bluuebunny/crossref_metadata_2025 huggingface dataset:
Apply Observation, Intervention, and Controlled Experiments
Authors: Shneiderman Ben
Published: March 2016

The spectrum of research methods ranges from observations, to interventions, to controlled experiments, with many variations along the way. The outcomes manifest in solutions and theories have four components: clear descriptions, causal explanations, reliable predictions, and practical guidelines. The opportunity to test environmental and made-world interventions at massive scale grows with the increasing availability of big data resources from sensors, commercial applications, government data, and open social media discussions. Rigorous guidelines for controlled experiments would accelerate their adoption and gain respect for large-scale quantitative studies. Rigorous guidelines would also be helpful for promoting the adoption of replicated case study research using qualitative methods such as interviews and ethnographic observations.
Form Teams with Diverse Individuals and Organizations
Authors: Shneiderman Ben
Published: March 2016

Teams often produce high-quality research because they bring complementary knowledge, skills, and attitudes, take on ambitious projects, apply diverse research methods, and have large networks. Teamwork is an increasingly popular way of doing research, probably because of the urgency of contemporary problems and the potential for high-impact work. Some funding agencies encourage or even require teamwork in their program announcements. However, teamwork is a complex strategy with many variations and occasionally goes badly, producing acrimonious fights and failed projects. Collaborations can come from business partnerships or interdisciplinary teams that span academic disciplines.
Promote Adoption and Assess Impact
Authors: Shneiderman Ben
Published: March 2016

Write well, promote thoughtfully, and assess with care. Strong story-telling skills, which build on compelling narratives, can increase research impact. Addressing appropriate audiences using effective media honors a researcher team’s work. Spreading ideas is a turbulent imperfect process, so vigorous promoters can influence the attention to their work. The best form of promotion is still good writing with striking visuals. Once this foundation is laid, spin-off presentations can be produced through slide decks, podcasts, videos, blog posts, and other forms of social media. This chapter describes the politics of promoting research outcomes in the marketplace of ideas. It also discusses mixing subjective and objective assessments of research impact.
Public, Private,…and Secret
Authors: Eidinow Esther
Published: March 2016

This chapter continues the examination of the role and pathways of gossip in and through ancient society. It turns to the genre of curse tablets or binding spells, as a vehicle for the expression of suspicion and aggression. Using conceptual blending analysis, this chapter provides an analysis of the metaphor of binding, in binding spells. This demonstrates the metaphoric connections between binding and civic punishment and gives some insight into the ancient experience of writing or fearing binding spells. In conclusion, it examines the emotions that were likely to motivate the creation of binding spells and argues that this is more likely to be phthonos than Schadenfreude (as some scholars have claimed).
Aesthetics as Philosophy of Perception
Authors: Nanay Bence
Published: March 2016

Aesthetics is about some special and unusual ways of experiencing the world. Not just artworks, but also nature and ordinary objects. But then if we apply the remarkably elaborate and sophisticated conceptual apparatus of philosophy of perception to questions in aesthetics, we can make real progress. The aim of this book is to bring the discussion of aesthetics and perception together. Many influential debates in aesthetics will look very different and maybe not as difficult to tackle if we clarify the assumptions they make about perception and about experiences in general. The focus of the book is the concept of attention and the ways in which this concept and especially the distinction between distributed and focused attention can help us re-evaluate various key concepts and debates in aesthetics. Some of the key concepts and debates that the book covers are picture perception and depiction, about aesthetic experiences, about formalism, about the importance of uniqueness in aesthetics, about the history of vision debate, and about our identification with fictional characters (among others).
Structure and Evolution of Invertebrate Nervous Systems
Authors: Schmidt-Rhaesa Andreas , Harzsch Steffen , Purschke Günter
Published: March 2016

For many biologists the nervous system is a particularly fascinating organ system. The nervous system is involved in or is even responsible for many features that are regarded as being characteristic of animals in general. Since the last comprehensive work was published about 50 years ago, the time has probably come to provide a new review on recent, newly gathered knowledge on the structure of invertebrate nervous systems, especially since new methods have come into use. These advances now enable us to demonstrate neuronal architecture down to the level of the genes and the cell types involved, allowing a new view on nervous systems and comparisons among different taxa. These new findings may help in development of new hypotheses, or support of existing hypotheses on phylogenetic relationships and evolutionary pathways in the nervous system. In spite of many open questions we already have a good knowledge of how nervous systems work, how they are constructed, and how they may have evolved. There is certain evidence that the first nervous systems are represented by rather simple sensory–motor circuits, followed by nerve nets (plexus) located within the epithelia, and finally neuronal circuits composed of sensory cells, interneurons, and brains. Therefore, this book concentrates on invertebrates and structure and these new evolutionary aspects, here discussed as ‘research highlights’ or ‘perspectives’. Sensory structures are only touched on peripherally. Whereas some taxa have been studied extensively and well-written reviews may already exist, in other taxa our knowledge on the nervous system is still scant and scarce.
Perspective—Evolution of Neural Cell Types
Authors: Arendt Detlev
Published: March 2016

The nervous system is composed of cell types. Thus, any attempt to elucidate the evolutionary origin of the nervous system requires comparison of the constituting neural cell types. This chapter surveys the state of the art in the comparative analysis of cell types in the nervous system, conceptually and by means of a few illustrative examples. First, what is a cell type? In essence, the definition of a ‘cell type’ is structural. It refers to the specific phenotype of a population of cells in the body that are structurally more similar to each other than to other cells. Therefore, neural cell types are defined by their specific structure reflecting their unique function. The structure of a given cell type is a manifestation of its molecular composition; and although cell types are more than the sum of their constituent parts, the comparative analysis of their molecular composition in various different ways is key to understanding cell type evolution. Typically, cellular functions require the cooperation of proteins and other biomolecules that constitute ‘modules’. We can thus envisage a neural cell type, as any other cell type, as an assembly of modules with discrete subfunctions. The focus of this chapter is on the evolutionary origin of ‘neural’ modules in early metazoans and their subsequent distribution to emergent sister cell types such as sensory neurons and interneurons.
Perspective—The First Brain
Authors: Riebli Nadia , Reichert Heinrich
Published: March 2016

In this spotlight chapter the question of whether the urbilaterian ancestor already possessed a complex brain, or whether the various brains found in extant bilaterians arose by convergent evolution is considered. Since current palaeontological data gives little insight into the origin of brains during evolution earlier than the Cambrium, evidence from comparative, developmental, and molecular genetic studies that sheds light on the origin of the first brain is reviewed. Comparative neuroanatomical data reveal complex CNS throughout the protostomes and deuterostomes, but do not resolve the question of whether the diverse brains of extant bilaterians all had a common urbilaterian origin. Studies on regionalized expression of developmental patterning genes, such as Cephalic gap genes and Hox genes, show that they not only show similar expression patterns, but also have comparable developmental roles in vertebrate and invertebrate brain development. Moreover, even conserved organizational features of complex brain circuitry such as the visual and olfactory system have recently been reported in both protostomes and deuterostomes. Taken together, there is now increasing evidence for a brain with relatively sophisticated sensory and associative brain centres in the urbilaterian ancestor of vertebrates and invertebrates, implying that the first urbilaterian brain might already have been quite complex.
Platyhelminthes: Neodermata
Authors: Biserova Natalia M.
Published: March 2016

In Neodermata, the brain consists of paired ganglia (right and left lateral lobes), connected by the brain commissure; paired anterior nerves and two posterior main nerve cords extending from the lobes and the commissure. The brain is composed of numerous serotoninergic, peptidergic, and cholinergic neurons. The bilobed neuropil is a compact integrative part of the brain. Except synaptic contacts, it usually has fibrillar and glial envelopes. The architecture and ultrastructure of the bilobed neuropil is different among Neodermata. Monogeneans and trematodes possess a bilateral symmetrical bilobed brain with a broad commissure dorsally behind the pharynx. The amphilinidean brain consists of the right and left non-symmetrical ganglia, connected by the median commissure located ventrally underneath the anterior pit. In Cestodes the brain has a complicated architecture. More prominent concentrations of neurons are located around the median commissure and two main neuropils. Scoleces with four sets of attachment organs have distinct double lateral lobes with two pairs of main neuropils. The central unpaired lobe with neuropil and neurons, and also the X (or +)-shaped commissures are evidenced in some cestodes species. Anterior nerves and ganglia innervate the mouth, pharynx, lappets, and the musculo-glandular organs of monogenea and trematoda. In cestodes, the anterior ganglia innervate suckers, proboscises, and glandular organs; and anterior nerves innervate the bothria. The sensory organs are presented by the unciliated, uni-ciliated, and multiciliated aggregations of free nerve endings in the neodermis. The position of the sensory organs correlates with the morphology of attachment and copulatory apparatus.
Mollusca: Caudofoveata, Monoplacophora, Polyplacophora, Scaphopoda, And Solenogastres
Authors: Sigwart Julia D. , Sumner-Rooney Lauren H.
Published: March 2016

Molluscs are the second most speciose metazoan phylum, and arguably molluscs demonstrate the largest morphological disparity. The dramatic body-plan modifications and changes among the molluscan clades leave few consistent characters that can be directly compared across all eight living classes. The five groups covered here—Caudofoveata (chaetoderms), Monoplacophora (headless deep-sea limpets), Polyplacophora (chitons), Scaphopoda (tusk shells), and Solenogastres (neomeniomorphs)—are all exclusively marine, and live as benthic or infaunal species. They are less commercially exploited than the other more speciose and edible groups of molluscs, but nonetheless demonstrate extensive diversification within each clade, and many are locally abundant and exert significant ecosystem control. They also possess fascinating specialized sensory structures, from the sensory shell ‘eyes’ or aesthetes within the shells of chitons, to the inordinate elastic sensory tentacles that scaphopods use for feeding. Neuroanatomy has long been crucial to the study of molluscs and molluscan phylogeny. Indeed, aplacophorans (Caudofoveata and Solenogastres) as well as scaphopods were historically considered to be worms, but the organization of their nervous systems helped early comparative anatomists to recognize these animals as molluscs. This assessment of the nervous systems across diverse body plans may prove essential to resolving larger questions about molluscan and metazoan evolutionary dynamics.
Bryozoa (Ectoprocta)
Authors: Gruhl Alexander , Schwaha Thomas
Published: March 2016

Bryozoa (or Ectoprocta) are a taxon of sessile aquatic suspension feeders with about 6000 described species, living in marine and about 100 in freshwater habitats. Bryozoans form clonal colonies composed of numerous millimetre-sized individuals, called zooids, which maintain tissue interconnections. Traditionally, two main body regions are distinguished in an individual zooid, the protective cystid, which harbours a spacious fluid-filled coelom and is attached to the substrate or to neighbouring zooids, and the distal polypide, which consists of the tentacular crown, the tentacle sheath, and the digestive tract. The brain (also referred to as cerebral ganglion or ganglion) is located in the base of the lophophore. Underlying and innervating the ring of tentacles are large nerve cords that embrace the pharynx and form the so-called circumpharyngeal nerve ring. Additional neurite bundles emerging from the lateral and basal parts of the brain innervate further epidermal areas, the intestine, the musclature, and coelomic epithelia. Adult bryozoans lack complex sensory organs, but have many mechano- and possibly chemoreceptor cells on their tentacles and other uncuticularized parts of their body wall. Photoreceptors have not been demonstrated, although some colonies show positive or negative phototropism. Pigmented ocelli occur in some but not all larvae. Larvae also bear more or less complex apical organs, composed of several ciliated sensory cells, and frontal pyriform organs comprising sensory and gland cells.
Brachiopoda
Authors: Lüter Carsten
Published: March 2016

Brachiopoda is an exclusively marine group of bivalved sessile filter feeders comprising some 400 extant as opposed to about 30,000 described fossil species. The nervous system in brachiopods was shown to run basi- to subepidermally. The main elements are a brain and a circum-oesophageal ring. The brain is a concentration of nervous tissue around the oesophagus forming a supraoesophageal and a suboesophageal ganglion. Only a few sensory organs are described in Brachiopoda. In linguliforms the swimming juvenile has a median tentacle with primary receptor cells of as yet unknown function at its tip, which directly project into a circum-oesophageal nerve ring. Additionally, linguliform swimming juveniles and adults are decribed to have a pair of statocysts.
Pycnogonida (Pantopoda)
Authors: Brenneis Georg
Published: March 2016

Pycnogonids (sea spiders) are marine arthropods, which are most plausibly placed within chelicerates, as sister group to all other taxa. This chapter gives a brief overview of pycnogonid morphology before summarizing the available information on nervous system architecture and neural development. The brain is a bipartite composite ganglion that encompasses the protocerebral region and the deutocerebrum. Apart from fine structure details on the two pairs of eyes and the two optic neuropils, its neuroarchitecture remains poorly understood. The ventral nerve cord comprises a chain of separate ganglia, each of which containing a complex system of transverse tracts and glomerulus-like neuropils. At least some of these neuropils appear to receive chemosensory input. During development, transient ganglion anlagen posterior to the last walking leg ganglion indicate the reduction of more posterior body segments (‘opisthosoma’) in the pycnogonid stem lineage – as is also suggested by fossil evidence. Variations of the gross neuroanatomy in extant pycnogonid taxa include the presence of additional walking leg ganglia in extra-legged species and the occasional occurrence of an ‘extended’ suboesophageal ganglion. The intricate stomatogastric nervous system forms a basket-like network of numerous neurite bundles and several small ganglia around the triradiate sucking pharynx. While early pycnogonid neurogenesis is similar to other chelicerates, it differs in advanced stages by differentiation of neural stem cells. Based on the likely phylogenetic position of pycnogonids as sister group to all other chelicerate taxa, their bipartite brain and the separate ventral ganglia are discussed as plesiomorphic features of the Chelicerata.
The role of in hospite zooxanthellae photophysiology and reef chemistry on elevated pCO2 effects in two branching Caribbean corals: Acropora cervicornis and Porites divaricata
Authors: Bedwell-Ivers Hayley E. , Koch Marguerite S. , Peach Katherine E. , Joles Luke , Dutra Elizabeth , Manfrino Carrie
Published: March 2016

Previous studies suggest uniform reductions in coral calcification under ocean acidification (OA); however, greater tolerance has been observed under natural diel metabolic signals present on reefs. In addition, few studies have examined the role of in hospite zooxanthellae energetics on coral OA tolerance. In this study, we examined zooxanthellae photosynthesis and coral calcification responses using seawater with natural metabolic dissolved inorganic carbon (DIC) dynamics from a fringing back reef on Little Cayman Island, Caribbean. The experimental design included Acropora cervicornis and Porites divaricata microcolonies grown in continuously flowing seawater with (∼1000 μatm) and without (∼500 μatm) CO2 enrichment to year 2100 predicted levels. Calcification rates were measured weekly, while linear extension and zooxanthellae photosynthesis were determined at the termination of the 28 d experiment. Results showed A. cervicornis microcolonies maintained both photosynthesis and calcification under elevated CO2 partial pressure (pCO2) relative to controls. However, photosynthesis and calcification rates of P. divaricata microcolonies were reduced by ∼80 and 20%, respectively, under relatively high [DIC]:[H+] ratios and aragonite saturation states (Ωarag). Porites divaricata calcification response to elevated pCO2 was linked to photophysiological dysfunction of the algal symbiont, an indicator that this species was metabolically depressed under elevated pCO2. In contrast to calcification, linear extension rates were unaffected by pCO2 in both species. Future studies should investigate how elevated pCO2 may compromise zooxanthellae–coral interactions with an emphasis on DIC uptake pathways.
New method for probing Kerr space-time based on imaging observation of in-falling gas blob
Authors: Moriyama Kotaro , Mineshige Shin
Published: March 2016

We propose a new observational method to probe the black hole space-time described by Einstein's theory. We consider a gas blob with an arc shape falling from the marginally stable orbit onto a black hole, carrying a finite amount of angular momentum. Previously, we proposed measuring the black hole spin from the flux variation data of the in-falling blob, assuming the Kerr space-time. We demonstrate here that we can independently measure the black hole spin solely by using the imaging data of the in-falling blob. We then introduce a Kerr-like hole (with one additional parameter which describes a stronger or weaker frame-dragging effect than that of the Kerr hole) and apply the two different methods of spin measurement: one based on the flux variation data and the other based on the imaging data. We obtain different spin values by the different methods for the Kerr-like hole. This is because these methods are sensitive to different components of the metric. We can in this way probe the black hole space-time through the comparison of the estimated spin values; that is, if the black hole space-time is described by the Kerr metric, all of them should coincide.
Self-assembly Controls Self-cleavage of HHR from ASBVd(-): a Combined SANS and Modeling Study
Authors: Leclerc Fabrice , Zaccai Giuseppe , Vergne Jacques , Řìhovà Martina , Martel Anne , Maurel Marie-Christine
Published: March 2016

In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.
Synthesis of titanium dioxide thin films and its application in reducing microbial load of milk
Authors: Kumar Shruthi N , Sarode Manjula , Ravi Shankar H. N.
Published: March 2016

Milk has rich nutritional content packed with fats, proteins and water. It also contains beneficiary and non-beneficiary microbes which account for its short shelf life. Currently cold storage, pasteurization, ultra-high temperature, microfiltration and addition of lactose peroxidase are the methods of choice to control milk spoilage and prolong its shelf life. Their limitations include high energy consumption and loss of variable proportion of heat sensitive nutrients. Titanium dioxide (TiO2) nanoparticle coated thin film was used in food packaging industry for its antimicrobial property. TiO2thin films were synthesized by sol gel process; it was characterized with scanning electron microscopy which showed pore size as 5 μm and Fourier transform infrared spectroscopy which showed metal present in sample is TiO2, zinc and silver. Exposure of raw milk at room temperature to TiO2thin films doped with zinc or copper for a couple of hours showed zone of inhibition in disc diffusion technique, reduction in acid production. It also showed reduction in optical density indicating inhibition of growth in growth curve analysis, increase in the time required for methylene blue reduction and a five log folds decrease in bacterial count estimated using serial dilution plate count. The present studies were carried out under room temperature and pressure which is an added advantage in terms of energy as well as retention of nutrients. Though TiO2is insoluble in water one needs to address it toxicity issues and adverse effects if any on the nutritional quality of milk before scaling up the process.
Modeling multi-particle complexes in stochastic chemical systems
Authors: Morrison Muir J. , Kinney Justin B.
Published: March 2016

Large complexes of classical particles play central roles in biology, in polymer physics, and in other disciplines. However, physics currently lacks mathematical methods for describing such complexes in terms of component particles, interaction energies, and assembly rules. Here we describe a Fock space structure that addresses this need, as well as diagrammatic methods that facilitate the use of this formalism. These methods can dramatically simplify the equations governing both equilibrium and non-equilibrium stochastic chemical systems. A mathematical relationship between the set of all complexes and a list of rules for complex assembly is also identified.
Functional data analysis techniques for the study of structural parameters in polymer composites
Authors: Urs Thejas Gopal Krishne , Bharath Karthik , Yallappa Sangappa , Rudrappa Somashekar
Published: March 2016

This article presents a novel method, based on functional data analysis, to analyse measurements of structural parameters of polymers and polymer composites. The method is demonstrated using newly developed biodegradable conducting polymer composites prepared via a solution casting technique. The measurements of the macro- and microstructural parameters that are used in the characterization of these films are obtained using X-ray diffraction, an impedance analyser and a UV–vis spectrometer. A functional representation of the measured values of the parameters at different dopant concentrations is adopted by viewing them as realizations of a continuous-time stochastic process observed with measurement error. This allows one to estimate the mean functional relationship between a parameter and the dopant concentration. A functional version of principal component analysis is performed, by which the major modes of variation are discovered and the correlations of parameter values at different concentrations are estimated. This provides insight into local and global features of the relationship between these parameters. Some comments are made on how the parameters vary as a function of dopant concentration.
A novel microseeding method for the crystallization of membrane proteins in lipidic cubic phase
Authors: Kolek Stefan Andrew , Bräuning Bastian , Shaw Stewart Patrick Douglas
Published: March 2016

Random microseed matrix screening (rMMS), in which seed crystals are added to random crystallization screens, is an important breakthrough in soluble protein crystallization that increases the number of crystallization hits that are available for optimization. This greatly increases the number of soluble protein structures generated every year by typical structural biology laboratories. Inspired by this success, rMMS has been adapted to the crystallization of membrane proteins, making LCP seed stock by scaling up LCP crystallization conditions without changing the physical and chemical parameters that are critical for crystallization. Seed crystals are grown directly in LCP and, as with conventional rMMS, a seeding experiment is combined with an additive experiment. The new method was used with the bacterial integral membrane protein OmpF, and it was found that it increased the number of crystallization hits by almost an order of magnitude: without microseeding one new hit was found, whereas with LCP-rMMS eight new hits were found. It is anticipated that this new method will lead to better diffracting crystals of membrane proteins. A method of generating seed gradients, which allows the LCP seed stock to be diluted and the number of crystals in each LCP bolus to be reduced, if required for optimization, is also demonstrated.
Crystal structure of a tankyrase 1–telomere repeat factor 1 complex
Authors: Li Bo , Qiao Ruihong , Wang Zhizhi , Zhou Weihong , Li Xin , Xu Wenqing , Rao Zihe
Published: March 2016

Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and a fragment of TNKS1 covering the second and third ankyrin-repeat clusters (ARC2-3) is presented at 2.2 Å resolution. The TNKS1–TRF1 complex crystals were optimized using an `oriented rescreening' strategy, in which the initial crystallization condition was used as a guide for a second round of large-scale sparse-matrix screening. This crystallographic and biochemical analysis provides a better understanding of the TRF1–TNKS1 interaction and the three-dimensional structure of the ankyrin-repeat domain of TNKS.
Trinuclear nickel coordination complexes of phenanthrene-9,10-dione dioxime
Authors: Williams Owen M. , Cowley Alan H.
Published: March 2016

A trinuclear nickel complex of phenanthrene-9,10-dione dioxime (H2pqd), namely bis[μ2-9,10-bis(oxidoimino)phenanthrene]bis[μ2-10-(oxidoimino)phenanthrene-9-one oxime](phenanthrene-9,10-dione dioxime)trinickel(II) toluene disolvate, [Ni3(C14H8N2O2)2(C14H9N2O2)2(C14H10N2O2)]·2C7H8, has been isolated and its crystal structure determined. This complex features three independent NiIIatoms that are arranged in a triangular fashion along with five supporting ligands. There are two square-planar NiIIatoms and a third pseudo-octahedral NiIIatom. While the square-planar NiIIatoms are stacked, there are no ligand bridges between them. Each square-planar NiIIatom, however, bridges with the pseudo-octahedral NiIIatom through Ni—N—O—Ni and Ni—O—Ni bonds. A fluoridoboration reaction of the proton-bridged species gave the analogous complex bis(μ2-bis{[10-(oxidoimino)-9,10-dihydrophenanthren-9-ylidene]amino}difluoridoborato)(phenanthrene-9,10-dione dioxime)trinickel(II) dichloromethane trisolvate, [Ni3(C28H16BF2N4O2)4(C14H10N2O2)]·3CH2Cl2, which shows the same binding structure, but features a widened Ni—Ni interaction between the square-planar NiIIatoms. The proton-bridged complex completes the macrocyclic coordination around the square-planar NiIIatoms by means of an O—H...O hydrogen bond. Both compounds feature O—H...N hydrogen bonds between the oxime and the N atoms attached to square-planar nickel atom. The nickel units show no direct interaction with their nearest neighbors in the extended lattice. Two π-stacking interactions between adjacent molecules are found: one with a centroid–centroid distance of 3.886 (2) Å and the other with a centroid–centroid distance of 4.256 (3) Å. In the latter case, although not aromatic, the distance to the centroid of the central phenanthrene ring is shorter, with a distance of 3.528 (3) Å. Toluene molecules occupy the solvent channels that are oriented along thecaxis. In the fluoridoboronate structure, the solvent (DCM) was too badly disordered to be modelled, so its contribution was removed using SQUEEZE [Spek (2015).Acta Cryst.C71, 9–18].
Crystal structures of bis[2-(pyridin-2-yl)phenyl-κ2N,C1]rhodium(III) complexes containing an acetonitrile or monodentate thyminate(1−) ligand
Authors: Sakate Mika , Hosoda Haruka , Suzuki Takayoshi
Published: March 2016

The crystal structures of bis[2-(pyridin-2-yl)phenyl]rhodium(III) complexes with the metal in an octahedral coordination containing chloride and acetonitrile ligands, namely (OC-6-42)-acetonitrilechloridobis[2-(pyridin-2-yl)phenyl-κ2N,C1]rhodium(III), [RhCl(C11H8N)2(CH3CN)] (1), thyminate(1−) and methanol, namely (OC-6-42)-methanol(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ido-κN1)bis[2-(pyridin-2-yl)phenyl-κ2N,C1]rhodium(III), [Rh(C11H8N)2(C5H5N2O2)(CH3OH)]·CH3OH·0.5H2O (2), and thyminate(1−) and ethanol, namely (OC-6-42)-ethanol(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ido-κN1)bis[2-(pyridin-2-yl)phenyl-κ2N,C1]rhodium(III), [Rh(C11H8N)2(C5H5N2O2)(C2H5OH)]·C2H5OH (3), are reported. The acetonitrile complex,1, is isostructural with the IrIIIanalog. In complexes2and3, the monodeprotonated thyminate (Hthym−) ligand coordinates to the RhIIIatom through the N atom, and the resulting Rh—N(Hthym) bond lengths are relatively long [2.261 (2) and 2.252 (2) Å for2and3, respectively] as compared to the Rh—N bonds in the related thyminate complexes. In each of the crystals of2and3, the complexes are linkedviaa pair of intermolecular N—H...O hydrogen bonds between neighbouring Hthym−ligands, forming an inversion dimer. A strong intramolecular O—H...O hydrogen bond between the thyminate(1−) and alcohol ligands in mutuallycispositions to each other is also observed.
Novel mode of inhibition byD-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants
Authors: Stellmacher Lena , Sandalova Tatyana , Schneider Sarah , Schneider Gunter , Sprenger Georg A. , Samland Anne K.
Published: March 2016

Transaldolase B (TalB) and D-fructose-6-phosphate aldolase A (FSAA) fromEscherichia coliare C—C bond-forming enzymes. Using kinetic inhibition studies and mass spectrometry, it is shown that enzyme variants of FSAA and TalB that exhibit D-fructose-6-phosphate aldolase activity are inhibited covalently and irreversibly by D-tagatose 6-phosphate (D-T6P), whereas no inhibition was observed for wild-type transaldolase B fromE. coli. The crystal structure of the variant TalBF178Ywith bound sugar phosphate was solved to a resolution of 1.46 Å and revealed a novel mode of covalent inhibition. The sugar is bound covalentlyviaits C2 atom to the ∊-NH2group of the active-site residue Lys132. It is neither bound in the open-chain form nor as the closed-ring form of D-T6P, but has been converted to β-D-galactofuranose 6-phosphate (D-G6P), a five-membered ring structure. The furanose ring of the covalent adduct is formedviaa Heyns rearrangement and subsequent hemiacetal formation. This reaction is facilitated by Tyr178, which is proposed to act as acid–base catalyst. The crystal structure of the inhibitor complex is compared with the structure of the Schiff-base intermediate of TalBE96Qformed with the substrate D-fructose 6-phosphate determined to a resolution of 2.20 Å. This comparison highlights the differences in stereochemistry at the C4 atom of the ligand as an essential determinant for the formation of the inhibitor adduct in the active site of the enzyme.
Structure of a quinolone-stabilized cleavage complex of topoisomerase IV fromKlebsiella pneumoniaeand comparison with a relatedStreptococcus pneumoniaecomplex
Authors: Veselkov Dennis A. , Laponogov Ivan , Pan Xiao-Su , Selvarajah Jogitha , Skamrova Galyna B. , Branstrom Arthur , Narasimhan Jana , Prasad Josyula V. N. Vara , Fisher L. Mark , Sanderson Mark R.
Published: March 2016

Klebsiella pneumoniaeis a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains ofKlebsiellahave become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown. In this paper, the structure of its DNA-cleavage complex is reported at 3.35 Å resolution. The complex is comprised of ParC breakage-reunion and ParE TOPRIM domains ofK. pneumoniaetopoisomerase IV with DNA stabilized by levofloxacin, a broad-spectrum fluoroquinolone antimicrobial agent. This complex is compared with a similar complex fromStreptococcus pneumoniae, which has recently been solved.
UHM–ULM interactions in the RBM39–U2AF65 splicing-factor complex
Authors: Stepanyuk Galina A. , Serrano Pedro , Peralta Eigen , Farr Carol L. , Axelrod Herbert L. , Geralt Michael , Das Debanu , Chiu Hsiu-Ju , Jaroszewski Lukasz , Deacon Ashley M. , Lesley Scott A. , Elsliger Marc-André , Godzik Adam , Wilson Ian A. , Wüthrich Kurt , Salomon Daniel R. , Williamson James R.
Published: March 2016

RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39–U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35–U2AF65 and RBM39–SF3b155, the RBM39-UHM–U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM–ULM binding interface, providing a rationale for the known specificity of UHM–ULM interactions. This study therefore establishes a structural basis for specific UHM–ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.
Microcrystal delivery by pulsed liquid droplet for serial femtosecond crystallography
Authors: Mafuné Fumitaka , Miyajima Ken , Tono Kensuke , Takeda Yoshihiro , Kohno Jun-ya , Miyauchi Naoya , Kobayashi Jun , Joti Yasumasa , Nango Eriko , Iwata So , Yabashi Makina
Published: March 2016

A liquid-droplet injector has been developed that delivers pristine microcrystals to an X-ray irradiation area for conducting serial femtosecond crystallography (SFX) with an X-ray free-electron laser (XFEL). By finely tuning the pulsed liquid droplets in time and space, a high hit rate of the XFEL pulses to microcrystals in the droplets was achieved for measurements using 5 µm tetragonal lysozyme crystals, which produced 4265 indexable diffraction images in about 30 min. The structure was determined at a resolution of 2.3 Å from <0.3 mg of protein. With further improvements such as reduction of the droplet size, liquid droplets have considerable potential as a crystal carrier for SFX with low sample consumption.
Bis[4-(2,4,4-trimethylpentan-2-yl)phenyl]amine
Authors: Wang Limin , Wang Shengpei , Liu Shenggao
Published: March 2016

In the title compound, C28H43N, the dihedral angle between the aromatic rings is 41.15 (12)° and both side chains exhibit extensive disorder. No directional interactions beyond van der Waals contacts could be identified in the crystal.
2-Methoxy-4-[3-(3-nitrophenyl)-4,5-dihydro-1H-pyrazol-5-yl]phenol
Authors: Inturi Bharathkumar , Roopashree K. R. , Pujar Gurubasavaraj V. , Mohammed Irfan Ali , Devarajegowda H. C.
Published: March 2016

In the title compound, C16H15N3O4, the pyrazole ring has an envelope conformation, with the C atom substituted by the 2-methoxyphenol ring as the flap. Its mean plane makes dihedral angles of 56.78 (9) and 9.7 (1)° with the 2-methoxyphenol and 3-nitrophenyl rings, respectively. The benzene rings are inclined to one another by 49.37 (8)°. In the crystal, molecules are linked by pairs of O—H...N hydrogen bonds, forming inversion dimers with anR22(16) ring motif. The dimers are linked by C—H...O hydrogen bonds, forming slabs parallel to theacplane. There are slipped parallel π–π interactions present within the slabs, involving inversion-related 2-methoxyphenol rings [intercentroid distance = 3.729 (1) Å] and inversion-related 3-nitrophenyl rings [intercentroid distance = 3.831 (1) Å].
N,N,N′,N′,N′′,N′′-Hexamethylguanidinium 1,1,3,3-tetracyanoprop-2-en-1-ide
Authors: Tiritiris Ioannis , Kress Ralf , Kantlehner Willi
Published: March 2016

The asymmetric unit of the title salt, C7H18N3+·C7HN4−, comprises one cation and one anion. TheN,N,N′,N′,N′′,N′′-hexamethylguanidinium ion shows orientational disorder and two sets of N- and C-atom positions were found, with an occupancy ratio of 0.535 (3):0.465 (3). The C—N bond lengths in the guanidinium ion range from 1.339 (16) to 1.35 (2) Å, indicating partial double-bond character pointing towards charge delocalization within the NCN planes. The negative charge in the 1,1,3,3-tetracyanoprop-2-en-1-ide ion is delocalized within the CCC planes with the C—C bonds ranging in length from 1.379 (3) to 1.427 (3) Å, also indicating partial double-bond character.
5-Nitro-1-(prop-2-yn-1-yl)-1H-indazole
Authors: Boulhaoua Mohammed , El Hafi Mohamed , Benchidmi Mohammed , Essassi El Mokhtar , Mague Joel T.
Published: March 2016

The packing of the title molecule, C10H7N3O2, features the formation of weak dimersviapairwise C—H...O interactions across centers of symmetry. The prop-2-yn-1-yl moiety is twisted out of the plane of the indazole unit by 78.53 (17)°.
Effectiveness of Google keyword suggestion on users’ relevance judgment
Authors: Fattahi Rahmatollah , Parirokh Mehri , Dayyani Mohammd Hosien , Khosravi Abdolrasoul , Zareivenovel Mojgan
Published: March 2016

Purpose

– One of the most effective ways information retrieval (IR) systems including Web search engines can improve relevance performance is to provide their users with tools for facilitating query expansion. Search engines such as Google provide users with keyword suggest tools. This paper aims to investigate users’ criteria in relevance judgment regarding Google’s keywords suggest tool and to see how such keywords would lead to more relevant results from the viewpoint of users.

Design/methodology/approach

– Through a mixed method approach, quantitative and qualitative data were collected from 60 postgraduate students at Ferdowsi University of Mashhad, Iran, using four different instruments (questionnaire, thinking aloud technique, query logs and interviews).

Findings

– Among other criteria, the “relation between suggested keywords and the information need” (with the mean rate of 3.53 of four) was considered the most important by searchers in selecting suggested keywords for query expansion. Also, the “relation between suggested Keywords and the retrieved items” (with the mean rate of 3.62) was considered the second most important criterion in judging the relevance of the retrieved results. The participants agreed that the suggested keywords by Google improved the retrieval relevance. The content analysis of the participants’ aloud-thinking sessions and the interviews approved such findings.

Originality/value

– This research makes a contribution to the need of designers of IR systems regarding the use of add words for query expansion. It also helps librarians how to instruct searchers with expanding their queries to retrieve more relevant results. Another contribution of the study is the identification of a number of new relevance judgment criteria for Web-based environments.
Effectuation and causation in new internet venture growth
Authors: Guo Runping , Cai Li , Zhang Weiyong
Published: March 2016

Purpose

– Research on new internet venture growth is lacking. The purpose of this paper is to address the gap by developing and testing a theoretical model that links venturing principles (effectuation or causation) to new internet venture growth through resource bundling (pioneering or stabilizing).

Design/methodology/approach

– The proposed theoretical model is developed upon the entrepreneurship literature and resource-based view. Empirical data are collected from entrepreneurs and top executives in China via a survey. The Baron and Kenny (1986) mediation model assessment procedure is used to analyze the data.

Findings

– Both effectuation and causation are positively associated with new internet venture growth. Effectuation leads to pioneering resource bundling, which in turn contributes to new internet venture growth. Causation also contributes to new internet venture growth, but through stabilizing resource bundling.

Research limitations/implications

– This research helps link the theory of effectuation to resource-based theory by revealing resource bundling as the mediator between effectuation, causation, and new venture growth. Moreover, the authors provide empirical evidence of the importance of resource bundling with entrepreneurial strategic decision logics to the growth of new internet ventures in transitional economies.

Practical implications

– Entrepreneurs and managers of new internet ventures should leverage both venturing principles to support growth. Internet ventures generally are creative and innovative in nature, hence favor effectuation. But it will be unwise to ignore causation, which also leads to growth.

Originality/value

– This is an original empirical research guided by theories. It is a novel insight to identify the mediating effect of resource bundling. This study likely will inspire more scholarly research on the subject. It also lays a solid foundation for further inquiry such as complementarities between effectuation and causation.
The Internet of Things: a security point of view
Authors: Li Shancang , Tryfonas Theo , Li Honglei
Published: March 2016

Purpose

– The purpose of this paper is to provide an in-depth overview of the security requirements and challenges for Internet of Things (IoT) and discuss security solutions for various enabling technologies and implications to various applications.

Design/methodology/approach

– Security requirements and solutions are analysed based on a four-layer framework of IoT on sensing layer, network layer, service layer, and application layer. The cross-layer threats are analysed followed by the security discussion for the enabling technologies including identification and tracking technologies, WSN and RFID, communication, networks, and service management.

Findings

– IoT calls for new security infrastructure based on the new technical standards. As a consequence, new security design for IoT shall pay attention to these new standards. Security at both the physical devices and service-applications is critical to the operation of IoT, which is indispensable for the success of IoT. Open problems remain in a number of areas, such as security and privacy protection, network protocols, standardization, identity management, trusted architecture, etc.

Practical implications

– The implications to various applications including supervisory control and data acquisition, enterprise systems, social IoT are discussed. The paper will serve as a starting point for future IoT security design and management. The security strategies for IoT should be carefully designed by managing the tradeoffs among security, privacy, and utility to provide security in multi-layer architecture of IoT.

Originality/value

– The paper synthesizes the current security requirements for IoT and provides a clear framework of security infrastructure based on four layers. Accordingly, the security requirements and potential threats in the four-layer architecture are provided in terms of general devices security, communication security, network security, and application security.
Internet of things capability and alliance
Authors: Yu Xiaoyu , Nguyen Bang , Chen Yi
Published: March 2016

Purpose

– The purpose of this paper is to examine the role of capability and alliance arising from the internet of things (IoT), specifically in the relationships between strategic orientations (entrepreneurial and market foci) with product and process innovations. In addition, it investigates the direct relationship between IoT capability and alliance. Improving these relationships assist in ensuring that new knowledge from the IoT can be translated into tangible business innovations that contribute to economic development.

Design/methodology/approach

– Data from 207 new high-technology IoT ventures in China were obtained after three-wave mailing (i.e. two reminders). Following a rigorous process to purify and validate the measurement scale items, the study used structural equation modeling to test the conceptual model.

Findings

– Findings demonstrate that an IoT capability only enhances product innovation, however, with the addition and support from IoT alliance, both product and process innovation can be achieved in new high-tech IoT ventures. This nuanced insight suggests that new high-tech IoT ventures should focus on building their IoT capability, and at the same time, develop IoT alliances with value chain partners in order to fully take advantage of IoT and gain a better position to formulate more novel offerings.

Originality/value

– The study is first to contribute with a much needed framework of IoT and entrepreneurship by examining the role of IoT capability further in the relationships between: entrepreneurial orientation and market orientation with product and process innovations arising from IoT; and the role of IoT alliance (interfirm relations, partnerships, etc.) on the relationship above.