bluuebunny/crossref_metadata_2025 huggingface dataset:
Crowdfunding in social finance
Authors: Lehner Othmar M.
Published: December 2015

This chapter examines crowdfunding, particularly as it relates to financing social enterprise. It suggests that crowdfunding offers a real opportunity to connect mass retail investors with social enterprise, and it highlights the significant research gaps to which this development has given rise. The chapter starts by examining various business models for crowdfunding and these are set out in detail. Then it explores debt- and equity-based models of crowdfunding in relation to social finance. Each model is considered in turn. Finally, the chapter proposes a range of future research themes and topics for scholarship concerned with crowdfunding in a social enterprise context.
Investing for social impact
Authors: Hinton Peter , Penemetsa Sweta
Published: December 2015

This chapter focuses on foreign direct investment (DFI) and private equity (PE) finance as a source of social impact. It assesses the current investment landscape of DFIs and PE in emerging markets with a special emphasis on the African and South Asian markets. It argues that DFIs have been providing a form of (largely unrecognized) social finance to emerging markets for many decades by dint of their impact mandates and ownership structures. Such finance stresses clear standards of environmental, social, and governance performance and aims to measure and account for them transparently. However, the chapter goes on to explore how various funds can be divided as being either ‘finance’ or ‘impact’ first with significant implications for their activities and structures. The chapter concludes by looking at a range of key issues with respect to FDI as social finance.
{A/a}spect/discourse interactions
Authors: Tasmowski Liliane
Published: December 2015

This chapter has its origin in the totally unexpected observation that in a translation of a narrative text from French into Bulgarian each and every preverbal weak indefinite subject in French of the form des N.pl has been rendered by a definite NP in Bulgarian. The chapter investigates the possible reasons for such a curious systematic correspondance. Can it be due to internal Aspect on the verbal level, to a topicalization strategy on the sentence level, or to the default value of the definite article on the morphosemantic level? All these solutions are ruled out by data to the contrary. It appears that the ultimate explanation for the difference consists in a combination of all of these factors as related to pragmatic differences between the use of articles in French and in Bulgarian. The solution to the problem must take into account both discourse structure, information structure, and world knowledge.
Time talk in narrative discourse: evidence from child and adult language acquisition
Authors: Hickmann Maya , Hendriks Henriëtte
Published: December 2015

Children’s acquisition of verbal morphology has been attributed to cognitive factors, leading them at first to focus on perceptible results. The chapter tests this hypothesis on the basis of narrative data elicited from children (four to ten years) and control groups of adults in four languages presenting relevant differences in their temporal–aspectual systems (English, French, German, Chinese). These data are then compared to the productions of Chinese adults learning a second language (English, French, German) using the same experimental procedure. The results show that discourse functions of tense–aspect take some time to emerge, enabling children to ground information after age seven. Cross-linguistic differences also show the role of language particulars in accounting for children’s development. Finally, the adult data suggest that cognitive factors cannot be the only determinants of development. In conclusion, the discussion highlights the complex interplay of cognitive, language-specific, and discourse determinants of temporal–aspectual markers.
Thepassé composéin Old French and Modern French: evolution or revolution?
Authors: Caudal Patrick
Published: December 2015

This chapter is concerned with determining how strictly ordered sequences of events described by the passé composé (PC) in Old French should be accounted for. The analysis here proposed will combine (i) insights from analyses claiming that this tense did not have (yet) a past perfective semantic content (e.g. Martin 1971), but really behaves like a resultative narrative (‘perfective’) present in many of the above configurations, with (ii) insights from analyses claiming that it had perfective uses in some specific types of sequence of events configurations, albeit at a pragmatic level. The chapter will also show how recurrent inter-clausal syntactic patterns, as well as non-syntactically marked related discourse structural patterns, simultaneously played a role in the rise of such uses—thus pointing to interesting convergences between syntax and discourse, and to some properties they might share, particularly with respect to grammatical processes.
Orthography
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter considers the way in which the morphological structure of words interacts with their spelling. After a general introduction to the basics of English spelling, the chapter discusses how vowel length is represented in English orthography, and the way in which this is affected by morphological processes of affixation. In particular, the relation between double consonant spellings and vowel length is laid out. Then some other orthographic processes are considered which influence the spelling of morphologically complex forms or the link between spelling and pronunciation. This includes phenomena such as silent , velar softening and hyphenation.
Function words
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter considers all other English word classes that might conceivably be subjected to inflectional analysis. First it discusses pronouns, then determiners of various sorts, wh-words, and deictics. The analyses looks at the extent to which parts of function words can be said to bear meaning. For example, the role of , and  in deictic expressions is discussed. It is concluded that there is little evidence to support a morphemic analysis of such forms.
Derived nouns: quality, collective, and other abstracts
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter deals with affixes whose primary purpose is to derive nouns other than event/state/result nouns or personal/participant nouns. Among these are affixes that create abstract and collective nouns of various sorts, including -ness, -ity, -dom, -ship, -hood, -ery, -ia, -y, -ana,and -age. The chapter also looks at the suffix -ism, which has a more specific meaning than the purely abstract or collective-forming affixes, but which nevertheless forms nouns that denote neither events nor participants in events. The first part of the chapter summarizes the formal properties of these derived nouns while the second part focuses on semantic issues.
Derived verbs
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter first discusses the verb-forming prefixes a‑, be‑, fore‑, and en‑. This is followed by a description of verbal suffixation by ‑ize, ‑ify, and ‑ate, conversion into verbs, back-formation, and other processes. The first part of the chapter covers formal properties and considers the phonological characteristics of the different types of affixed forms. The second part of the chapter is devoted to the semantic characteristics of the various kinds of derived verb. Finally, the competition between the different verb-deriving processes is summarized.
Locatives of time and space
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter surveys the affixes used in English to express spatial and temporal concepts. All such affixes are prefixal, and many of them do double duty with spatial or temporal readings depending on context. English has two cohorts of such prefixes, non-native ones and native ones, and there are generally pairs (or sets) that overlap in meaning, with only subtle differences apparent. Several of the prefixes (super-, sur-, extra-, over-, under-) mix spatial readings with quantitative (or at least scalar) readings. Issues of polysemy are discussed.
Combination of affixes
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter discusses complex words that have more than one affix. First it looks at combinations of suffixes and combinations of prefixes, the areas on which research on affix combination has traditionally focused. Then it discusses types of derivative that have received little attention in the literature, those in which a prefix and a suffix are found in a single word, considering the issue of parasynthetic affixation as well. It also takes up the intersection of conversion with affixation, combinations including inflections, and derivatives involving more than two affixes. This chapter focuses on the extent to which a complexity-based approach predicts the behaviour of complex words in English.
Affixation on compounds and phrases
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter addresses the issue of derivation on bases that are compounds or phrases. It is shown that it is not at all rare to find derivational affixes in English appearing on compound bases, and that phrasal bases are also not as rare as intuitions or the literature might suggest. First the data are reviewed, much of which can be found in previous chapters treating specific types of derivation. Then the factors are considered that might contribute to the ability of an affix to take a compound or phrasal base. Finally, the chapter raises the issue of whether affixation to compounds and phrases is restricted to those structures that are highly lexicalized, and concludes that this is not the case.
Paradigmatic processes
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter takes up the vexed question of the difference between inflection and derivation as it applies to English. It considers the kinds of criteria that might distinguish between inflection and derivation, the value of the distinction where English is concerned, and features of English that make applying the distinction awkward. Special attention is paid to the cases of plural-marking, adverbial marking with ‑ly, the status of ordinal ‑th and other number-forming affixes, as well as to participles. It is concluded that the distinction is not very helpful in understanding other aspects of the morphology of English.
English morphology and theories of morphology
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This last chapter takes a broader view of what the English data tell us about morphological theory in general. First a range of theoretical models are considered (Item and Arrangement, Item and Process, Word and Paradigm), and it is concluded that the facts of English morphology do not allow us to argue strongly for or against most extant frameworks. The chapter then looks at a variety of theoretical principles that are relatively independent of broader frameworks. Here it is argued that the corpus data provide strong arguments against many of the specific claims or principles that have been proposedin the literature such as the righthandhead rule, the unitary base, hypothesis, theunitary output hypotheses, blocking, lexical phonology and morphology, the monosuffixconstraint, the first sister principle, and the lexical integrity hypothesis. Finally, the chapter turns to what we do know, and how that knowledge should help us to frame new theoretical models.
Dirac notation
Authors: Manousakis Efstratios
Published: December 2015

This chapter considers a two-state system in order to review the Dirac notation in the simplest realization of quantum mechanics, that is, a Hilbert space spanned by a basis of just two states.
Angular momentum and spherical symmetry
Authors: Manousakis Efstratios
Published: December 2015

This chapter presents orbital angular momentum as the generator or rotations in space. The operators which carry out rotations in space form a group, which is a symmetry group of the Hamiltonian when the interaction is spherically symmetric. In such a case, there are certain useful statements which we can make about the role of invariant and irreducible subspaces of the Hilbert space under the group operations and how to calculate matrix elements of tensor operators within such spaces, that is, the Wigner-Eckart theorem.
Adding angular momenta
Authors: Manousakis Efstratios
Published: December 2015

This chapter discusses addition of angular momentum. This implies that it discusses how to build eigenstates of the total angular momentum and its projection from eigenstates of the individual angular momenta and their projections. It discusses Clebsh–Gordan coefficients.
Quantization of the free electromagnetic field
Authors: Manousakis Efstratios
Published: December 2015

This chapter, in a manner analogous to that used to quantize the one-dimensional chain of atoms coupled via spring-like constants to its neighboring atoms (see Chapter 28), it will quantize the electromagnetic field in a space of volume V with periodic boundary conditions and free of sources (no static charges nor currents).
Elementary relativistic quantum mechanics
Authors: Manousakis Efstratios
Published: December 2015

This chapter is seeking relativistic wave equations, which are invariant under Lorentz transformations, in an attempt to obtain a quantum mechanical description of relativistic particles. First, the chapter starts with the Klein–Gordon equation and then it discusses the Dirac equation. It also takes the non-relativistic limit of the Dirac equation to derive the Schrödinger equation with two additional terms, the Zeeman term and the spin–orbit coupling term. These two terms emerge naturally from the Dirac equation, and thus the spin, as an internal quantum number which behaves like angular momentum, is clearly identified. Finally, the existence of antimatter is clearly supported by the nature of the solutions to the Dirac equation.
Introduction
Authors: Pinkster Harm
Published: December 2015

This chapter is, on the one hand, a very brief introduction to Latin, including information on the sources and the diversity of the corpus used, the language’s regional and historical variation, and the periodization used in the work, On the other hand, it provides a description of the methodological approach of the work, its structure and organization and some technical information concerning text editions used, translations and the selection of examples.
Latin word classes and inflectional categories
Authors: Pinkster Harm
Published: December 2015

This chapter is intended to provide those who are not well acquainted with Latin with an overview of the main Latin word classes and their morphology. It is divided into three sections: (i) nominal word classes, (ii) verbs, and (iii) non-nominal, non-verbal word classes. The first–nominal word classes–deals with the inflectional categories of number, case, and gender of nouns, and with adjectives, pronouns/determiners, and numerals. The section on verbs deals with the inflectional categories of tense and mood as well as the various verbal forms; the distinction between finite and non-finite verb forms (including substantival and adjectival verb forms and supines) receives special attention. The third main section includes adverbs, prepositions, particles and clitics.
Active/passive, reflexivity, and intransitivization
Authors: Pinkster Harm
Published: December 2015

In this chapter three uses of the verbs that are normally treated in different chapters are discussed together. It is shown that from a semantic point of view the passive, reflexive, and intransitive uses of verbs overlap. In the section on the passive a distinction is made between true passive, decausative and autocausative uses, which also applies to reflexive uses. A further distinction is made between agentful and agentless use of the passive. The degree to which these distinctions are relevant differs from text type to text type. Deponent verbs receive a separate discussion. The voice value of the gerund and the gerundive verb forms are also discussed.
Sentence type and illocutionary force
Authors: Pinkster Harm
Published: December 2015

Four sentence types are distinguished: declarative, imperative, interrogative, and exclamatory sentences. The form of negation is the main formal criterion to distinguish imperative sentences (negation ne) from the others (negation non). Each sentence type has a basic illocutionary force, but may be used with a different illocutionary force (the so-called indirect illocutionary force). Further subtypes of the four sentence types are discussed in detail. For imperative sentences a distinction can be made between wishes and orders, depending on whether the agent of the sentence is supposed to control the event the sentence refers to. For interrogative sentences a distinction is made between sentence questions and constituent questions. Additional attention is given to responses.
Syntactic functions of arguments and the categories of constituents that may fulfil them
Authors: Pinkster Harm
Published: December 2015

This chapter contains a detailed survey of the types of constituents that may function in one of the argument positions of a clause: subject, object, indirect object, other third arguments, subject complement, and object complement. The two main types of constituents found in these positions are noun phrases (including nouns and pronouns) and clauses (which are dealt with in detail in Vol. II). Subject constituents are often not expressed. Attention is paid to the conditions determining this situation. In the section on the object, constituents functioning as ‘pseudo-objects’ are discussed as well. The number of types of constituent that may function as subject and object complement is higher, including also adjectives, numerals, determiners and noun phrases in the genitive, dative, and ablative case.
The noun phrase
Authors: Pinkster Harm
Published: December 2015

‘Noun phrase’ is used in a broad sense, including nouns, noun phrases proper, and pronouns. Furthermore, attention is paid to the internal structure of adjective phrases. Typical noun phrases consist of a head and a modifier. The function of head can be fulfilled by various constituents, the most frequent being common nouns, but many other categories can be used ‘substantively’, such as adjectives and infinitives. With some nouns a modifier is required (an adnominal argument). All nouns can be modified by one or more optional attributes, the range of which is very wide including adjectives, determiners, quantifiers and others. Noun phrases are either referring or non-referring. Referring noun phrases are either specific or generic, and if specific, either definite or indefinite. In Latin there is often no formal marking corresponding to these distinctions. The traditional category of pronouns contains in reality pronouns proper and determiners, which have very diverse properties.
Buddhist Permutations and Symbolism of Fire
Authors: Skorupski Tadeusz
Published: December 2015

This chapter examines the history of fire-related ritual practices and symbolism starting from the earliest period of religious history in the Indian subcontinent, the Vedic hymns and Upaniṣads. The variety of symbolic characterizations includes fire as a natural phenomenon, as a cosmic force, as the fire of digestion, and as a key element of Brahmanic ritual. Fire is also personified as Agni, who in addition to all of these different forms is also the ritual intermediary, purifying the offerings made by humans and carrying them to the gods. Buddhism reinterpreted and adapted this fire symbolism and yogic practices employing fire symbolism were integrated into Buddhism. This study includes meditative practices, such as the kasiṇas, and esoteric physiological interpretations of fire, relating to the psycho-physical internalization of ritual practice. Fire is identified with bodhicitta, the luminous consciousness of the Buddhist practitioner.
Ritual Subjects
Authors: Orzech Charles D.
Published: December 2015

This chapter demonstrates the ongoing relation between India and China, in which changes to the practice of the homa in China are the consequence of developments in India. Although mentioned earlier, in conjunction with image consecration, the homa is described in detail around the end of the sixth century. It is then only in the middle of the next century that forms comparable to contemporary homas—including for example evocations of Agni and the summoning and enthronement of deities in a maṇ ḍala—make their first appearance. More fully developed forms were introduced by Vajrabodhi and Amoghavajra in the eighth century. This chapter also examines key differences in the social context of the ritual in China and Japan, indicating that the use of the homa in the two was actually significantly different. The theoretical issue it addresses following the historical inquiry is the role of ritual practice in subject formation.
Citizen Makers
Authors: Orgad Liav
Published: December 2015

The question whether the majority has a right to defend its culture has not been the subject of much discussion in law and political liberalism. Theories of cultural minority rights have been put forward, but it has been generally assumed by most thinkers either that the majority culture is not threatened, or that liberal states should not attempt to promote a particular culture but instead should remain neutral in the public sphere. Reality, however, has changed. The changing patterns of immigration and the changing face of the West have generated a form of majority nationalism and given rise to a series of new questions. The book addresses one of the most divisive questions—is it justified for a liberal state to restrict immigration in order to protect the culture of majority groups? It seeks to offer a form of cultural defense that is morally defensible and politically wise.
New Challenge
Authors: Orgad Liav
Published: December 2015

This chapter argues that contemporary global migration presents a new challenge. It challenges a fundamental premise in liberal thought under which majority groups can perpetuate their culture by controlling entry into the state. Grouping together nine macro and micro—level changes, the chapter traces a transformation in the relationship between majority groups and minority groups. The nine changes occur in migration patterns (scale, character, intensity), in Western society (population decline, changing lifestyles, new human rights regime), and in the world (geopolitics, technology, globalization). Each of these changes, individually, may not be entirely new, yet the combination of them all together at one time has no historical precedent. This reality brings about political and legal responses and raises normative questions. The aim of this chapter is to document the changing reality and show that it is not adequately addressed by political theory and international human rights law.
CG2AA: backmapping protein coarse-grained structures
Authors: Lombardi Leandro E. , Martí Marcelo A. , Capece Luciana
Published: December 2015

Summary: Coarse grain (CG) models allow long-scale simulations with a much lower computational cost than that of all-atom simulations. However, the absence of atomistic detail impedes the analysis of specific atomic interactions that are determinant in most interesting biomolecular processes. In order to study these phenomena, it is necessary to reconstruct the atomistic structure from the CG representation. This structure can be analyzed by itself or be used as an onset for atomistic molecular dynamics simulations. In this work, we present a computer program that accurately reconstructs the atomistic structure from a CG model for proteins, using a simple geometrical algorithm.

Availability and implementation: The software is free and available online at http://www.ic.fcen.uba.ar/cg2aa/cg2aa.py

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  lula@qi.fcen.uba.ar
Testing Antarctic resilience: the effects of elevated seawater temperature and decreased pH on two gastropod species
Authors: Schram Julie B. , Schoenrock Kathryn M. , McClintock James B. , Amsler Charles D. , Angus Robert A.
Published: December 2015

Ocean acidification has been hypothesized to increase stress and decrease shell calcification in gastropods, particularly in cold water habitats like the western Antarctic Peninsula (WAP). There is limited information on how calcified marine benthic invertebrates in this region will respond to these rapidly changing conditions. The present study investigated the effects of elevated seawater temperature and decreased pH on growth (wet mass and shell morphometrics), net calcification, and proximate body composition (protein and lipid) of body tissues in two common benthic gastropods. Individuals of the limpet Nacella concinna and the snail Margarella antarctica collected from the WAP were exposed to seawater in one of four treatment combinations: current ambient conditions (1.5°C, pH 8.0), near-future decreased pH (1.5°C, pH 7.8), near-future elevated temperature (3.5°C, pH 8.0), or combination of decreased pH and elevated temperature (3.5°C, pH 7.8). Following a 6-week exposure, limpets showed no temperature or pH effects on whole body mass or net calcification. Despite no significant differences in whole body mass, the shell length and width of limpets at elevated temperature tended to grow less than those at ambient temperature. There was a significant interaction between the sex of limpets and pH. There were no significant temperature or pH effects on growth, net calcification, shell morphologies, or proximate body composition of snails. Our findings suggest that both gastropod species demonstrate resilience to initial exposure to temperature and pH changes predicted to occur over the next several hundred years globally and perhaps sooner along the WAP. Despite few significant impacts of elevated temperature or decreased pH, any response to either abiotic variable in species with relatively slow growth and long lifespan is of note. In particular, we detected modest impacts of reduced pH on lipid allocation in the reproductive organs of the limpet N. concinna that warrants further study.
Why No Signals? Cerebral Anatomy Predicts Success of Intraoperative Neuromonitoring During Correction of Scoliosis Secondary to Cerebral Palsy
Authors: Mo Andrew Z. , Asemota Anthony O. , Venkatesan Arun , Ritzl Eva K. , Njoku Dolores B. , Sponseller Paul D.
Published: December 2015

Background:

Intraoperative neuromonitoring (IONM) is widely used to reduce postoperative neurological complications during scoliosis correction. IONM allows intraoperative detection of neurological insults to the spinal cord and enables surgeons to react in real time. IONM failure rates can reach 61% in patients with cerebral palsy (CP). Factors decreasing the quality of IONM signals or making IONM impossible in CP patients undergoing scoliosis correction have not been well described.

Methods:

We categorized IONM data from 206 children with CP who underwent surgical scoliosis correction at a single institution from 2002 through 2013 into 3 groups: (1) “no signals,” if neither somatosensory-evoked potentials (SSEP) nor transcranial motor-evoked potentials (TcMEP) could be obtained; (2) “no sensory,” if no interpretable SSEP were obtained regardless of interpretable TcMEP; and (3) “no motor,” if no interpretable TcMEP were obtained regardless of interpretable SSEP. We analyzed preexisting neuroimaging, available for 93 patients, and neurological status of the full cohort against these categories. Statistical analysis of univariate and multivariate associations was performed using logistic regression. Odds ratios (ORs) were calculated with significance set at P<0.05.

Results:

Multivariate analysis showed significant associations of periventricular leukomalacia (PVL), hydrocephalus, and encephalomalacia with lack of meaningful and interpretable signals. Focal PVL (Fig. 1) was associated with no motor (OR=39.95; P=0.04). Moderate hydrocephalus was associated with no signals (OR=32.35; P<0.01), no motor (OR=10.14; P=0.04), and no sensory (OR=8.44; P=0.03). Marked hydrocephalus (Fig. 2) was associated with no motor (OR=20.46; P<0.01) and no signals (OR=8.83; P=0.01). Finally, encephalomalacia (Fig. 3) was associated with no motor (OR=6.99; P=0.01) and no signals (OR=4.26; P=0.03).

Conclusion:

Neuroanatomic findings of PVL, hydrocephalus, and encephalomalacia are significant predictors of limited IONM signals, especially TcMEP.

Level of Evidence:

Level IV.
Minimally Invasive Cardiac Surgery Using a 3D High-Definition Endoscopic System
Authors: Ruttkay Tamas , Götte Julia , Walle Ulrike , Doll Nicolas
Published: December 2015

We describe a minimally invasive heart surgery application of the EinsteinVision 2.0 3D high-definition endoscopic system (Aesculap AG, Tuttlingen, Germany) in an 81-year-old man with severe tricuspid valve insufficiency. Fourteen years ago, he underwent a Ross procedure followed by a DDD pacemaker implantation 4 years later for tachy-brady-syndrome. His biventricular function was normal. We recommended minimally invasive tricuspid valve repair. The application of the aformentioned endoscopic system was simple, and the impressive 3D depth view offered an easy and precise manipulation through a minimal thoracotomy incision, avoiding the need for a rib spreading retractor.
Force fields for simulating the interaction of surfaces with biological molecules
Authors: Martin Lewis , Bilek Marcela M. , Weiss Anthony S. , Kuyucak Serdar
Published: December 2015

The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide–surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.
Cell–matrix interaction during strain-dependent remodelling of simulated collagen networks
Authors: Gyoneva Lazarina , Hovell Carley B. , Pewowaruk Ryan J. , Dorfman Kevin D. , Segal Yoav , Barocas Victor H.
Published: December 2015

The importance of tissue remodelling is widely accepted, but the mechanism by which the remodelling process occurs remains poorly understood. At the tissue scale, the concept of tensional homeostasis, in which there exists a target stress for a cell and remodelling functions to move the cell stress towards that target, is an important foundation for much theoretical work. We present here a theoretical model of a cell in parallel with a network to study what factors of the remodelling process help the cell move towards mechanical stability. The cell-network system was deformed and kept at constant stress. Remodelling was modelled by simulating strain-dependent degradation of collagen fibres and four different cases of collagen addition. The model did not lead to complete tensional homeostasis in the range of conditions studied, but it showed how different expressions for deposition and removal of collagen in a fibre network can interact to modulate the cell's ability to shield itself from an imposed stress by remodelling the surroundings. This study also showed how delicate the balance between deposition and removal rates is and how sensitive the remodelling process is to small changes in the remodelling rules.
Changing planetary rotation rescues the biological clock mutantlhy cca1ofArabidopsis thaliana
Authors: Millar Andrew J. , Carrington Jamie T. , Tee Wei Ven , Hodge Sarah K.
Published: December 2015

Background: Pervasive, 24-hour rhythms from the biological clock affect diverse biological processes in metabolism and behaviour, including the human cell division cycle and sleep-wake cycle, nightly transpiration and energy balance in plants, and seasonal breeding in both plants and animals. The clock mechanism in the laboratory model plant species Arabidopsis thaliana is complex, in part due to the multiple interlocking, negative feedback loops that link the clock genes. Clock gene mutants are powerful tools to manipulate and understand the clock mechanism and its effects on physiology. The LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK ASSOCIATED 1 genes encode dawn-expressed, Myb-related repressor proteins that delay the expression of other clock genes until late in the day. Double mutant plants (lhy cca1) have low-amplitude, short-period rhythms that have been used in multiple studies of the plant circadian clock. Results: We used in vivo imaging of several luciferase (LUC) reporter genes to test how the rhythmic gene expression of wild-type and lhy cca1 mutant plants responded to light:dark cycles. Red, blue and red+blue light were similarly able to entrain these gene expression rhythms. The timing of expression rhythms in double mutant plants showed little or no response to the duration of light under 24h light:dark cycles (dusk sensitivity), in contrast to the wild type. As the period of the mutant clock is about 18h, we tested light:dark cycles of different duration (T cycles), simulating altered rotation of planet Earth. lhy cca1 double mutants regained as much dusk sensitivity in 20h T cycles as the wild type in 24h cycles, though the phase of the rhythm in the mutants was much earlier than wild type. The severe, triple lhy cca1 gi mutants also regained dusk sensitivity in 20h cycles. The double mutant showed some dusk sensitivity under 28h cycles. lhy cca1 double mutants under 28h cycles with short photoperiods, however, had the same apparent phase as wild-type plants. Conclusion: Simulating altered planetary rotation with light:dark cycles can reveal normal circadian performance in clock mutants that have been described as arrhythmic under standard conditions. The features rescued here comprise a dynamic behaviour (apparent phase under 28h cycles) and a dynamic property (dusk sensitivity under 20h cycles). These conditional clock phenotypes indicate that parts of the clock mechanism continue to function independently of LHY and CCA1, despite the major role of these genes in wild-type plants under standard conditions. Accessibility: Most results here will be published only in this format, citable by the DOI. Data and analysis are publicly accessible on the BioDare resource (www.biodare.ed.ac.uk), as detailed in the links below. Transgenic lines are linked to Stock Centre IDs below (Table 7).
Neural oscillations as a signature of efficient coding in the presence of synaptic delays
Authors: Chalk Matthew , Gutkin Boris , Deneve Sophie
Published: December 2015

Cortical networks exhibit “global oscillations”, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a “prediction error” while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is achieved when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code.
BrowseVCF: a web-based application and workflow to quickly prioritise disease-causative variants in VCF files
Authors: Salatino Silvia , Ramraj Varun
Published: December 2015

As sequencing costs associated with fast advancing Next Generation Sequencing (NGS) technologies continue to decrease, variant discovery is becoming a more affordable and popular analysis method among research laboratories. Following variant calling and annotation, accurate variant filtering is a crucial step to extract meaningful biological information from sequencing data and to investigate disease etiology. However, the standard variant call file format (VCF) used to store this valuable information is not easy to handle without bioinformatics skills, thus preventing many investigators from directly analysing their data. Here, we present BrowseVCF, an easy-to-use stand-alone software that enables researchers to browse, query and filter millions of variants in a few seconds. Key features include the possibility to store intermediate search results, to query user-defined gene lists, to group samples for family or tumour/normal studies, to download a report of the filters applied, and to export the filtered variants in spreadsheet format. Additionally, BrowseVCF is suitable for any DNA variant analysis (exome, whole-genome and targeted sequencing), can be used also for non-diploid genomes, and is able to discriminate between Single Nucleotide Polymorphisms (SNPs), Insertions/Deletions (InDels), and Multiple Nucleotide Polymorphisms (MNPs). Owing to its portable implementation, BrowseVCF can be used either on personal computers or as part of automated analysis pipelines. The software can be initialised with a few clicks on any operating system without any special administrative or installation permissions. It is actively developed and maintained, and freely available for download fromhttps://github.com/BSGOxford/BrowseVCF/releases/latest.
A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
Authors: Ettwiller Laurence , Buswell John , Yigit Erbay , Schildkraut Ira
Published: December 2015

We have developed Cappable-seq that specifically captures primary RNA transcripts by enzymatically modifying the 5’ triphosphorylated end of RNA with a selectable tag. We first applied Cappable-seq toE. coli, achieving up to 50 fold enrichment of primary transcripts and identifying an unprecedented 16539 transcription start sites (TSS) genome-wide at single base resolution. We also applied Cappable-seq to a mouse cecum sample and for the first time identified TSS in a microbiome. Furthermore, Cappable-seq universally depletes ribosomal RNA and reduces the complexity of the transcriptome to a single quantifiable tag per TSS enabling digital profiling of gene expression in any microbiome.
Meta3C analysis of a mouse gut microbiome
Authors: Marbouty Martial , Baudry Lyam , Cournac Axel , Koszul Romain
Published: December 2015

Microbial populations as well as they biochemical activities are important components of environmental ecosystems, including the human microbiome. Deciphering the genomic content of these complex mixes of species is an important challenge but is essential to fully understand the regulation of their ecological balance. Here we apply meta3C, an experimental and computational approach that exploits the physical contacts between chromosomes to characterize large genomic regions of bacterial species mixed together, on a truly complex ecosystem: the mouse gut microbiota. Meta3C, which was initially described and applied onto controlled mixes of microorganisms, allowed thede novoassembly and scaffolding of numerous bacteria present into this natural mix. Importantly, the scaffolds analyzed exhibit the structural properties expected from typical bacterial chromosomes. Meta3C therefore paves the way to the in-depth analysis of genomic structuration of complex populations.
Crystal structure of 4-{2-[4-(dimethylamino)phenyl]diazen-1-yl}-1-methylpyridinium iodide
Authors: Chulvi Katherine , Costero Ana , Ochando Luis E. , Gaviña Pablo
Published: December 2015

The molecular geometry of the ionic title compound, C14H17N4+·I−or DAZOP+·I−, is essentially featureless. Regarding the crystal structure, in addition to the obvious cation–anion Coulombic interactions, the packing is mostly directed by non-covalent interactions involving both ring systems, as well as the iodide anion. It consists of cationic molecules aligned along [101] and disposed in an antiparallel fashion while linked into π-bonded dimeric entities by a stacking contact involving symmetry-related phenyl rings, with a centroid–centroid distance of 3.468 (3) Å and a slippage of 0.951 Å. The dimers are, in addition, sustained by a number of C—H...I and I...π (I...centroid = 3.876 Å) interactions involving the anion. Finally, interdimeric contacts are of the C—H...I and C—H...π types.
Crystal structure of (Z)-4-methylbenzyl 3-[1-(5-methylpyridin-2-yl)ethylidene]dithiocarbazate
Authors: Ravoof Thahira Begum S. A. , Tiekink Edward R. T. , Omar Siti Aminah , Begum Sharifa Zaithun , Tahir Mohamed I. M.
Published: December 2015

In the title dithiocarbazate compound, C17H19N3S2, the central CN2S2residue is essentially planar (r.m.s. deviation = 0.0288 Å) and forms dihedral angles of 9.77 (8) and 77.47 (7)° with the substituted-pyridyl andp-tolyl rings, respectively, indicating a highly twisted molecule; the dihedral angle between the rings is 85.56 (8)°. The configuration about the C=N bond isZ, which allows for the formation of an intramolecular N—H...N(pyridyl) hydrogen bond. The packing features tolyl-methyl-C—H...N(imine), pyridyl-C—H...π(tolyl) and π–π interactions [between pyridyl rings with a distance = 3.7946 (13) Å], which generates jagged supramolecular layers that stack along thebaxis with no directional interactions between them.
A new default restraint library for the protein backbone inPhenix: a conformation-dependent geometry goes mainstream
Authors: Moriarty Nigel W. , Tronrud Dale E. , Adams Paul D. , Karplus P. Andrew
Published: December 2015

Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.
SMEs and social capital: exploring the Brazilian context
Authors: Clarke Ruth , Chandra Ramdas , Machado Marcilio
Published: December 2015

Purpose

– This study aims to explore the extent to which social capital plays a role in firm development, internationalization and growth, in the context of an emerging market, Brazil. The study aims to provide a new context and perspective on the role social capital plays in fostering growth and internationalization among small and medium enterprises (SMEs) in an emerging market.

Design/methodology/approach

– This is an exploratory study. First, empirical data are drawn from a commodity industry, the Brazilian Stone industry, which is a competitive, well-established sector in the country. Using a previously validated questionnaire from the World Bank, the extent of social capital possessed and used by the firms in this industry is correlated to their growth and performance. Based on the exploratory results, a set of research propositions are developed that point the way to questions that are important and interesting to further understand the role of social capital in this context.

Findings

– The results point to fairly low levels of social capital among Brazilian SMEs in this sector and relatively low levels of awareness of the potential opportunities to exploit social capital to further development and internationalization.

Research limitations/implications

– Social capital matters for firm growth and performance, but the extent of development of social capital in this context is fairly low. The limitations include the sample size and the homogeneity of the sample, which restricts generalizability.

Practical implications

– Building and exploiting social capital is a void that currently exists in the commodity sector in Brazil. Developing this can lead to more positive firm performance and growth, especially as the institutional context in Brazil continues to develop.

Originality/value

– The paper offers a unique context, as well as a new perspective on the role of firm social capital, by using an emerging market and a commodity industry that has been rarely studied in the literature.
Spatial health and life sciences business ecosystem: a case study of San Diego
Authors: Majava Jukka , Leviäkangas Pekka , Kinnunen Tuomo , Kess Pekka , Foit Del
Published: December 2015

Purpose

– Increasing competition in global markets requires many countries to seek new growth sectors. In addition, the nature of competition is changing. This paper applies the business ecosystem concept and studies San Diego as a spatial health and life sciences ecosystem. The purpose of this paper is to identify issues that should be considered in design of innovation policies and regional industry development.

Design/methodology/approach

– The research approach is built on a literature review of business ecosystems and spatial innovation. The empirical study is based on semi-structured interviews, observations, and information gathering and verification during field research.

Findings

– The results include a description of the ecosystem structure and dynamics. This paper demonstrates the bottom-up nature of San Diego’s health and life sciences ecosystem without a dominant lead actor, and presents prerequisites for fostering spatial ecosystems.

Research limitations/implications

– A single case may not be able to offer a generalized picture of this topic. However, the study raises several considerations for researchers and decision-makers involved in innovation policy design. Future work should extend the study and involve other spatial and substance contexts to compare findings and to pursue a more generic picture of innovation ecosystems and networks.

Originality/value

– This paper demonstrates that applying the concept of business ecosystems to the spatial context provides new insights in terms of dynamic mechanisms and factors contributing to economic growth in a particular location. Understanding how to facilitate the creation of successful spatial ecosystems is in the focal point of innovation policies.