bluuebunny/crossref_metadata_2025 huggingface dataset:
Bioinspired morphing wings for extended flight envelope and roll control of small drones
Authors: Di Luca M. , Mintchev S. , Heitz G. , Noca F. , Floreano D.
Published: December 2016

Small-winged drones can face highly varied aerodynamic requirements, such as high manoeuvrability for flight among obstacles and high wind resistance for constant ground speed against strong headwinds that cannot all be optimally addressed by a single aerodynamic profile. Several bird species solve this problem by changing the shape of their wings to adapt to the different aerodynamic requirements. Here, we describe a novel morphing wing design composed of artificial feathers that can rapidly modify its geometry to fulfil different aerodynamic requirements. We show that a fully deployed configuration enhances manoeuvrability while a folded configuration offers low drag at high speeds and is beneficial in strong headwinds. We also show that asymmetric folding of the wings can be used for roll control of the drone. The aerodynamic performance of the morphing wing is characterized in simulations, in wind tunnel measurements and validated in outdoor flights with a small drone.
Coevolving advances in animal flight and aerial robotics
Authors: Lentink David
Published: December 2016

Our understanding of animal flight has inspired the design of new aerial robots with more effective flight capacities through the process of biomimetics and bioinspiration. The aerodynamic origin of the elevated performance of flying animals remains, however, poorly understood. In this themed issue, animal flight research and aerial robot development coalesce to offer a broader perspective on the current advances and future directions in these coevolving fields of research. Together, four reviews summarize and 14 reports contribute to our understanding of low Reynolds number flight. This area of applied aerodynamics research is challenging to dissect due to the complicated flow phenomena that include laminar–turbulent flow transition, laminar separation bubbles, delayed stall and nonlinear vortex dynamics. Our mechanistic understanding of low Reynolds number flight has perhaps been advanced most by the development of dynamically scaled robot models and new specialized wind tunnel facilities: in particular, the tiltable Lund flight tunnel for animal migration research and the recently developed AFAR hypobaric wind tunnel for high-altitude animal flight studies. These world-class facilities are now complemented with a specialized low Reynolds number wind tunnel for studying the effect of turbulence on animal and robot flight in much greater detail than previously possible. This is particular timely, because the study of flight in extremely laminar versus turbulent flow opens a new frontier in our understanding of animal flight. Advancing this new area will offer inspiration for developing more efficient high-altitude aerial robots and removes roadblocks for aerial robots operating in turbulent urban environments.
Mathematical constraints onFST: biallelic markers in arbitrarily many populations
Authors: Alcala Nicolas , Rosenberg Noah A
Published: December 2016

FSTis one of the most widely used statistics in population genetics. Recent mathematical studies have identified constraints onFSTthat challenge interpretations ofFSTas a measure with potential to range from 0 for genetically similar populations to 1 for divergent populations. We generalize results obtained for population pairs to arbitrarily many populations, characterizing the mathematical relationship betweenFST, the frequencyMof the more frequent allele at a polymorphic biallelic marker, and the number of subpopulationsK. We show that for fixedK,FSThas a peculiar constraint as a function ofM, with a maximum of 1 only ifM=i/Kfor integersiwith ⌈K/2⌉ ≤i≤K− 1. For fixedM, asKgrows large, the range ofFSTbecomes the full closed or half-open unit interval. For fixedK, however, someM< (K− 1)/Kalways exists at which the upper bound onFSTis constrained to be below. In each of three migration models—island, rectangular stepping-stone, and linear stepping-stone—we use coalescent simulations to show that under weak migration,FSTdepends strongly on the allele frequencyMwhenKis small, but not whenKis large. Finally, using data on human genetic variation, we employ our results to explain the generally smallerFSTvalues between pairs of continents relative to globalFSTvalues. We discuss implications for the interpretation and use ofFST.
The Bayesian-Laplacian Brain
Authors: Zeki Semir , Chén Oliver Y.
Published: December 2016

We outline what we believe could be an improvement in future discussions of the brain acting as a Bayesian-Laplacian system. We do so by distinguishing between two broad classes of priors on which the brain’s inferential systems operate: in one category are biological priors (β priors) and in the other artifactual ones (α priors). We argue thatβ priors, of which colour categories and faces are good examples, are inherited or acquired very rapidly after birth, are highly or relatively resistant to change through experience, and are common to all humans. The consequence is that the probability of posteriors generated fromβ priorshaving universal assent and agreement is high. By contrast, αpriors, of which man-made objects are examples, are acquired post-natally and modified at various stages throughout post-natal life; they are much more accommodating of, and hospitable to, new experiences. Consequently, posteriors generated from them are less likely to find universal assent. Taken together, in addition to the more limited capacity of experiment and experience to alter theβ priorscompared toα priors, another cardinal distinction between the two is that the probability of posteriors generated fromβ priorshaving universal agreement is greater than that forα priors. The two categories are not, however, always totally distinct and can merge into one another to varying extents, resulting in posteriors that draw upon both categories.
De novoIdentification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
Authors: Stoiber Marcus , Quick Joshua , Egan Rob , Eun Lee Ji , Celniker Susan , Neely Robert K. , Loman Nicholas , Pennacchio Len A , Brown James
Published: December 2016

Advances in nanopore sequencing technology have enabled investigation of the full catalogue of covalent DNA modifications. We present the first algorithm for the identification of modified nucleotides without the need for prior training data along with the open source software implementation,nanoraw.Nanorawaccurately assigns contiguous raw nanopore signal to genomic positions, enabling novel data visualization, and increasing power and accuracy for the discovery of covalently modified bases in native DNA. Ground truth case studies utilizing synthetically methylated DNA show the capacity to identify three distinct methylation marks, 4mC, 5mC, and 6mA, in seven distinct sequence contexts without any changes to the algorithm. We demonstrate quantitative reproducibility simultaneously identifying 5mC and 6mA in native E. coli across biological replicates processed in different labs. Finally we propose a pipeline for the comprehensive discovery of DNA modifications in any genome withouta prioriknowledge of their chemical identities.
Memory trace reactivation and behavioral response during retrieval are differentially modulated by amygdalar glutamate receptors activity: interaction between amygdala and insular cortex
Authors: Osorio-Gómez Daniel , Guzmán-Ramos Kioko , Bermúdez-Rattoni Federico
Published: December 2016

The insular cortex (IC) is required for conditioned taste aversion (CTA) retrieval. However, it remains unknown which cortical neurotransmitters levels are modified upon CTA retrieval. Using in vivo microdialysis, we observed that there were clear elevations in extracellular glutamate, norepinephrine, and dopamine in and around the center of the gustatory zone of the IC during CTA retrieval. Additionally, it has been reported that the amygdala–IC interaction is highly involved in CTA memory establishment. Therefore, we evaluated the effects of infusions of an AMPA receptor antagonist (CNQX) and a NMDA receptor antagonist (APV) into the amygdala on CTA retrieval and IC neurotransmitter levels. Infusion of APV into the amygdala impaired glutamate augmentation within the IC, whereas dopamine and norepinephrine levels augmentation persisted and a reliable CTA expression was observed. Conversely, CNQX infusion into the amygdala impaired the aversion response, as well as norepinephrine and dopamine augmentations in the IC. Interestingly, CNQX infusion did not affect glutamate elevation in the IC. To evaluate the functional meaning of neurotransmitters elevations within the IC on CTA response, we infused specific antagonists for the AMPA, NMDA, D1, and β-adrenergic receptor before retrieval. Results showed that activation of AMPA, D1, and β-adrenergic receptors is necessary for CTA expression, whereas NMDA receptors are not involved in the aversion response.
Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography
Authors: Coughlan H. D. , Darmanin C. , Kirkwood H. J. , Phillips N. W. , Hoxley D. , Clark J. N. , Vine D. J. , Hofmann F. , Harder R. J. , Maxey E. , Abbey B.
Published: December 2016

The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed.
Crystal structure of 1-[2-(4-chlorophenyl)-4,5-diphenyl-1H-imidazol-1-yl]propan-2-ol
Authors: Mohamed Shaaban K. , Marzouk Adel A. , Albayati Mustafa R. , Abdelhamid Antar A. , Simpson Jim
Published: December 2016

The title compound, C24H21ClN2O, crystallizes with two unique molecules in the asymmetric unit. In each molecule, the central imidazole ring is substituted at the 2-, 4- and 5-positions by benzene rings. The 2-substituted ring carries a Cl atom at the 4-position. One of the imidazole N atoms in each molecule has a propan-2-ol substituent. In the crystal, a series of O—H...N, C—H...O and C—H...Cl hydrogen bonds, augmented by several C—H...π(ring) interactions, generate a three-dimensional network of molecules stacked along thea-axis direction.
Synthesis and crystal structure ofN-(4-chlorophenyl)-5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidin-2-amine
Authors: Repich Hlib , Orysyk Svitlana , Savytskyi Pavlo , Pekhnyo Vasyl
Published: December 2016

The title compound, C13H12ClN5, was synthesized by the cyclization of 1-(4,6-dimethylpyrimidin-2-yl)-4-phenylthiosemicarbazide in the presence of Ni(NO3)2. The molecular structure of the compound is essentially planar. In the crystal, molecules form dimersviapairs of N—H...N hydrogen bonds between the H atom of the exocyclic amino group and the N atom at the 4-position of the triazole ring. The resulting dimers are packed into layers which are connected by π-stacking interactions between the aromatic systems of the pyrimidine and benzene nuclei, and between the triazole cores.
2,3,5,6-Tetrakis{[(pyridin-2-yl)sulfanyl]methyl}pyrazine
Authors: Assoumatine Tokouré , Stoeckli-Evans Helen
Published: December 2016

The title compound, C28H24N6S4, synthesized by the reaction of 2,3,5,6-tetrakis(bromomethyl)pyrazine with 2-mercaptopyridine, crystallizes with one half-molecule in the asymmetric unit. The whole molecule is generated by inversion symmetry, the centre of the pyrazine ring being located about an inversion centre. The pyridine rings of the unique (pyridin-2-ylsulfanyl)methyl substituents are inclined to the pyrazine ring by 38.7 (3) and 75.6 (2)°, and by 66.0 (3)° to one another. In the crystal, molecules are linkedviaC—H...π interactions, forming chains along theb-axis direction. The chains are linked by offset π–π interactions [intercentroid distance = 3.682 (3) Å], forming layers lying parallel to thebcplane.
1-Benzyl-4-phenyl-1H-1,5-benzodiazepin-2(3H)-one
Authors: Essaghouani Abdelhanine , Boulhaoua Mohammed , Lahmidi Sanae , El Hafi Mohamed , Essassi El Mokhtar , Mague Joel T.
Published: December 2016

In the title molecule, C22H18N2O, the seven-membered ring adopts a boat conformation with the planes of the pendant phenyl rings nearly perpendicular to the plane of the aromatic portion of the benzodiazepine core. Pairwise C—H...π(ring) interactions form inversion dimers which pack in zigzag layers associated through weak C—H...O hydrogen bonds.
Cellular manufacturing system selection with multi-lean measures using optimization and simulation
Authors: Bocanegra-Herrera Claudia Cristina , Orejuela-Cabrera Juan Pablo
Published: December 2016

The cellular manufacturing technique is widely used in many industries. This research proposes an alternative to design and balance a cellular manufacturing system of an assembly company, with the purpose to obtain an optimal configuration under different criteria such as Process, Total Cost, Idle Time and Reliability. The methodology consists in: I) To obtain candidate solutions using optimization models where the objectives are to minimize Cycle Time and Total Cost II) To find the performance measures of each candidate solution using discrete-event simulation III) To choose the optimal configuration using the multi-criteria decision analysis ANP. The best configuration was found to have the bottleneck in the starting, a smoothness index in 0, the highest Reliability and Idle Time of 0%, although it was not the solution with the lower cost.
Localized defect states and charge trapping in atomic layer deposited-Al2O3 films
Authors: Henkel Karsten , Kot Malgorzata , Schmeißer Dieter
Published: December 2016

In this study, the authors compared different Al2O3 films grown by atomic layer deposition (ALD) with the same aluminum precursor but on different substrates. The authors employed different process parameters such as thermal-ALD and plasma-enhanced-ALD using different substrate temperatures ranging from 280 °C down to room temperature. They characterized these films by resonant photoelectron spectroscopy and by electrical measurements. They established that generally the ALD-Al2O3 films show characteristic features of bulk Al2O3. For all films investigated, the authors found intrinsic defect states within the electronic band gap and identified excitonic, polaronic, and charge-transfer defect states. The authors gave an atomistic model to explain these intrinsic defects and found that their relative abundance is subject of the choice of ALD parameters and of the substrate used. They were able to relate the spectroscopic assigned in-gap defect states with the electronic charges as determined in our electrical measurements.
Ambient noise correlations on a mobile, deformable array
Authors: Naughton Perry , Roux Philippe , Yeakle Riley , Schurgers Curt , Kastner Ryan , Jaffe Jules S. , Roberts Paul L. D.
Published: December 2016

This paper presents a demonstration of ambient acoustic noise processing on a set of free floating oceanic receivers whose relative positions vary with time. It is shown that it is possible to retrieve information that is relevant to the travel time between the receivers. With thousands of short time cross-correlations (10 s) of varying distance, it is shown that on average, the decrease in amplitude of the noise correlation function with increased separation follows a power law. This suggests that there may be amplitude information that is embedded in the noise correlation function. An incoherent beamformer is developed, which shows that it is possible to determine a source direction using an array with moving elements and large element separation. This incoherent beamformer is used to verify cases when the distribution of noise sources in the ocean allows one to recover travel time information between pairs of mobile receivers.
Effects of spectral smearing on performance of the spectral ripple and spectro-temporal ripple tests
Authors: Narne Vijaya Kumar , Sharma Mridula , Van Dun Bram , Bansal Shalini , Prabhu Latika , Moore Brian C. J.
Published: December 2016

The main aim of this study was to use spectral smearing to evaluate the efficacy of a spectral ripple test (SRt) using stationary sounds and a recent variant with gliding ripples called the spectro-temporal ripple test (STRt) in measuring reduced spectral resolution. In experiment 1 the highest detectable ripple density was measured using four amounts of spectral smearing (unsmeared, mild, moderate, and severe). The thresholds worsened with increasing smearing and were similar for the SRt and the STRt across the three conditions with smearing. For unsmeared stimuli, thresholds were significantly higher (better) for the STRt than for the SRt. An amplitude fluctuation at the outputs of simulated (gammatone) auditory filters centered above 6400 Hz was identified as providing a potential detection cue for the STRt stimuli. Experiment 2 used notched noise with energy below and above the passband of the SRt and STRt stimuli to reduce confounding cues in the STRt. Thresholds were almost identical for the STRt and SRt for both unsmeared and smeared stimuli, indicating that the confounding cue for the STRt was eliminated by the notched noise. Thresholds obtained with notched noise present could be predicted reasonably accurately using an excitation-pattern model.
Talker variability effects on vocal emotion recognition in acoustic and simulated electric hearing
Authors: Luo Xin
Published: December 2016

Vocal emotion production varies across talkers. Effects of talker variability (i.e., same talker vs different talkers across trials) on vocal emotion recognition were tested in babble noise and with cochlear implant (CI) simulations in normal-hearing listeners. Results showed significant talker variability effects in noise but not with CI simulations, suggesting that the degree of talker variability effects on vocal emotion recognition may vary with listeners' weighting of acoustic cues for emotions (e.g., pitch and duration) and the availability of these cues in different listening conditions. Vocal emotion recognition significantly improved with higher signal-to-noise ratio and more vocoder channels.
Extensive water ice within Ceres’ aqueously altered regolith: Evidence from nuclear spectroscopy
Authors: Prettyman T. H. , Yamashita N. , Toplis M. J. , McSween H. Y. , Schörghofer N. , Marchi S. , Feldman W. C. , Castillo-Rogez J. , Forni O. , Lawrence D. J. , Ammannito E. , Ehlmann B. L. , Sizemore H. G. , Joy S. P. , Polanskey C. A. , Rayman M. D. , Raymond C. A. , Russell C. T.
Published: December 2016

Water ice beneath the surface of Ceres

The dwarf planet Ceres in the inner solar system is thought to have a crust made of a mixture of rock and ice. Prettyman
et al.
used neutron and gamma-ray spectroscopy from the Dawn spacecraft to peer below Ceres' surface and map the subsurface composition. They found evidence for water ice across the dwarf planet, with water making up a larger fraction of the material near the poles than around the equator. Together with their measurements of other elements, these results aid our understanding of Ceres' composition and constrain models of its formation.

Science
, this issue p.
55
Use of the Bacillus subtilis subtilisin signal peptide for efficient secretion of TEM beta-lactamase during growth
Authors: Wong S L , Kawamura F , Doi R H
Published: December 2016

We report the development of an efficient Bacillus subtilis secretory system, with the secreted product stably maintained in the medium for 100 h. The system is based on characterization of the subtilisin signal peptidase cleavage site and promoters, catabolite repression of sporulation, presence of a vegetative secreting mechanism, and availability of a protease-deficient strain.
Expression of the bacteriophage T4 denV structural gene in Escherichia coli
Authors: Recinos A , Augustine M L , Higgins K M , Lloyd R S
Published: December 2016

The expression of the T4 denV gene, which previously had been cloned in plasmid constructs downstream of the bacteriophage lambda hybrid promoter-operator oLpR, was analyzed under a variety of growth parameters. Expression of the denV gene product, endonuclease V, was confirmed in DNA repair-deficient Escherichia coli (uvrA recA) by Western blot analyses and by enhancements of resistance to UV irradiation.
Cloning and nucleotide sequence of the Bacillus megaterium gene coding for small, acid-soluble spore protein B
Authors: Hackett R H , Setlow B , Setlow P
Published: December 2016

The Bacillus megaterium gene coding for small, acid-soluble spore protein (SASP) B was cloned and its nucleotide sequence was determined. The amino acid sequence predicted from the DNA sequence was identical to that determined previously for SASP B, with the exception of the amino-terminal methionine predicted from the gene sequence which is presumably removed posttranslationally and an asparagine residue predicted at position 21 which was originally identified as an aspartate residue. The mRNA encoded by the SASP B gene is synthesized for only a discrete period midway in sporulation, in parallel with mRNAs coding for other SASPs. The small size of the SASP B mRNA (365 nucleotides) indicated that the mRNA is monocistronic. The SASP B gene itself hybridized strongly to only one band in Southern blots of restriction enzyme digests of B. megaterium DNA, suggesting that the SASP B gene is not a member of a highly conserved multigene family, as is the case for other SASP genes.
Primary and secondary chloride transport in Halobacterium halobium
Authors: Duschl A , Wagner G
Published: December 2016

Chloride uptake in intact cells of Halobacterium halobium was characterized by rates of influx and efflux of 36Cl- under conditions of light, respiration, or both. Halobacterial mutant strains with and without retinal transport proteins allowed study of the effects of halorhodopsin and bacteriorhodopsin under illumination. Two structurally independent chloride transport systems could be distinguished: halorhodopsin, the already known light-driven chloride pump, and a newly described secondary uptake system, which was energized by respiration or by light via bacteriorhodopsin.
Poly-beta-hydroxybutyrate membrane structure and its relationship to genetic transformability in Escherichia coli
Authors: Reusch R N , Hiske T W , Sadoff H L
Published: December 2016

The effects of competence-inducing treatments on the composition and organization of membrane lipids in Escherichia coli K-12, DH1, DH5, HB101, and RR1 were investigated for two widely used protocols in which transformability is developed at low temperatures in Ca2+ buffers. At stages during each procedure, the lipid compositions of the cells were determined, and the thermotropic lipid phase transitions were observed in whole cell culture by fluorescence assay with the hydrophobic probe N-phenyl-1-naphthylamine. Competence was evaluated by determining transformation efficiencies with plasmid pBR322 DNA. The competence-inducing procedures effected only slight changes in phospholipid compositions which did not correlate with transformability. However, the induction of competence was coincident with de novo synthesis and incorporation of poly-beta-hydroxybutyrate into the cytoplasmic membranes and with the appearance of a sharp lipid phase transition above physiological temperatures. Transformation efficiencies correlated with poly-beta-hydroxybutyrate concentrations and with the intensity of the new phase transition. Transformability, poly-beta-hydroxybutyrate synthesis and the new phase transition were not significantly affected by inhibition of protein synthesis with chloramphenicol or inhibition of respiration or ATP synthesis with azide, cyanide, arsenate, or 2,4-dinitrophenol; however, when poly-beta-hydroxybutyrate synthesis was inhibited with acetaldehyde, the new phase transition was not observed, and competence failed to develop. These studies suggest that genetic transformability in E. coli may be physiologically regulated.
Evidence against direct involvement of cyclic GMP or cyclic AMP in bacterial chemotactic signaling
Authors: Tribhuwan R C , Johnson M S , Taylor B L
Published: December 2016

Defects in phosphotransferase chemotaxis in cya and cpd mutants previously cited as evidence of a cyclic GMP or cyclic AMP intermediate in signal transduction were not reproduced in a study of chemotaxis in Escherichia coli and Salmonella typhimurium. In cya mutants, which lack adenylate cyclase, the addition of cyclic AMP was required for synthesis of proteins that were necessary for phosphotransferase transport and chemotaxis. However, the induced cells retained normal phosphotransferase chemotaxis after cyclic AMP was removed. Phosphotransferase chemotaxis was normal in a cpd mutant of S. typhimurium that has elevated levels of cyclic GMP and cyclic AMP. S. typhimurium crr mutants are deficient in enzyme III glucose, which is a component of the glucose transport system, and a regulator of adenylate cyclase. After preincubation with cyclic AMP, the crr mutants were deficient in enzyme II glucose-mediated transport and chemotaxis, but other chemotactic responses were normal. It is concluded that cyclic GMP does not determine the frequency of tumbling and is probably not a component of the transduction pathway. The only known role of cyclic AMP is in the synthesis of some proteins that are subject to catabolite repression.
Effect of glutamine on growth and heterocyst differentiation in the cyanobacterium Anabaena variabilis
Authors: Thiel T , Leone M
Published: December 2016

Mutants of the cyanobacterium Anabaena variabilis that were capable of increased uptake of glutamine, as compared with that in the parental strains, were isolated. Growth of these mutants and their parental strains was measured in media containing N2, ammonia, or glutamine as a source of nitrogen. All strains grew well with any one of these sources of fixed nitrogen. Much of the glutamine taken up by the cells was converted to glutamate. The concentrations of glutamine, glutamate, arginine, ornithine, and citrulline in free amino acid pools in glutamine-grown cells were high compared with the concentrations of these amino acids in ammonia-grown or N2-grown cells. All strains capable of heterocyst differentiation, including a strain which produced nonfunctional heterocysts, grew and formed heterocysts in the presence of glutamine. However, nitrogenase activity was repressed in glutamine-grown cells. Glutamine may not be the molecule directly responsible for repression of the differentiation of heterocysts.
Binding specificity of the periplasmic oligopeptide-binding protein from Escherichia coli
Authors: Guyer C A , Morgan D G , Staros J V
Published: December 2016

The structural properties required for the binding of peptide substrates to the Escherichia coli periplasmic protein involved in oligopeptide transport were surveyed by measuring the ability of different peptides to compete for binding in an equilibrium dialysis assay with the tripeptide Ala-Phe-[3H]Gly. The protein specifically bound oligopeptides and failed to bind amino acids or dipeptides. Acetylation of the peptide amino terminus of (Ala)3 severely impaired binding, whereas esterification of the carboxyl terminus significantly reduced but did not completely eliminate binding. Peptides composed of L-amino acids competed more effectively than did peptides containing D-residues or glycine. Experiments with a series of alanyl peptide homologs demonstrated a decrease in competitive ability with increasing chain length beyond tripeptide. Competition studies with tripeptide homologs indicated that a wide variety of amino acyl side chains were tolerated by the periplasmic protein, but side-chain composition did affect binding. Fluorescence emission data suggested that this periplasmic protein possesses more than one substrate-binding site capable of distinguishing peptides on the basis of amino acyl side chains.
Transport of gamma-butyrobetaine in an Agrobacterium species isolated from soil
Authors: Nobile S , Deshusses J
Published: December 2016

An Agrobacterium sp. isolated from soil by selective growth on gamma-butyrobetaine (gamma-trimethylaminobutyrate) as the sole source of both carbon and nitrogen has been shown to possess an inducible transport system for this growth substrate. This transport system has a Kt of 0.5 microM and a maximal velocity of 3.8 nmol/min per mg (dry weight). The influx of gamma-butyrobetaine is optimal at pH 8.5 and operates against a concentration gradient. The transport system shows a high specificity for trimethylamine carboxylic acid molecules of defined chain length. gamma-Butyrobetaine uptake was significantly reduced in osmotically shocked cells and a gamma-butyrobetaine binding activity was detected in the crude shock fluid. This suggests a transport mechanism involving a periplasmic gamma-butyrobetaine binding protein.
Multigeneric aggregations among oral bacteria: a network of independent cell-to-cell interactions
Authors: Kolenbrander P E , Andersen R N
Published: December 2016

A radioactivity-based assay was developed to define the participation of radioactively labeled cell types within the milieu of unlabeled partners in multigeneric aggregates. The cell types in these multigeneric aggregations consisted of various combinations of 21 strains representing five genera of human oral bacteria. The coaggregation properties of each cell type, when paired individually with various strains, were delineated and were unchanged when the microbes took part in the more complex multigeneric aggregations. Competition between homologous labeled and unlabeled cells for binding to a partner cell type was achieved only when the homologous cells were mixed together before the addition of their partner cells. Attempts to displace a labeled cell type from an aggregate by subsequent addition of a large excess of the same unlabeled cell type were unsuccessful, which suggested that the forces that bound different cell types together were very strong and the cell-to-cell interactions were stable. However, a cell type that exhibited only lactose-reversible coaggregations with partners was easily and selectively released by the addition of lactose to multigeneric aggregates otherwise consisting solely of lactose-nonreversible cell-to-cell interactions. This not only indicates the independent nature of individual coaggregations but also suggests the involvement of lectinlike adhesins in these sugar-inhibitable coaggregations. Although the molecular mechanisms responsible for multigeneric aggregations are unknown, the principle of a common partner cell type serving as a bridge between two otherwise noncoaggregating cell types was firmly established by the observation of sequential addition of one cell type to another. Thus, competition, bridging, coaggregate stability, independent nature of interactions, and partner specificity are the key principles of adherence that form the framework for continued studies of multigeneric aggregates. While the human oral cavity is a prime example of a complex microbial community, collectively the community appears to consist of simple and testable individual interactions.
recA (Srf) suppression of recF deficiency in the postreplication repair of UV-irradiated Escherichia coli K-12
Authors: Wang T C , Smith K C
Published: December 2016

The mechanism by which recA (Srf) mutations (recA2020 and recA801) suppress the deficiency in postreplication repair shown by recF mutants of Escherichia coli was studied in UV-irradiated uvrB and uvrA recB recC sbcB cells. The recA (Srf) mutations partially suppressed the UV radiation sensitivity of uvrB recF, uvrB recF recB, and uvrA recB recC sbcB recF cells, and they partially restored the ability of uvrB recF and uvrA recB recC sbcB recF cells to repair DNA daughter-strand gaps. In addition, the recA (Srf) mutations suppressed the recF deficiency in the repair of DNA double-strand breaks in UV-irradiated uvrA recB recC sbcB recF cells. The recA2020 and recA801 mutations do not appear to affect the synthesis of UV radiation-induced proteins, nor do they appear to produce an altered RecA protein, as detected by two-dimensional gel electrophoresis. These results are consistent with the suggestion (M. R. Volkert and M. A. Hartke, J. Bacteriol. 157:498-506, 1984) that the recA (Srf) mutations do not act by affecting the induction of SOS responses; rather, they allow the RecA protein to participate in the recF-dependent postreplication repair processes without the need of the RecF protein.
Tn5-mediated integration of the delta-endotoxin gene from Bacillus thuringiensis into the chromosome of root-colonizing pseudomonads
Authors: Obukowicz M G , Perlak F J , Kusano-Kretzmer K , Mayer E J , Bolten S L , Watrud L S
Published: December 2016

Gene replacement mediated by Tn5 sequences was used to integrate the Bacillus thuringiensis subsp. kurstaki HD-1 delta-endotoxin gene (tox) into the chromosome of two corn root-colonizing strains of Pseudomonas fluorescens. A Tn5 transposase deletion element containing the tox gene (delta Tn5-tox) was substituted for a Tn5 element previously present in the P. fluorescens chromosome. Two classes of delta Tn5-tox elements were made. The first class encodes kanamycin resistance in addition to the Tox protein, whereas the second class encodes only the Tox protein. Both classes of delta Tn5-tox elements can no longer transpose, owing to a 324-base-pair deletion in the transposase gene of IS50R, minimizing the potential for horizontal gene transfer of the tox gene to other bacterial species. A frameshift mutation in the transposase gene of IS50L was also constructed to eliminate the possibility of suppression or of a spontaneous reversion at the ochre termination codon that would create an active transposase. Expression of the Tox protein in P. fluorescens strains 112-12 and Ps3732-3-7 was demonstrated by an immunological assay (Western blot) and toxicity against larvae of the tobacco hornworm (Manduca sexta).
Dominance relationships among mutant alleles of regulatory gene araC in the Escherichia coli B/R L-arabinose operon
Authors: Sheppard D E
Published: December 2016

The araBAD operon of Escherichia coli B/r is positively and negatively regulated by the araC+ regulatory protein. Mutations in gene araC can result in a variety of different regulatory phenotypes: araC null mutants (those carrying a null allele exhibiting no repressor or activator activity) are unable to achieve operon induction; araC-constitutive (araCc) mutants are partially constitutive, inducible by D-fucose, and resistant to catabolite repression; araCh mutants are hypersensitive to catabolite repression; and araCi mutants are resistant to catabolite repression. Various mutant alleles of gene araC were cloned into a derivative of plasmid pBR322 by in vivo recombination. Various heterozygous araC allelic combinations were constructed by transformation. Analysis of isomerase (araA) specific activity levels under various growth conditions indicated the following dominance relationships with regard to sensitivity to catabolite repression: araCh greater than araC+ greater than (araCc and araCi) greater than araC. It was concluded that the araCh protein may form a repressor complex that is refractory to removal by cyclic AMP receptor protein-cyclic AMP complex. This was interpreted in terms of the known nucleoprotein interactions between ara regulatory proteins and ara regulatory DNA.
Pharmacokinetics of metformin in the rat: assessment of the effect of hyperlipidemia and evidence for its metabolism to guanylurea
Authors: Gabr Raniah Q. , El-Sherbeni Ahmed A. , Ben-Eltriki Mohamed , El-Kadi Ayman O. , Brocks Dion R.
Published: December 2016

Metformin pharmacokinetics are highly dependent upon organic cationic transporters. There is evidence of a change in its renal clearance in hyperlipidemic obese patients, and no information on its metabolic fate. To study some of these aspects, the influence of poloxamer 407 (P407)-induced hyperlipidemia on metformin pharmacokinetics was assessed. Control and P407-treated adult male rats were administered 30 mg/kg metformin intravenously (i.v.). The pharmacokinetic assessments were performed at 2 time points, 36 and 108 h, following the intraperitoneal dose of P407 (1 g/kg). mRNA and protein expressions of cationic drug transporters were also measured. There was no evidence of a change in metformin pharmacokinetics after i.v. doses as a consequence of short-term hyperlipidemia, and a change in transporter mRNA but not protein expression was observed in the P407- treated rats 108 h after P407 injection. Urinary recovery of unchanged drug was high (>90%) but incomplete. Presumed metabolite peaks were detected in chromatograms of hepatocytes and microsomal protein spiked with metformin. Comparative chromatographic elution times and mass spectra suggested that one of the predominant metabolites was guanylurea. Hyperlipidemia by itself did not affect the pharmacokinetics of metformin. Guanylurea is a putative metabolite of metformin in rats.
Inelastic Buckling of FGM Cylindrical Shells Subjected to Combined Axial and Torsional Loads
Authors: Huang Huaiwei , Zhang Yongqiang , Han Qiang
Published: December 2016

A semi-analytical procedure is presented to solve the elastoplastic buckling problem of cylindrical shells made of functionally groded materials (FGMs) under combined axial and torsional loads. The elastoplastic properties are assumed to vary smoothly according to the power law distribution rule, introduced in the J2 deformation theory for formulation of the constitutive relation of FGMs in the framework of the Tamura–Tomota–Ozawa (TTO) model, which is a volume fraction-based material model. The critical condition is deduced by the Ritz method. Assuming the uniform prebuckling strain, a biaxial stress state analysis is conducted to determine the analytical position of the elastoplastic interface, which is used in the integration of the elastoplastic internal force and all the material-related structural parameters. Finally, an iterative procedure is adopted to find the exact elastoplastic critical load. Numerical results indicate the effects of the inhomogeneous parameter and the elastoplastic material properties of their constituents on the stability region and plastic flow region of the materials.
A construction of quantum turbo product codes based on CSS-type quantum convolutional codes
Authors: Xiao Hailin , Ni Ju , Xie Wu , Ouyang Shan
Published: December 2016

As in classical coding theory, turbo product codes (TPCs) through serially concatenated block codes can achieve approximatively Shannon capacity limit and have low decoding complexity. However, special requirements in the quantum setting severely limit the structures of turbo product codes (QTPCs). To design a good structure for QTPCs, we present a new construction of QTPCs with the interleaved serial concatenation of [Formula: see text]-type quantum convolutional codes (QCCs). First, [Formula: see text]-type QCCs are proposed by exploiting the theory of CSS-type quantum stabilizer codes and QCCs, and the description and the analysis of encoder circuit are greatly simplified in the form of Hadamard gates and C-NOT gates. Second, the interleaved coded matrix of QTPCs is derived by quantum permutation SWAP gate definition. Finally, we prove the corresponding relation on the minimum Hamming distance of QTPCs associated with classical TPCs, and describe the state diagram of encoder and decoder of QTPCs that have a highly regular structure and simple design idea.
Quantum mutual information matrices
Authors: Liu Feng
Published: December 2016

For any [Formula: see text]-partite state [Formula: see text], we define its quantum mutual information matrix as an [Formula: see text][Formula: see text][Formula: see text][Formula: see text][Formula: see text] matrix whose [Formula: see text]-entry is given by quantum mutual information [Formula: see text]. Although each entry of quantum mutual information matrix, like its classical counterpart, is also used to measure bipartite correlations, the similarity ends here: quantum mutual information matrices are not always positive semidefinite even for collections of up to 3-partite states. In this work, we define the genuine n-partite mutual information which can be easily calculated. This definition is symmetric, nonnegative, bounded and more accurate for measuring multipartite states.
An assessment of the Upper Succession and the related secondary reservoirs in the Welton Field, onshore UK
Authors: Steventon James , Bowman Mike
Published: December 2016

The Welton oil field has produced nearly 20 MMBO (million barrels of oil) since discovery in 1981. Now in post-plateau decline, there is increasing reliance on a series of secondary reservoirs. Production has been from a suite of stacked reservoirs deposited by large-scale prograding delta-plain systems of early Westphalian age. Whilst the bulk of production has been from the Basal Succession, a considerable upside is considered to exist in the less well-studied Upper Succession that comprises predominantly distributary channel and crevasse splay deposits which have produced in excess of 3 MMBO. These accumulations occur within the Deep Soft Rock, Deep Hard Rock and Tupton reservoirs.

This paper focuses on a sedimentological analysis of cored intervals, integrated with petrophysical logs and detailed production data to enable further recommendations to identify areas of undrained pay, along with identifying additional reservoir management activities that could optimize future offtake from the field. These reservoirs consist predominantly of very fine-grained sandstone, with permeability values rarely attaining 100 mD and average porosity values of 10–12%.

Recommendations include executing tracer communication tests and building a detailed field model, as well as a pilot water-injection scheme to increase production from some of Welton's secondary reservoirs.

Supplementary material:
A full set of detailed sedimentological logs for each of the cored wells in this study is available at
https://doi.org/10.6084/m9.figshare.c.3593984
miR-200b inhibits TNF-α-induced IL-8 secretion and tight junction disruption of intestinal epithelial cells in vitro
Authors: Shen Yujie , Zhou Min , Yan Junkai , Gong Zizhen , Xiao Yongtao , Zhang Cong , Du Peng , Chen Yingwei
Published: December 2016

Inflammatory bowel diseases (IBDs) are chronic, inflammatory disorders of the gastrointestinal tract with unclear etiologies. Intestinal epithelial cells (IECs), containing crypt and villus enterocytes, occupy a critical position in the pathogenesis of IBDs and are a major producer of immunoregulatory cytokines and a key component of the intact epithelial barrier. Previously, we have reported that miR-200b is involved in the progression of IBDs and might maintain the integrity of the intestinal epithelial barrier via reducing the loss of enterocytes. In this study, we further investigated the impact of miR-200b on intestinal epithelial inflammation and tight junctions in two distinct differentiated states of Caco-2 cells after TNF-α treatment. We demonstrated that TNF-α-enhanced IL-8 expression was decreased by microRNA (miR)-200b in undifferentiated IECs. Simultaneously, miR-200b could alleviate TNF-α-induced tight junction (TJ) disruption in well-differentiated IECs by reducing the reduction in the transepithelial electrical resistance (TEER), inhibiting the increase in paracellular permeability, and preventing the morphological redistribution of the TJ proteins claudin 1 and ZO-1. The expression levels of the JNK/c-Jun/AP-1 and myosin light chain kinase (MLCK)/phosphorylated myosin light chain (p-MLC) pathways were attenuated in undifferentiated and differentiated enterocytes, respectively. Furthermore, a dual-luciferase reporter gene detection system provided direct evidence that c-Jun and MLCK were the specific targets of miR-200b. Collectively, our results highlighted that miR-200b played a positive role in IECs via suppressing intestinal epithelial IL-8 secretion and attenuating TJ damage in vitro, which suggested that miR-200b might be a promising strategy for IBD therapy.

NEW & NOTEWORTHY This was the first time that the inhibitory role of miR-200b on intestinal epithelial inflammation and paracellular permeability has been reported. Moreover, we further divided the intestinal epithelial cells (IECs) into two differentiated conditions and investigated the distinct impacts of miR-200b. Finally, we put forward and proved that myosin light chain kinase (MLCK) was a novel target of miR-200b.
Repeated Long-Term DT Application in the DEREG Mouse Induces a Neutralizing Anti-DT Antibody Response
Authors: Wang Junhua , Siffert Myriam , Spiliotis Markus , Gottstein Bruno
Published: December 2016

Regulatory T (Tregs) cells play an important role in mediating tolerance to self-antigens but can also mediate detrimental tolerance to tumours and pathogens in a Foxp3-dependent manner. Genetic tools exploiting the foxp3 locus including bacterial artificial chromosome- (BAC-) transgenic DEpletion of REGulatory T cells (DEREG) mice have provided essential information on Treg biology and the potential therapeutic modulation of tolerance. In DEREG mice, Foxp3+ Tregs selectively express enhanced green fluorescent protein (eGFP) and diphtheria toxin (DT) receptor, allowing for the specific depletion of Tregs through DT administration. We here provide a detailed overview about an important consideration that long-term administration of DT induces a humoral immune response with an appropriate production of anti-DT antibodies that can inactivate DT and thus abrogate its effect in the DEREG mouse. Additionally, we showed that anti-DT mouse serum partially neutralized DT-induced Foxp3 inhibition.
The Efficiency of Sclerotherapy in the Treatment of Vascular Malformations: A Retrospective Study of 63 Patients
Authors: Veräjänkorva Esko , Rautio Riitta , Giordano Salvatore , Koskivuo Ilkka , Savolainen Otto
Published: December 2016

Background and Aims. Vascular malformations are a vast group of congenital malformations that are present at birth. These malformations can cause pain, pressure, and cosmetic annoyance as well as downturn growth and development in a child in the case of high flow. Sclerotherapy has become an important tool in the treatment of vascular malformations. However, little is known about the success rate of sclerotherapy. Material and Methods. In this study, the efficiency of sclerotherapy in the treatment of vascular anomalies was investigated retrospectively in 63 patients treated in Turku University Hospital between 2003 and 2013. Results. Out of the 63 patients investigated, 83% (53) had venous malformations (VMs) and 9% (5) were defined as having arteriovenous malformations (AVMs). Patients with a VM were operated on, in 14% (8) out of all VM cases. Hence 86% (45) of patients with a VM received adequate help to their symptoms solely from sclerotherapy. The duration of treatment for the 14% of the VM patients that needed a surgical procedure was prolonged by 7–9 months, that is, by 41%. Conclusions. Sclerotherapy is an effective method in the treatment of VMs with a satisfactory clinical response in patients symptoms in 84% of cases.