack of lymphoid cells in insects and other simpler animals, however, led to the common notion that they might simply lack the capacity defend themselves with humoral factors. This view was challenged by microbiologist Hans G. Boman and co-workers in a series of publications that led to the advent of antimicrobial peptides as a universal arm of the immune system. Besides ingenious research, Boman ignited his work by posing the right questions. He started off by asking himself a simple question: ‘Antibodies take weeks to produce while many microbes divide hourly; so how come we stay healthy?’. This led to two key findings in the field: the discovery of an inducible and highly potent antimicrobial immune response in
Drosophila
in 1972, followed by the characterization of cecropin in 1981. Despite broadly being considered an insect-specific response at first, the work of Boman and co-workers eventually created a bandwagon effect that unravelled various aspects of innate immunity.

This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.
Odd-paired controls frequency doubling inDrosophilasegmentation by altering the pair-rule gene regulatory network
Authors: Clark Erik , Akam Michael
Published: May 2016

TheDrosophilaembryo transiently exhibits a double segment periodicity, defined by the expression of seven “pair-rule” genes, each in a pattern of seven stripes. At gastrulation, interactions between the pair-rule genes lead to frequency doubling and the patterning of fourteen parasegment boundaries. In contrast to earlier stages ofDrosophilaanteroposterior patterning, this transition is not well understood. By carefully analysing the spatiotemporal dynamics of pair-rule gene expression, we demonstrate that frequency-doubling is precipitated by multiple coordinated changes to the network of regulatory interactions between the pair-rule genes. We identify the broadly expressed but temporally patterned transcription factor, Odd-paired (Opa/Zic), as the cause of these changes, and show that the patterning of the even-numbered parasegment boundaries relies on Opa-dependent regulatory interactions. Our findings indicate that the pair-rule gene regulatory network has a temporally-modulated topology, permitting the pair-rule genes to play stage-specific patterning roles.
The interaction of PRC2 with RNA or chromatin is mutually antagonistic
Authors: Beltran Manuel , Yates Christopher M. , Skalska Lenka , Dawson Marcus , Reis Filipa P. , Viiri Keijo , Fisher Cynthia L. , Sibley Christopher R. , Foster Benjamin M. , Bartke Till , Ule Jernej , Jenner Richard G.
Published: May 2016

Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon–intron boundaries and the 3′ UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, the release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome.
Trisodium citrate, Na3(C6H5O7)
Authors: Rammohan Alagappa , Kaduk James A.
Published: May 2016

The crystal structure of anhydrous trisodium citrate, Na3(C6H5O7), has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory (DFT). There are two independent five-coordinate Na+and one six-coordinate Na+cations in the asymmetric unit. The [NaO5] and [NaO6] polyhedra share edges and corners to form a three-dimensional framework. There are channels parallel to theaandbaxes in which the remainder of the citrate anions reside. The only hydrogen bonds are an intramolecular one between the hydroxy group and one of the terminal carboxylate O atoms and an intermolecular one between a methylene group and the hydroxyl O atom.
The nature of memorisation for embodiment
Authors: Hardaker Glenn , Sabki Aishah
Published: May 2016

Purpose

The purpose of this paper is to provide insights on the interconnectedness of the Muslim community, madrasah and memorisation in realising the process of embodiment.

Design/methodology/approach

Our anthropological study was conducted in 2011 at a prominent madrasah for higher education in England. The madrasah has approximately 400 adult learners that are studying Islamic studies programme. For our anthropological study, the notion of Islamic teaching and embodiment was integral to each other and was illustrative of a long educational tradition of the pedagogy of Islam. For this research, we follow a sensory narrative style in expressing our descriptions.

Findings

The findings provide an insight into the nature of memorisation for embodiment. The research suggests that the madrasah was teaching memorisation with a purpose to support the process of personal embodiment. Moreover, what we also see when considering madrasah life is that the notion of the “walking Qur’an” endures, and it transcends in the form of locally flavoured articulations of embodiment. To reiterate, the Islamic approach to memorisation for embodiment was found to be a practice relevant to all of us, as individuals, communities and institutions, reflexively engaging in the world around us. For the British madrasah, this was seen to be pivotal to the Islamic pedagogy shaped by the interplay between orality, facilitating memorisation and the didactic approach towards the sacred. From our observations, embodiment has a physical and spiritual dimension where prophecy is retained and is inherent to existence and daily madrasah practice.

Originality/value

Our narrative experiences bring a spiritual order to the pedagogical matters of memorisation represented by the inseparable nature of knowledge and the sacred. The interweaving of experiential narrative with a theoretical perspective brings forth our understanding towards the nature of memorisation for embodiment.