bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultimate Curiosity
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

This chapter first describes the cognitive science of religion, a multidisciplinary field that draws from anthropology, cognitive science, and evolutionary psychology to study the nature of religious thoughts and actions. It then explains the meaning of the terms ‘ultimate curiosity’ and ‘slipstream’, and asks how slipstream effects might provide a way of thinking about human curiosity. It suggests that particular configurations of ‘ultimate curiosity’ seem to have produced a powerful motivational slipstream in which the consequences of ‘penultimate curiosity’ became ever more spectacular. The temptation to close the gap between them—to make religion answer scientific questions or vice versa—and the ‘chutes’ that result are part of this story that must be considered.
The Two Students
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

In 2005 excavations in Alexandria uncovered a large complex of twenty lecture theatres from the fifth or sixth century ad. While there is to date no inscriptional proof, it seems almost certain that this was the site of a famous school where two men of different religions, one Christian, the other pagan, began their studies. This chapter focusses on the dispute between these two students, Simplicius the Cicilian and John Philoponus, which was not so much about the character of God as about the nature of the world. While each man’s thinking was grounded in their own religious viewpoint, both shared the assumption that the truths of religion and the truths discovered by reason and observation were part of a single seamless fabric. Hence their dispute was conducted not by pitting one claim to revelation against another, but through a series of closely reasoned philosophical arguments.
Against Aristotle
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

This chapter focusses on Galileo’s campaign against Aristotelian ideas, which began during his time at the University of Pisa. Galileo cites Philoponus a number of times in his manuscript notes on motion, describing him as one of those forced ‘by the power of truth’ to realize the falsity of Aristotle’s views. In 1592, Galileo moved from Pisa to Padua where he was appointed professor of mathematics. During this time he was able to extend dramatically his attack on Aristotle’s picture of the world with the help of a new instrument of discovery, the telescope. When he directed this instrument up at the night sky, Galileo discovered evidence that the heavenly bodies were not the perfect and unchanging entities that Aristotle had supposed. Rather they showed every sign of being formed from the same kind of elements as the Earth.
Free Philosophizing
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

This chapter focusses on Galileo’s support for Nicholas Copernicus’ idea that the Earth and the other planets all revolved around the Sun. His theologically informed intellectual optimism made him particularly anxious that the Church not condemn Copernicanism. In his Letter to Castelli, Galileo argued that there was no contradiction between science and Scripture. Holy writ was given to teach us the path to salvation but it was not necessary ‘to believe that the same God who has furnished us with senses, language and intellect would want to bypass their use and … the information we can obtain with them’. He then argued that the passage in the Book of Joshua, which describes God lengthening a day of battle by making the Sun stand still (which was used by opponents of the Copernican theory to show it contradicted Scripture), actually made better sense if Copernicus was right.
The Freedom of Intellect
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

This chapter focusses on Galileo’s The Assayer, his contribution to a debate that began with the appearance in August 1618 of the first of three comets. These had been observed by the Jesuits of the Collegio Romano using their Galilean telescope. Orazio Grassi, the professor of mathematics at the college, published a report arguing that the comet was located between the Moon and the Sun, supporting this with arguments that included the suggestion that the more distant an object, the less it was magnified by a telescope. Galileo responded to this publication with The Assayer, which reads almost as a manifesto of his approach to natural philosophy. Although barred from directly advocating Copernicus’ system, Galileo sought to ‘teach a method which would inevitably transform all natural philosophy and thus sooner or later establish a true system of the universe and demolish Aristotelian physics’.
Simplicius Reborn
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

This chapter focusses on Galileo’s Dialogue Concerning the Two Chief World Systems, which takes the form of a conversation conducted over the course of four days. A discussion between three men takes place in the Venetian palazzo of one of the three who is called Sagredo. Sagredo is an intelligent layman who is at first neutral in the debate between the other two. Galileo’s own arguments are put into the mouth of one of these two, Salviati, and a third character, Simplicius, described as a philosopher ‘whose greatest obstacle in apprehending the truth seemed to be the reputation he had acquired by his interpretations of Aristotle’. Galileo says that this character (who is recognizably modelled on two of Galileo’s opponents), ‘because of his excessive affection towards the commentaries of Simplicius, I have thought fit to leave ... under the name of the author he so much revered’.
Two Journeys
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

This chapter focusses on the scientific expeditions of Charles Darwin and Sir John Herschel in the early 1830s. For both men, the journey on which they were about to embark would yield a harvest of observations that would occupy them for years to come. Although each had rejected the idea of taking holy orders, both men shared a scientific outlook which had at its heart an essentially religious idea. The younger of the two men and the first to depart was Charles Darwin, who set sail from Plymouth in late December 1831 as an unpaid naturalist accompanying a five-year hydrographical survey voyage. In November 1833, Sir John Herschel (the son of William) began what was to be a five-year astronomical survey of the southern hemisphere. For Darwin, Herschel was a scientific hero whose understanding of science influenced the formation and conclusions of his own most famous book.
Breaking the Seals
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

This chapter describes the opening of the sealed packets sent by William Henry Fox Talbot, Dr Julius Oppert, Dr Edward Hincks, and Sir Henry Creswicke Rawlinson, and the comparison of their respective translations of the same ancient text. When the seals were broken and the manuscripts compared, three of the translations were more or less identical, ‘while it appeared to be merely owing to Dr Oppert’s very imperfect acquaintance with the English language that a difficulty was found in bringing his version into unison with the others’. The committee concluded that there was a ‘sufficient variety of words to test … the extent of the knowledge claimed by the translators of the sound of the words, and of the language to which the words are supposed to belong’. They noted that ‘the two principle scholars in the field’, Rawlinson and Hincks, often agreed word for word.
By the Waters of Babylon
Authors: Wagner Roger , Briggs Andrew
Published: March 2016

The story of the exile and the seemingly miraculous return of the Jewish people to their homeland was the apparent context for the writing and editing of a large percentage of the Old Testament. The Book of Kings and the Book of Chronicles both end with descriptions of the fall of Jerusalem and the forced transport of its people to Babylon. But had these events actually happened? While late-nineteenth-century evangelicals were committed to reading every word of Scripture as literal truth, late-nineteenth-century sceptics were equally committed to reading it as wholly mythological. This chapter shows that the archaeological traces of the Babylonian captivity were dug up in reverse order.
Bose-Einstein Condensation and Superfluidity
Authors: Pitaevskii Lev , Stringari Sandro
Published: March 2016

This volume introduces the basic concepts of Bose–Einstein condensation and superfluidity. It makes special reference to the physics of ultracold atomic gases; an area in which enormous experimental and theoretical progress has been achieved in the last twenty years. Various theoretical approaches to describing the physics of interacting bosons and of interacting Fermi gases, giving rise to bosonic pairs and hence to condensation, are discussed in detail, both in uniform and harmonically trapped configurations. Special focus is given to the comparison between theory and experiment, concerning various equilibrium, dynamic, thermodynamic, and superfluid properties of these novel systems. The volume also includes discussions of ultracold gases in dimensions, quantum mixtures, and long-range dipolar interactions.
Coherence, Interference, and the Josephson Effect
Authors: Pitaevskii Lev , Stringari Sandro
Published: March 2016

This chapter discusses several phenomena related to the coherence of trapped Bose–Einstein condensates. These include the long-range behaviour of the one-body density matrix and the interference fringes exhibited by two expanding condensates overlapping in space. Interference patterns in the momentum distribution are also discussed. A special section is devoted to the Josephson oscillations in the double-well potential, including the plasma oscillation and self-trapping phenomena. The procedures required to quantize the Josephson Hamiltonian, the phenomena of decoherence and fluctuations of the phase, and the derivation of the Bose–Hubbard model in the problem of the double well, are also discussed.
Spin-polarized Fermi Gases
Authors: Pitaevskii Lev , Stringari Sandro
Published: March 2016

This chapter discusses the magnetic properties of interacting Fermi gases. It considers the transition to the ferromagnetic phase (itinerant ferromagnetism) of a repulsive Fermi gas as a consequence of the Stoner instability. The dependence of the magnetic susceptibility on the relevant interaction coupling constant is explicitly discussed. The chapter then investigates the competition between superfluidity and ferromagnetism and the nature of the Clogston–Chandrasekhar transition, both in uniform and harmonically trapped Fermi gases, with special focus on the behaviour at unitarity, where systematic experimental data are available. It finally addresses the problem of the polaron in highly polarized configurations and the transition from the polaron to molecular binding along the BCS–BEC crossover.
Quantum Gases in Cigar and One-dimensional Regimes
Authors: Pitaevskii Lev , Stringari Sandro
Published: March 2016

This chapter discusses the behaviour of one-dimensional quantum gases. It discusses both the so-called cigar configurations, where the system is locally three-dimensional despite its one-dimensional-like geometrical shape, and the deep one-dimensional regime where the motion is frozen in the radial direction. The cigar configuration is well suited to investigating the novel features exhibited by quantized vortices and solitons. In the deep one-dimensional regime Bose gases exhibits a very different behaviour with respect to usual three-dimensional BECs as a consequence of the quantum and thermal fluctuations of the phase. The Lieb–Liniger transition between the one-dimensional mean-field and the Tonks–Girardeau regimes is discussed, and important features concerning the frequency of the collective oscillations and the superfluid behaviour are pointed out. Finally, the chapter discusses some key features exhibited by one-dimensional Fermi gases.
Aesthetically Relevant Properties
Authors: Nanay Bence
Published: March 2016

This chapter introduces the concept of ‘aesthetically relevant properties’—properties that are such that attending to them makes an aesthetic difference—and argues that it is a more useful concept for a number of debates in aesthetics than that of ‘aesthetic properties’. The aim then is to encourage a turn from the concept of ‘aesthetic properties’—properties like being beautiful and being graceful—towards that of ‘aesthetically relevant properties’. A detailed case study of how this could be done is given in a specific debate about whether aesthetic properties are perceived—one of the most important debates about aesthetic properties. It is pointed out that while there is no principled way of answering this question about aesthetic properties, if we shift this debate to be about aesthetically relevant properties, we can make real progress in understanding the relation between perception and the domain of aesthetics
Perspective—How to Write an Invertebrate Anatomy Book
Authors: Horridge Adrian
Published: March 2016

This personal view back in time spans the period from 1949, when the chapter's author was a PhD student at the Zoology Department in the University of Cambridge, until he met Ted Bullock and wrote with him the book Structure and Function in the Nervous Systems of Invertebrates
Acoelomorpha
Authors: Hejnol Andreas
Published: March 2016

The nervous system architecture of the Acoelomorpha is very diverse, ranging from a simple basiepidermal nerve plexus over basiepidermal condensations into neurite bundles and—in more derived lineages—an internalization of brain and cords below the muscle sheet. Characteristic for this animal taxon is the lack of a stomatogastric nervous system. The chapter describes details in the different organizations of nemertodermatid and acoel nervous systems and compares them with those of other taxa. It describes a step-wise internalization of the nervous system during evolution.
Annelida: Myzostomida
Authors: Helm Conrad , Bleidorn Christoph
Published: March 2016

Myzostomida comprise a taxon of mainly soft-bodied, flattened, oval, and disc-like marine protostomes. They are usually associated with echinoderms. Most myzostomids exhibit five pairs of uniramous parapodia comprising aciculae and hooked setae, but a distinct head, pygidium, or signs of external segmentation are lacking. In Myzostoma cirriferum, development comprises four free-swimming trochophora-like larval stages and juvenile development, including segment formation, takes place on its echinoderm host. The position of the group within Metazoa is under discussion, but recent phylogenomic data strongly support a close relationship with annelids or even a grouping of Myzostomida within the errant Annelida. The nervous system of myzostomids exhibits a circum-oral ring, nerves within the axial sucking pharynx, a prominent ventral nerve mass, and peripheral nerves leading towards the parapodia and lateral organs. The myzostomid brain is located dorso-laterally within the pharynx (introvert). The stomatogastric nerves originate in the region of the terminal nerve ring, located apically in the pharynx and run towards the posterior into the pharynx. The ventral nerve mass represents a ventrally oriented ring-shaped neuropil each consisting of two longitudinal nerve cords. The neuroanatomical data available for Myzostomida indicate a segmented ancestry of Myzostomida, and it supports recent molecular and morphological analyses that reveal myzostomids as part of the Annelida, such as the annelid-like nervous system comprising a dorsal anterior ganglion, presence of distinct circumoesophageal connectives, longitudinal nerves connected via twelve commissures, serial clusters of somata, and paired lateral nerves that run from the longitudinal nerves towards the body margin.
Phoronida
Authors: Temereva Elena
Published: March 2016

Phoronids are marine invertebrates with biphasic life cycles. Development of the nervous system starts at the stage of late gastrula on the animal pole of the embryo, which acquires several 5HT-like immunoreactive (-lir) cells in the epidermis of the apical plate. With time, the apical organ—a larval brain—is formed here. It consists of numerous 5HT-lir and FMRF-lir perikarya, which then give rise to the postoral neurite bundle. The development and organization of the nervous system in phoronid larvae has more in common with the deuterostomian than with the protostomian nervous system. During metamorphosis the apical organ is consumed by the juvenile, whereas the postoral neurite bundle retains and gives rise to the definitive tentacular nerve ring. The juvenile inherits from the larva the complex structure of the lophophore nervous system: the regular alternation of the intertentacular and abfrontal neurite bundles. In adult phoronids, the nervous system is represented by the intraepithelial nerve plexus, which is thickened in several areas and forms here the dorsal ganglion and tentacular nerve. All phoronids have two (right and left) or one (only left) giant nerve fibres, which start from the dorsal ganglion and pass along the left and right sides of the trunk. Each tentacle is innervated by six longitudinal neurite bundles connected to the tentacular nerve ring. All nerve elements have a similar cytological organization and stratified structure that is related to the cellular layers. Simplification of the definitive nervous system in comparison with complex larval nervous system may correlate with a sessile life style of adult phoronids.
Xiphosura
Authors: Battelle Barbara A. , Sombke Andy , Harzsch Steffen
Published: March 2016

Xiphosura are an early branching sister taxa to Arachnida, which together comprise the group Euchelicerata. Because they appear to have retained many plesiomorphic features, xiphosurans are seen as a proxy of the (Eu)chelicerate ancestor. Xiphosurans probably acquired many new characteristics during the course of their evolution; nevertheless, the structure of the xiphosuran nervous system can inform discussions of the phylogenetic relationships among arthropods and the plesiomorphic characteristics of Euarthropoda. Of the four extant species of Xiphosura, Limulus polyphemus Linnaeus, 1758, the American horseshoe crab, is the most extensively studied. The architecture of its central nervous system has been studied for more than a century, and because it has been a favourite preparation for vision scientists, there is an extensive literature detailing the structure and function of its visual system, including projections to the brain from the animal’s lateral compound eyes, median ocelli, and ventral larval eyes. Furthermore, the distribution of biogenic amines and peptides in its central nervous system and peripheral visual system have been explored. This chapter summarizes current knowledge of the L. polyphemus nervous system, focusing on the two most extensively studied subsystems of the brain, the visual system and the corpora pedunculata (mushroom bodies). The chapter describes the visual organs, their projections to the central nervous system, the sources and effects of efferent projections to the eyes, and the distribution and hypothesized functions of extraocular photoreceptors. The chapter also reviews current knowledge of the architecture and synaptic chemistry of the corpora pedunculata and compare it to that of insects.
Scorpiones
Authors: Wolf Harald
Published: March 2016

Scorpions are the oldest known terrestrial metazoans and thus an ancient and lastingly successful arthropod group. Some 1600 extant species inhabit a broad range of habitats, despite highly conserved body morphology. The first sets of appendages are the chelicers, identifying scorpions as Chelicerata; the second set are the pedipalps bearing the characteristic pincers, followed by four pairs of walking legs. The pectines are derived ventral posterior appendages for mechanical and chemical substrate probing; further chemosensors are on legs and mouthparts. A ‘tail’ with stinger is another typical scorpion characteristic. Mechanosensors are numerous on body and appendages, ranging from hair sensilla (trichobothria) to slit-sense organs. They allow high sensitivity to substrate- and air-borne vibrations, air currents, and can fulfil proprioceptive functions. Eyes are not well developed in these nocturnal animals; they also serve circadian entrainment. The scorpion central nervous system conforms to the basic pattern of the arthropod ventral nerve cord. The protocerebrum is fused with the following ten neuromeres, including deuto- and tritocerebrum of chelicers and pedipalps, into one circumoesophageal ganglion mass. Seven unfused ganglia supply posterior metasoma and ‘tail’ segments. Unfused ganglia and neuromeres of the circumoesophageal ganglion apparently conform to the basic structure of the arthropod segmental ganglion, with the respective tracts, commissures, neuropils, and soma groups. This includes immunocytochemically characterized neuron groups (5HT, GABA etc.) and inhibitory motoneurons. An intriguing characteristic is an about five- to ten-fold larger number of nerve cells supplying a given structure, from leg muscle to sensory hair, compared to most other arthropods.
Research Spotlight—Adult Neurogenesis In The Decapod Crustacean Brain: The Immune System Supplies Neural Progenitors
Authors: Sandeman David C. , Benton Jeannie L. , Beltz Barbara S.
Published: March 2016

It is firmly established that new neurons are born and integrated into the central nervous systems of both invertebrate and vertebrate organisms, throughout their adult lives. The identity and source of neuron progenitors, however, is still a matter of much debate. Freshwater crayfish represent a useful model for the study of persistent neurogenesis in long-lived animals and have provided some remarkable insights. All decapod crustaceans so far examined possess a pair of unique structures, the neurogenic niches, within their brains. In crayfish, it has been shown that cells from the niches divide and both daughters migrate along streams to neuron cell clusters in the olfactory centres where they differentiate, express appropriate transmitters, and become anatomically integrated into local circuits. In spite of providing a continual supply of cells, the niche is never depleted of precursors, implying the presence of a source from which the niche is replenished. A variety of techniques, including pulse chase labelling of cells with mitotic markers and adoptive transfer experiments in which labelled haemocytes from donor crayfish were transferred to the vascular systems of recipient crayfish, have been used in the investigation of the crayfish niche. Together these studies show that the immune system in crayfish produces cells that are transformed into precursors that generate adult-born neurons. The innate immune system in these animals, and perhaps in other organisms, is therefore a critical contributor in terms of providing neural progenitors and regulating the process of persistent neurogenesis.
Branchiopoda
Authors: Fritsch Martin , Richter Stefan
Published: March 2016

In over 150 years of nervous system research on Branchiopoda, numerous detailed descriptions are available. Branchiopods constitute one of the morphologically most disparate taxa in Crustacea, but the nervous system architecture appears to be fairly homogeneous across the taxon. As in all other crustaceans, the branchiopod brain consists of a proto-, deuto-, and tritocerebrum and is connected posteriorly to the ventral nerve cord. Proto- and deutocerebra are often completely confluent and are both connected posteriorly with the tritocerebrum by circumoral connectives. Each brain part is connected to sensory or mechanosensory organs by nerves (antennule, antenna) or tracts (compound eyes), and possesses a discrete centre for integrative processing (central body, optical neuropils, deutocerebral lobes). The presence of olfactory glomeruli is still uncertain; hemiellipsoid bodies, however, appear to be absent. The ventral nerve cord consists of a well-separated pair of ganglia in each appendage-bearing segment, which are interconnected by two parallel longitudinal connectives and two transversal commissures. Laterally, each ganglion projects nerves into the appendages and also sends nerves into the integument and the visceral body cavity. At the posterior end, two longitudinal neurite bundles extend into the telson and innervate the proctodaeum and the dorsal setae. Investigations into neuro-active substances have revealed a uniform distribution pattern of individually identifiable neurons (e.g. serotonin-like immunoreactive neurons). Although the phylogenetic position of Branchiopoda within Tetraconata is still uncertain, it appears more likely that the branchiopod brain is secondarily simplified instead of being primitive. It is uncertain whether or not this also concerns the ventral nerve cord.
Perspective—The Origin Of Vertebrate Neural Organization
Authors: Lacalli Thurston
Published: March 2016

The closest invertebrate relatives of vertebrates have brains that are smaller and organizationally much simpler that those of vertebrates, but there are similarities in basic architecture from which an evolutionary trajectory from simple to complex can be inferred. The molecular data show that many of the patterning signals are common to a range of taxa, including insects and annelids, indicating that some features are ancient and widely shared. Among protochordates, amphioxus provides the best model for the basic circuitry of the basal brainstem, including the hypothalamus and reticular formation. These have key roles in homeostasis and locomotory control, using circuits where paracrine transmission, neuropeptides, and open tract organization predominate. What is missing from amphioxus are the expanded dorsal centres, used by vertebrates for processing inputs from the paired sense organs of the head, which are themselves vertebrate innovations. Signals from these are routed through stacked arrays of cells in cortex and related structures that act as parallel array processors. In pallial derivatives in the forebrain, this has led to the emergence of primary consciousness, exemplified by awareness of the visual field, which is probably widespread in vertebrates. The function of consciousness is suggested here to relate to the adaptive advantage of generating a searchable display of sensory data, i.e. a searchable database.
Testing the ‘microbubble effect’ using the Cavitron technique to measure xylem water extraction curves
Authors: Pivovaroff Alexandria L. , Burlett Régis , Lavigne Bruno , Cochard Hervé , Santiago Louis S. , Delzon Sylvain
Published: March 2016

Plant resistance to xylem cavitation is a major drought adaptation trait and is essential to characterizing vulnerability to climate change. Cavitation resistance can be determined with vulnerability curves. In the past decade, new techniques have increased the ease and speed at which vulnerability curves are produced. However, these new techniques are also subject to new artefacts, especially as related to long-vesselled species. We tested the reliability of the ‘flow rotor’ centrifuge technique, the so-called Cavitron, and investigated one potential mechanism behind the open vessel artefact in centrifuge-based vulnerability curves: the microbubble effect. The microbubble effect hypothesizes that microbubbles introduced to open vessels, either through sample flushing or injection of solution, travel by buoyancy or mass flow towards the axis of rotation where they artefactually nucleate cavitation. To test the microbubble effect, we constructed vulnerability curves using three different rotor sizes for five species with varying maximum vessel length, as well as water extraction curves that are constructed without injection of solution into the rotor. We found that the Cavitron technique is robust to measure resistance to cavitation in tracheid-bearing and short-vesselled species, but not for long-vesselled ones. Moreover, our results support the microbubble effect hypothesis as the major cause for the open vessel artefact in long-vesselled species.
Radiation therapy for localized duodenal low-grade follicular lymphoma
Authors: Harada Arisa , Oguchi Masahiko , Terui Yasuhito , Takeuchi Kengo , Igarashi Masahiro , Kozuka Takuyo , Harada Ken , Uno Takashi , Hatake Kiyohiko
Published: March 2016

The aim of this study was to evaluate the initial treatment results and toxicities of radiation therapy for patients with early stage low-grade follicular lymphoma (FL) arising from the duodenum. We reviewed 21 consecutive patients with early stage duodenal FL treated with radiation therapy between January 2005 and December 2013 at the Cancer Institute Hospital, Tokyo. The characteristics of patients were: median age 62 years (range, 46–79 years), gender (male, 6; female, 15), clinical stage (I, 20; II 1, 1), histological grade (I, 17; II, 4). All patients were treated with radiation therapy alone. The median radiation dose was 30.6 Gy (range, 30.6–39.6) in 17 fractions. The involved-site radiation therapy was delivered to the whole duodenum. The median follow-up time was 43.2 months (range 21.4–109.3). The 3-year overall survival (OS), relapse-free survival (RFS) and local control (LC) rates were 94.7%, 79.3% and 100%, respectively. There were four relapses documented outside the treated volumes: two in the gastrointestinal tract (jejunum, terminal ileum), one in an abdominal lymph node (mesenteric lymph node) and one in the bone marrow. None died of the disease; one death was due to acute myeloid leukemia. No toxicities greater than Grade 1 were observed during treatment and over the follow-up time. The 30.6 Gy of involved-site radiation therapy provided excellent local control with very low toxicities. Radiation therapy could be an effective and safe treatment option for patients with localized low grade FL arising from the duodenum.
The “Rise–Peak–Fall” Pattern of Time Dependency of the Cardiovascular Pleiotropic Effects of Treatment With Low-dose Atorvastatin, Losartan, and a Combination Thereof in Rats
Authors: Janic Miodrag , Lunder Mojca , Cerne Darko , Marc Janja , Jerin Ales , Skitek Milan , Drevensek Gorazd , Sabovic Miso
Published: March 2016

Treatment with low, subtherapeutic doses of statins and sartans expresses beneficial pleiotropic effects on the arterial wall. The present study explored whether these effects depend on treatment duration. Wistar rats were randomly divided into 4 groups and received low-dose atorvastatin, low-dose losartan, their combination, or saline (control) daily. After 4, 6, 8, and 10 weeks of treatment, the animals were anesthetized, blood samples taken, and hearts and thoracic aortas isolated. Thoracic aorta endothelium–dependent relaxation and parameters of the isolated heart exposed to ischemic–reperfusion injury were assessed along with blood serum parameters and vasoactive genes expression. Low-dose atorvastatin, losartan, and especially their combination showed the characteristic time dependency of all studied parameters (thoracic aorta relaxation, isolated heart parameters, C-reactive protein values, genes encoding endothelial nitric oxide synthase, and CD40). The peak in efficacy was observed after 6 weeks of treatment and subsequently steadily declined. The peak versus control values were significant for all measured parameters. Only a combination of atorvastatin and losartan increased nitric oxide and decreased asymmetric dimethylarginine. A characteristic time-dependent “rise–peak–fall” pattern of the cardiovascular pleiotropic effects of statins and sartans in subtherapeutic low doses was revealed. Evidently, resistance to the explored treatment occurs after a certain period.
Herbs, Spices, and Flavoring Agents
Authors: Grivetti Louis E.
Published: March 2016

Each plant has a story, one that reflects the distance traveled from its ancient geographical origins, from wild to domesticated forms, and ultimately to culinary, cultural, medical, and social uses in the 21st century. Herbs and spices have taken these winding historical paths and the journeys reflect myriad of uses by widely different cultures as they ultimately reach our kitchens, serving plates, and palates.
Single-Cell Gene Expression Profiling and Cell State Dynamics: Collecting Data, Correlating Data Points and Connecting the Dots
Authors: Marr Carsten , Zhou Joseph X. , Huang Sui
Published: March 2016

Single-cell analyses of transcript and protein expression profiles – more precisely, single-cell resolution analysis of molecular profiles of cell populations – have now entered the center stage with widespread applications of single-cell qPCR, single-cell RNA-Seq and CyTOF. These high-dimensional population snapshot techniques are complemented by low-dimensional time-resolved, microscopy-based monitoring methods. Both fronts of advance have exposed a rich heterogeneity of cell states within uniform cell populations in many biological contexts, producing a new kind of data that has stimulated a series of computational analysis methods for data visualization, dimensionality reduction, and cluster (subpopulation) identification. The next step is now to go beyond collecting data and correlating data points: to connect the dots, that is, to understand what actually underlies the identified data patterns. This entails interpreting the “clouds of points” in state space as a manifestation of the underlying molecular regulatory network. In that way control of cell state dynamics can be formalized as a quasi-potential landscape, as first proposed by Waddington. We summarize key methods of data acquisition and computational analysis and explain the principles that link the single-cell resolution measurements to dynamical systems theory.
Light sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development
Authors: Girstmair Johannes , Zakrzewski Anne , Lapraz François , Handberg-Thorsager Mette , Tomancak Pavel , Pitrone Peter Gabriel , Simpson Fraser , Telford Maximilian J.
Published: March 2016

BACKGROUND

Selective plane illumination microscopy (SPIM a type of light-sheet microscopy) involves focusing a thin sheet of laser light through a specimen at right angles to the objective lens. As only the thin section of the specimen at the focal plane of the lens is illuminated, out of focus light is naturally absent and toxicity due to light (phototoxicity) is greatly reduced enabling longer term live imaging. OpenSPIM is an open access platform (Pitrone et al. 2013 andOpenSPIM.org) created to give new users step-by-step instructions on building a basic configuration of a SPIM microscope, which can in principle be adapted and upgraded to each laboratory’s own requirements and budget. Here we describe our own experience with the process of designing, building, configuring and using an OpenSPIM for our research into the early development of the polyclad flatwormMaritigrella crozieri– a non-model animal.

RESULTS

Our OpenSPIM builds on the standard design with the addition of two colour laser illumination for simultaneous detection of two probes/molecules and dual sided illumination, which provides more even signal intensity across a specimen. Our OpenSPIM provides high resolution 3d images and time lapse recordings, and we demonstrate the use of two colour lasers and the benefits of two color dual-sided imaging. We used our microscope to study the development of the embryo of the polyclad flatwormMaritigrella crozieri. The capabilities of our microscope are demonstrated by our ability to record the stereotypical spiral cleavage pattern ofMaritigrellawith high-speed multi-view time lapse imaging. 3D and 4D (3D + time) reconstruction of early development from these data is possible using image registration and deconvolution tools provided as part of the open source Fiji platform. We discuss our findings on the pros and cons of a self built microscope.

CONCLUSIONS

We conclude that home-built microscopes, such as an OpenSPIM, together with the available open source software, such as MicroManager and Fiji, make SPIM accessible to anyone interested in having continuous access to their own light-sheet microscope. However, building an OpenSPIM is not without challenges and an open access microscope is a worthwhile, if significant, investment of time and money. Multi-view 4D microscopy is more challenging than we had expected. We hope that our gained experience during this project will help future OpenSPIM users with similar ambitions.
Human mismatch repair system corrects errors produced during lagging strand replication more effectively
Authors: Andrianova Maria A. , Bazykin Georgii A. , Nikolaev Sergey I. , Seplyarskiy Vladimir B.
Published: March 2016

Mismatch repair (MMR) is one of the main systems maintaining fidelity of replication. Different effectiveness in correction of errors produced during replication of the leading and the lagging DNA strands was reported in yeast, but this effect is poorly studied in humans. Here, we use MMR-deficient (MSI) and MMR-proficient (MSS) cancer samples to investigate properties of the human MMR. MSI, but not MSS, cancers demonstrate unequal mutation rates between the leading and the lagging strands. The direction of strand asymmetry in MSI cancers matches that observed in cancers with mutated exonuclease domain of polymerase δ, indicating that polymerase δ contributes more mutations than its leading-strand counterpart, polymerase ε. As polymerase δ primarily synthesizes DNA during the lagging strand replication, this implies that mutations produced in wild type cells during lagging strand replication are repaired by the MMR ~3 times more effectively, compared to those produced on the leading strand.
Deep mutational scanning reveals characteristics important for targeting of the tail-anchored protein Fis1
Authors: Keskin Abdurrahman , Akdoğan Emel , Dunn Cory D.
Published: March 2016

Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of theSaccharomyces cerevisiaeFis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl-terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening the Fis1 TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs at specific organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong,in vivoevidence that lysine and arginine can “snorkel,” or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.

Abbreviations

TA

tail anchor

OM

outer membrane

MAD

membrane-anchoring domain

3-AT

3-aminotriazole

CHX

cycloheximide
DENFERT version 2: extension of ab initio structural modelling of hydrated biomolecules to the case of small-angle neutron scattering data
Authors: Koutsioubas Alexandros , Jaksch Sebastian , Pérez Javier
Published: March 2016

Following the introduction of the program DENFERT [Koutsioubas & Pérez (2013). J. Appl. Cryst.
46, 1884–1888], which takes into account the hydration layer around solvated biological molecules during ab initio restorations of low-resolution molecular envelopes from small-angle X-ray scattering data, the present work introduces the second version of the program, which provides the ability to treat neutron scattering data sets. By considering a fully interconnected and hydrated model during the entire minimization process, it has been possible to simplify the user input and reach more objective shape reconstructions. Additionally, a new method is implemented for the subtraction of the contribution of internal inhomogeneities of biomolecules to the measured scattering. Validation of the overall approach is performed by successfully recovering the shape of various protein molecules from experimental neutron and X-ray solution scattering data.
Multigrain indexing of unknown multiphase materials
Authors: Wejdemann Christian , Poulsen Henning Friis
Published: March 2016

A multigrain indexing algorithm for use with samples comprising an arbitrary number of known or unknown phases is presented. Noa prioricrystallographic knowledge is required. The algorithm applies to data acquired with a monochromatic beam and a conventional two-dimensional detector for diffraction. Initially, candidate grains are found by searching for crystallographic planes, using a Dirac comb convoluted with a box function as a filter. Next, candidate grains are validated and the unit cell is optimized. The algorithm is validated by simulations. Simulations of 500 cementite grains and ∼100 reflections per grain resulted in 99.2% of all grains being indexed correctly and 99.5% of the reflections becoming associated with the right grain. Simulations with 200 grains associated with four mineral phases and 50–700 reflections per grain resulted in 99.9% of all grains being indexed correctly and 99.9% of the reflections becoming associated with the right grain. The main limitation is in terms of overlap of diffraction spots and computing time. Potential areas of use include three-dimensional grain mapping, structural solution and refinement studies of complex samples, and studies of dilute phases.
Errors inCrystal structure of HINT from Helicobacter pylori
Authors: Maize Kimberly M.
Published: March 2016

Inaccuracies in the article,Crystal structure of HINT from Helicobacter pyloriby Tariqueet al.[(2016)Acta Cryst.F72, 42–48] are presented, and a brief history of HINT nomenclature is discussed.
DimethylN-cyanodithioiminocarbonate
Authors: Diop Mouhamadou Birame , Diop Libasse , Oliver Allen G.
Published: March 2016

The title compound, C4H6N2S2, crystallizes with four independent molecules in the asymmetric unit. Two of the molecules are disordered about a pseudo twofold rotation axis. The mean values of the C—N bonds are 1.143 (5) Å for C[triple-bond]N, 1.302 (5) Å for C=N and 1.341 (5) Å for the C—N single bond. In the crystal, molecules are linkedviaC—H...N hydrogen bonds, forming slabs parallel to thebcplane.
Factors affecting the implementation of Web 2.0 applications in Omani academic libraries
Authors: Al-Kharousi Rahma , Jabur Naeema H , Bouazza Abdelmajed , Al-Harrasi Nabhan
Published: March 2016

Purpose

– The purpose of this paper is to investigate the different factors that affect using Web 2.0 applications in Omani academic libraries (OALs).

Design/methodology/approach

– In all, 29 interviews with directors and library staff of five OALs were conducted for the purpose of collecting data for the current research.

Findings

– The results indicated that there are nine internal factors and four external factors that affect using Web 2.0 applications in OALs. Internal factors include the low motivation of directors and library staff regarding using of Web 2.0 applications, lack of training and constant changes in the management structure. Meanwhile, the external factors are related to lack of policy and regulations and weakness and low speed of the internet.

Practical implications

– Most academic libraries in Oman have not yet adopted Web 2.0 applications to enhance their services. Therefore, this study intends to open insight into the state of Web 2.0 adoption in academic libraries and will help library managers to understand factors facing the use of Web 2.0 applications in their libraries, and this could signal a basis for policy shift in the internet infrastructure especially in the institutions of the higher education.

Originality/value

– This research is the first study in the field of Web 2.0 applications in OALs that investigates the factors affecting the use of Web 2.0 applications in academic libraries in general and in OALs specifically.
Integrated library management systems
Authors: Madhusudhan Margam , Singh Vikas
Published: March 2016

Purpose

– The purpose of this paper is to analyze the various features and functions of Koha, Libsys, NewGenLib and Virtua with the help of specially designed evaluation checklist and rank them based on features/functions of integrated library management system (ILMS).

Design/methodology/approach

– The evaluation approach taken in this paper is similar to that of Singh and Sanaman (2012) and Madhusudhan and Shalini (2014) with minor modifications, comprising 306 features/functions and categorized as ten broad categories.

Findings

– The paper explores different features of open source (OS) and commercial ILMS, which reveals that Virtua got the highest total score of 218 (77.86 per cent), followed by Koha ILMS with 204 score (72.86 per cent). Interestingly, NewGenLib got the lowest total score, that is, 163 (58.21 per cent). ILMS under study are lagging behind in exploiting the full potential of the Web 2.0 features, including cloud computing features, and needs to be addressed in their future development.

Practical implications

– It is hoped that both the OS and commercial software will attend to the lacunae and soon develop fully functional Web 2.0/3.0 and cloud-based technologies.

Originality/value

– The findings of this paper will not only guide the librarians in the selection of a good ILMS, which can cater to the needs of their libraries, but also abreast the knowledge of evaluation of ILMS for the students of Library and Information Science. And the findings will help the ILMS vendors to know the limitations of their ILMS, so that they can overcome the limitations faced by users and improve their products.
Applying the DEMATEL approach to identify the focus of library service quality
Authors: Chen Yen-Ting
Published: March 2016

Purpose

– This paper aims to apply the decision-making trial and evaluation laboratory (DEMATEL) to validate the service factors of an academic library.

Design/methodology/approach

– First, the service criteria were extracted from the SERVQUAL model and then their values were examined in the user’s mind. Second, the DEMATEL was applied to estimate the importance of the criteria and identify the causal factors. Next, an empirical study was conducted to demonstrate and validate the proposed approach. Finally, this paper offers some practical suggestions for academic libraries based on the analysis.

Findings

– According to the analysis’ results, “Empathy” is the causal factor in the cause–effect diagram; i.e. the library should pay more attentions to “Empathy” rather than “Reliability”, “Responsiveness” and “Assurance” factors.

Originality/value

– DEMATEL is a useful tool to identify the prominence and relationship of service factors; the evaluation is easy to apply and has not been used before in the discussion of library service. This paper provides an alternative for libraries to sort out the priorities of service improvement. The correspondence improvement can be addressed based on the causal analysis to make notable enhancement in service quality.