bluuebunny/crossref_metadata_2025 huggingface dataset:
The interpretation of clefting (a)symmetries between Italian and German
Authors: Frascarelli Mara , Ramaglia Francesca
Published: December 2014

This paper proposes a comparative investigation of clefts in German and Italian. Assuming a specificational copular analysis, the properties of clefts in these languages are argued to rely on independent properties of relative clauses and nominal predicates. The major morpho-syntactic (a)symmetries are therefore discussed, and semantic, discourse and prosodic evidence supports a derivational analysis in which the clefted Focus is a predicate and the relative DP is a right-hand Topic connected with a non-expletive resumptive pronoun. As for post-copular agreement, the conditions on null subject licensing are considered: though they are very restricted in German and combine with V2 requirements, clefts represent a type of impersonal construction in which this option applies. Finally, data concerning quantifier scope and connectedness are discussed, providing further support for the present analysis.
Against the matrix left peripheral analysis of English it-clefts
Authors: Haegeman Liliane , Meinunger André , Vercauteren Aleksandra
Published: December 2014

In the wake of the proposals for the articulated left periphery (Rizzi 1997), Meinunger (1997, 1998), Frascarelli & Ramaglia (2009, 2013) and Sleeman (2011) assign to it-clefts a representation modeled on that of wh-interrogatives and of focus fronting. This paper first outlines one precise cartographic implementation of this analysis and then it is shown that such an analysis presents a number of problems of implementation, which concern the external and internal syntax of it-clefts. Distributionally, it-clefts are shown to pattern differently from sentences with focus fronting. Moreover the monoclausal analysis raises problems of implementation, in particular given that the cleft focus can itself undergo focus fronting and wh-movement.
A pragmatic analysis of the differences between NPIs and FCIs
Authors: Colinet Margot
Published: December 2014

The paper presents an analysis for a systematic distinction between NPIs and FCIs cross-linguistically. It first relates to a range of analyses that treat NPIs and FCIs as indefinites (in the sense of Kamp (1981) and Heim (1982)) that obey a particular semantic/pragmatic constraint that distinguishes them from plain indefinites. For example, Jayez and Tovena (2005) analyse this constraint as an "equity" constraint which demands that all the entities in the referential domain of the indefinite are equally likely referents for this indefinite. The new contribution of this paper consists in proposing that NPIs and FCIs differ on the fact that this "equity" constraint has a different informational status whether it enters the semantic composition of NPIs or FCIs. This is supported by evidence based on the study of three ways of coercing the interpretation of this kind of items.
The derivation of Classical Latin Aux-final clauses
Authors: Danckaert Lieven
Published: December 2014

The focus of this paper is the syntax of Latin clauses in which a finite auxiliary occurs in clause-final position, which in Classical Latin (ca. 100 BC–200 AD) is the most frequently attested word order pattern. I argue that these structures are derived through VP movement, which is analysed as an instance of EPP-driven A-movement rather than as phrasal roll-up (as in Ledgeway 2012). Evidence comes from the interaction between sentential negation and verb movement, as well as from the availability of the order VOAux. The present proposal supports the claim that in some languages, the EPP-feature on T0 attracts a VP rather than a DP (Travis 2005; Biberauer and Roberts 2005).
Partial Control in Romance Languages
Authors: Sheehan Michelle
Published: December 2014

This article considers the availability of partial Control in European Portuguese, French, Spanish and Italian and argues that many apparent examples of partial Control actually involve exhaustive control with a covert comitative, along the lines proposed by Boeckx, Hornstein & Nunes (2010) for English. The low level differences between French, Spanish, Italian and European Portuguese are argued to reduce to lexical differences concerning which verbs happen to be comitative in these varieties. This is the case even though the covert comitative approach is actually problematic as an analysis of partial Control in English. The implication for theories of Control is that surface instances of partial Control can have different underlying analyses.
‘Rippled’ low topics
Authors: Torregrossa Jacopo
Published: December 2014

This paper is concerned with low topics in the sentential left periphery. It builds on two main assumptions: (1) postfocal material is right-dislocated (Samek-Lodovici 2006); (2) fronted focus in Italian triggers a phonological process called ‘ripple effect of focus’ (Zubizarreta 2010). First, I will provide experimental evidence in favor of the second assumption and I will claim that a syntactic account of low topics is not tenable. Then, I will show that the free word order exhibited by postfocal constituents and the occurrence of low topics arise as side effects of the ripple effect of focus. This line of investigation argues in favor of a prosodic account of the phenomena at stake.
A comparison of fricative voicing and lateral velarization phenomena in Barcelona
Authors: Davidson Justin
Published: December 2014

This investigation constitutes a quantitative variationist approach toward Spanish in contact with Catalan in Barcelona, Spain. It seeks to empirically measure concrete usage patterns of two phonetic variants, [ɫ] and [z], in the Spanish of Catalan-Spanish bilinguals, as well as establish the extent to which both variants are conditioned by linguistic factors and Catalan dominance. The careful Spanish speech of 20 Barcelonan females (ages 18–27) was elicited through a word-reading task. Goldvarb binomial logistic regression analyses revealed that sensitivity to linguistic factors varied according to Catalan dominance. Moreover, although both variants were favored most by Catalan-dominant speakers, usage patterns among more Spanish-dominant speakers were divergent, consistent with claims of negative social value linked solely to [ɫ]
The tense-aspect system of Khorchin Mongolian
Authors: Brosig Benjamin
Published: December 2014

Khorchin, a Mongolian dialect spoken in eastern Inner Mongolia, has a tense-aspect system slightly simpler than Middle Mongol and considerably simpler than Central Mongolian dialects (Khalkha, Chakhar). While it can express the time stability of ongoing events with many nuances, present habitual and generic events are not distinguished. The existence of a present perfect category is doubtful, but in any case it doesn’t extend to the past as participle-copula-combinations are impossible. Evidentiality was lost in the central verbal system, but a non-obligatory quotative/hearsay marker exists. This article is an attempt to fit these phenomena into a coherent system of tense, aspect and related notions and to explore some of its diachronic implications.
Conspiring motivations for causative and passive isomorphism:
Authors: Jang Taeho , Payne Thomas E.
Published: December 2014

In many languages a single morphological category exists that expresses both causative and passive functions. Such “causative/passive isomorphism” appears anomalous from the point of view of much work in linguistic typology in that a causative is often considered a “valence increasing” construction, while passive is a “valence decreasing” construction. Nevertheless causative/passive isomorphism is fairly common and can prove stable over multiple generations of language change. In this paper we show how an analytic causative construction can become a morphological permissive causative, and finally take on the functions of canonical passive constructions. This path is motivated by well-documented processes of metaphorical extension, reanalysis and grammaticalization. We illustrate this development with data from Xibe (Sibe), a Tungusic language spoken in Northwestern China.
A survey of alignment features in the Greater Hindukush with special references to Indo-Aryan
Authors: Liljegren Henrik
Published: December 2014

The Hindukush Indo-Aryan (‘Dardic’) languages (Pakistan, Afghanistan, Kashmir) display a great range of variation in alignment patterns. The diversity is primarily evidenced in the case-marking of core argument noun phrases and verbal person marking properties. Along these parameters, six distinct alignment types emerge, each, in combination with language-specific developments, reflecting contact-induced changes that can be attributed to three significant areas or subareas that conflate in the region: first, a large Persian-dominated area overlapping with the Western part of the region, characterized by overt patient marking; second, an area in the East with e.g. ancient Tibetan influences, characterized by overt agent marking; and third, an area in the South bordering on the influential Hindi-Urdu belt, stretching over large parts of the Indian Subcontinent, characterized by patient agreement in the perfective.
Non-past copular markers in Turkish
Authors: Karakoç Birsel
Published: December 2014

The present paper aims to investigate non-past copular markers in modern Standard Turkish from a comparative point of view. The following markers are analysed by taking into account their semantic, discursive and clausal properties as a whole: (1) the simple subject markers of pronominal type, including the zero realization in third person; (2) the enclitic -DIr developed from a verbal copular predication; (3) the copular markers olur and oluyor consisting of the verb ol- ‘to be(come)’ and the non-past forms -(V)r or (Ø)Iyor, respectively. The underlying research questions are: (1) What semantic contents are inherently denoted by the respective copular strategies? (2) Are there any preferences and/or restrictions in the combinability of these copular markers with subject and predicate nouns, as well as with other clausal elements? (3) Is there any distributional relation between the copular markers and the semantic types of their copular clauses? (4) What are the discursive and pragmatic properties of these copular forms? The analysis suggests that the enclitic -DIr functions as a propositional stance marker, while olur and oluyor mainly operate on predicational level, though they occur as stance markers in special pragmatic constellations.
On the distribution of the contrastive-concessive discourse connectives ama ‘but/yet’ and fakat ‘but’ in written Turkish
Authors: Zeyrek Deniz
Published: December 2014

This chapter analyzes the similarities and differences between two contrastive-concessive discourse connectives in written Turkish, namely ama ‘but/yet’ and fakat ‘but’. The analysis is mainly based on Turkish Discourse Bank, a corpus annotated for discourse connectives and the discourse units they relate. A modular approach to discourse is adopted in the study, where the connectives are analyzed considering the characteristics of their arguments, their position in the sentence, the senses they convey, and how they are distributed across genres. The analyses are carried out quantitatively and qualitatively. One of the major findings of the study is that ama signals concession and pragmatic interpretations more readily than fakat does, suggesting that ama has a better ability to access inferences in discourse. The study also finds that while ama is the preferred discourse connective of fiction, fakat is the preferred discourse connective of more formal genres (e.g. research papers, monographs).
Evidentiality in Dzungar Tuvan
Authors: Rind-Pawlowski Monika
Published: December 2014

Dzungar Tuvan is a Turkic language variety spoken in North-West China. This article describes the strategies of Dzungar Tuvan to express information source both in finite and infinite sentences. In finite sentences, the interplay between the suffixes -D, GAn, -(I)pdur and the copula irgin provide the means to distinguish direct-perceptive, inferential and reportive type of evidentiality. The functions of these elements are, however, text type dependent. Regarding infinite or a temporal interpretation, can be subordinated to an omitted sentences, the direct or indirect reading of perception verbs will be discussed, which depends on the aspecto-temporal marking of the complement predicate. Converbial -sA clauses, which allow a conditional perception clause to which the finite main clause constitutes a complement.
On the evolution of Russian subject reference
Authors: Sidorova Evgeniya
Published: December 2014

Personal pronouns in Russian have replaced verbal inflection forms as the main reduced referential devices marking subject. Some possible internal scenarios of this process are examined, namely the present perfect reconstruction in Old Russian and the semantic similarity between Old Russian present nominal clauses and present verbal ones. Further testing of both hypotheses is based on the detailed chronological survey on 50 Old Russian texts (about 2000 relevant verbal clauses) from the 11th till the 17th century with the help of statistical methods (Student’s t-test and Lilliefors test). The diachronic study of Old Russian documents disproves the hypothesis of initial perfect tense destruction but admits the possibility of semantic factors as a trigger to the subject reference alternation.
The development of negation in the Transeurasian languages
Authors: Robbeets Martine
Published: December 2014

In this article, the historical development of sentential negation is compared across the Japonic, Koreanic, Tungusic, Mongolic, and Turkic languages to make inferences about the expression of negation in the common Transeurasian proto-language. Integrating typological considerations, including grammaticalization theory, into the argumentation, the approach taken here differs from previous studies, which are limited to form–function comparison of individual markers. The historical development of negation in the Transeurasian languages is argued to involve a grammaticalization pathway whereby an independent negative verb developed into a preposed negative auxiliary and then, either transferred its inflection to the lexical verb to become an invariant preposed particle or, else, moved to a postposed position to become a suffix on the lexical verb. Taken together with the form–function correspondences of the negative markers, these correlations lead to the reconstruction of genealogically motivated cycles of grammaticalization in the Transeurasian family.
The 2013 Josephine Waters Bennett Lecture: Machiavelli and History*
Authors: Najemy John M.
Published: December 2014

History is the foundation of Machiavelli’s political thought. Dismissing the celebratory traditions of humanist historiography and never fully sharing humanism’s idealization of antiquity, Machiavelli sought in history the causes of political failure. He acknowledged the fragmentary and fleeting character of historical knowledge and exposed fashionable philosophies of history (cyclical recurrence, unchanging human passions, celestial influences, laws of nature, fortune) as seductive fictions purveying false consolations for history’s adversities and afflictions. Machiavelli proposed instead a critical history focused on how social conflicts shape power and its abuses. His analysis of ancient Roman and more recent Florentine conflicts turns on a crucial distinction between conflicts contained within institutional frameworks and public law and those fought with instruments of private power (political patronage, wealth, and factions) that undermine public authority. Useful history, Machiavelli insists, must show how the constant pursuit, particularly by elites, of privatized power caused both the collapse of the Roman Republic and the failures of modern Italy’s ruling classes.
Diseased Bodies, Defiled Souls: Corporality and Religious Difference in the Reformation*
Authors: Parker Charles H.
Published: December 2014

This study examines Catholic and Reformed Protestant readings of the body among pastoral and polemical writers from the mid-sixteenth to the late seventeenth century. Both Catholics and Calvinists utilized bodily corruption as a motif to promote piety and unmask religious difference in a period of intense confessional conflict. This corporal hermeneutic coincided with a pivotal moment in the history of medicine, in which a widespread enthusiasm for anatomy mixed uneasily with time-honored notions of Galenic physiology until the ascendancy of a mechanical Cartesian outlook in the late 1600s. In this intellectual milieu, Catholic and Calvinist pastoral treatises generally relied on similar corporal features to signify a sinful state, but polemical texts made important distinctions about the effects of religious difference. Catholic writers identified the heretical body as the site of humoral contamination, whereas Calvinist theorists regarded the idolatrous body as the locus of inordinate sensuality.
Arc index of pretzel knots of type (-𝑝,𝑞,𝑟)
Authors: Lee Hwa Jeong , Jin Gyo Taek
Published: December 2014

We computed the arc index for some of the pretzel knots

K
=
P
(
−
p
,
q
,
r
)

K=P(-p,q,r)

with

p
,
q
,
r
≥
2

p,q,r\ge 2

,

r
≥
q

r\geq q

and at most one of

p
,
q
,
r

p,q,r

is even. If

q
=
2

q=2

, then the arc index

α
(
K
)

\alpha (K)

equals the minimal crossing number

c
(
K
)

c(K)

. If

p
≥
3

p\ge 3

and

q
=
3

q=3

, then

α
(
K
)
=
c
(
K
)
−
1

\alpha (K)=c(K)-1

. If

p
≥
5

p\ge 5

and

q
=
4

q=4

, then

α
(
K
)
=
c
(
K
)
−
2

\alpha (K)=c(K)-2

.
Mixed effects: a unifying framework for statistical modelling in fisheries biology
Authors: Thorson James T. , Minto Cóilín
Published: December 2014

Fisheries biology encompasses a tremendous diversity of research questions, methods, and models. Many sub-fields use observational or experimental data to make inference about biological characteristics that are not directly observed (called “latent states”), such as heritability of phenotypic traits, habitat suitability, and population densities to name a few. Latent states will generally cause model residuals to be correlated, violating the assumption of statistical independence made in many statistical modelling approaches. In this exposition, we argue that mixed-effect modelling (i) is an important and generic solution to non-independence caused by latent states; (ii) provides a unifying framework for disparate statistical methods such as time-series, spatial, and individual-based models; and (iii) is increasingly practical to implement and customize for problem-specific models. We proceed by summarizing the distinctions between fixed and random effects, reviewing a generic approach for parameter estimation, and distinguishing general categories of non-linear mixed-effect models. We then provide four worked examples, including state-space, spatial, individual-level variability, and quantitative genetics applications (with working code for each), while providing comparison with conventional fixed-effect implementations. We conclude by summarizing directions for future research in this important framework for modelling and statistical analysis in fisheries biology.
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape
Authors: Griffon Aurélien , Barbier Quentin , Dalino Jordi , van Helden Jacques , Spicuglia Salvatore , Ballester Benoit
Published: December 2014

The large collections of ChIP-seq data rapidly accumulating in public data warehouses provide genome-wide binding site maps for hundreds of transcription factors (TFs). However, the extent of the regulatory occupancy space in the human genome has not yet been fully apprehended by integrating public ChIP-seq data sets and combining it with ENCODE TFs map. To enable genome-wide identification of regulatory elements we have collected, analysed and retained 395 available ChIP-seq data sets merged with ENCODE peaks covering a total of 237 TFs. This enhanced repertoire complements and refines current genome-wide occupancy maps by increasing the human genome regulatory search space by 14% compared to ENCODE alone, and also increases the complexity of the regulatory dictionary. As a direct application we used this unified binding repertoire to annotate variant enhancer loci (VELs) from H3K4me1 mark in two cancer cell lines (MCF-7, CRC) and observed enrichments of specific TFs involved in biological key functions to cancer development and proliferation. Those enrichments of TFs within VELs provide a direct annotation of non-coding regions detected in cancer genomes. Finally, full access to this catalogue is available online together with the TFs enrichment analysis tool (http://tagc.univ-mrs.fr/remap/).
Revealing missing isoforms encoded in the human genome by integrating genomics, transcriptomics and proteomics data
Authors: Hu Zhiqiang , Scott Hamish S. , Qin Guangrong , Zheng Guangyong , Chu Xixia , Xie Lu , Adelson David L. , Oftedal Bergithe E , Venugopal Parvathy , Babic Milena , Hahn Christopher N , Zhang Bing , Wang Xiaojing , Li Nan , Wei Chaochun
Published: December 2014

Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing and is much larger than the number of human genes.

In this paper, we detected 31,566 novel transcripts with coding potential by filtering ourab initiopredictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.

Author summary

The identification of all human proteins is an important and open problem. In this report we first develop anab initiopredictor to collect candidate gene models as many as possible. Next, comprehensive sets of RNA-seq data from diverse tissues and cell lines are used to select confident transcripts. Experimental validation of a subset of predictions confirms a high accuracy for the predicted coding transcript set and has added about 30,000 new protein-coding transcripts to the existing corpus of knowledge in this area. This is significant progress given that the existing protein-coding transcript number in public databases is about 60,000. Our newly found transcripts are more tissue specific. Based on our results, we show that L1's high impact on gene origin and genes with high number of transcripts are enriched in specific functions. At last, we estimate that the total number of human protein-coding transcripts is in excess of 200,000.
Global geographic patterns of sexual size dimorphism in birds: Support for a latitudinal trend?
Authors: Friedman Nicholas R. , Remeš Vladimír
Published: December 2014

Sexual size dimorphism (SSD) is widespread among animals, and is a common indication of differential selection among males and females. Sexual selection theory predicts that SSD should increase as one sex competes more fiercely for access to mates, but it is unclear what effect spatial variation in ecology may have on this behavioral process. Here, we examine SSD across the class Aves in a spatial and phylogenetic framework, and test several a priori hypotheses regarding its relationship with climate. We mapped the global distribution of SSD from published descriptions of body size, distribution, and phylogenetic relationships across 2581 species of birds. We examined correlations between SSD and nine predictor variables representing a priori models of physical geography, climate, and climate variability. Our results show guarded support for a global latitudinal trend in SSD based on a weak prevalence of species with low or female-biased SSD in the North, but substantial spatial heterogeneity. While several stronger relationships were observed between SSD and climate predictors within zoogeographical regions, no global relationship emerged that was consistent across multiple methods of analysis. While we found support for a global relationship between climate and SSD, this support lacked consistency and explanatory power. Furthermore the strong phylogenetic signal and conspicuous lack of support from phylogenetically corrected analyses suggests that any such relationship in birds is likely due to the idiosyncratic histories of different lineages. In this manner, our results broadly agree with studies in other groups, leading us to conclude that the relationship between climate and SSD is at best complex. This suggests that SSD is linked to behavioral dynamics that may at a global scale be largely independent of environmental conditions.
SpeedSeq: Ultra-fast personal genome analysis and interpretation
Authors: Chiang Colby , Layer Ryan M , Faust Gregory G , Lindberg Michael R , Rose David B , Garrison Erik P , Marth Gabor T , Quinlan Aaron R , Hall Ira M
Published: December 2014

Comprehensive interpretation of human genome sequencing data is a challenging bioinformatic problem that typically requires weeks of analysis, with extensive hands-on expert involvement. This informatics bottleneck inflates genome sequencing costs, poses a computational burden for large-scale projects, and impedes the adoption of time-critical clinical applications such as personalized cancer profiling and newborn disease diagnosis, where the actionable timeframe can measure in hours or days. We developed SpeedSeq, an open-source genome analysis platform that vastly reduces computing time. SpeedSeq accomplishes read alignment, duplicate removal, variant detection and functional annotation of a 50X human genome in <24 hours, even using one low-cost server. SpeedSeq offers competitive or superior performance to current methods for detecting germline and somatic single nucleotide variants (SNVs), indels, and structural variants (SVs) and includes novel functionality for SV genotyping, SV annotation, fusion gene detection, and rapid identification of actionable mutations. SpeedSeq will help bring timely genome analysis into the clinical realm.

Availability:SpeedSeq is available athttps://github.com/cc2qe/speedseq.
Networks that learn the precise timing of event sequences
Authors: Veliz-Cuba Alan , Shouval Harel , Josić Krešimir , Kilpatrick Zachary P.
Published: December 2014

Neuronal circuits can learn and replay firing patterns evoked by sequences of sensory stimuli. After training, a brief cue can trigger a spatiotemporal pattern of neural activity similar to that evoked by a learned stimulus sequence. Network models show that such sequence learning can occur through the shaping of feedforward excitatory connectivity via long term plasticity. Previous models describe how event order can be learned, but they typically do not explain how precise timing can be recalled. We propose a mechanism for learning both the order and precise timing of event sequences. In our recurrent network model, long term plasticity leads to the learning of the sequence, while short term facilitation enables temporally precise replay of events. Learned synaptic weights between populations determine the time necessary for one population to activate another. Long term plasticity adjusts these weights so that the trained event times are matched during playback. While we chose short term facilitation as a time-tracking process, we also demonstrate that other mechanisms, such as spike rate adaptation, can fulfill this role. We also analyze the impact of trial-to-trial variability, showing how observational errors as well as neuronal noise result in variability in learned event times. The dynamics of the playback process determine how stochasticity is inherited in learned sequence timings. Future experiments that characterize such variability can therefore shed light on the neural mechanisms of sequence learning.
Evolutionary dynamics of collective action in spatially structured populations
Authors: Peña Jorge , Nöldeke Georg , Lehmann Laurent
Published: December 2014

Many models proposed to study the evolution of collective action rely on a formalism that represents social interactions asn-player games between individuals adopting discrete actions such as cooperate and defect. Despite the importance of spatial structure in biological collective action, the analysis ofn-player games games in spatially structured populations has so far proved elusive. We address this problem by considering mixed strategies and by integrating discrete-actionn-player games into the direct fitness approach of social evolution theory. This allows to conveniently identify convergence stable strategies and to capture the effect of population structure by a single structure coefficient, namely, the pairwise (scaled) relatedness among interacting individuals. As an application, we use our mathematical framework to investigate collective action problems associated with the provision of three different kinds of collective goods, paradigmatic of a vast array of helping traits in nature: “public goods” (both providers and shirkers can use the good, e.g., alarm calls), “club goods” (only providers can use the good, e.g., participation in collective hunting), and “charity goods” (only shirkers can use the good, e.g., altruistic sacrifice). We show that relatedness promotes the evolution of collective action in different ways depending on the kind of collective good and its economies of scale. Our findings highlight the importance of explicitly accounting for relatedness, the kind of collective good, and the economies of scale in theoretical and empirical studies of the evolution of collective action.
Consequences of a Deficit in Vitamin B6 Biosynthesis de Novo for Hormone Homeostasis and Root Development in Arabidopsis
Authors: Boycheva Svetlana , Dominguez Ana , Rolcik Jakub , Boller Thomas , Fitzpatrick Teresa B.
Published: December 2014

Vitamin B6 (pyridoxal 5′-phosphate) is an essential cofactor of many metabolic enzymes. Plants biosynthesize the vitamin de novo employing two enzymes, pyridoxine synthase1 (PDX1) and PDX2. In Arabidopsis (Arabidopsis thaliana), there are two catalytically active paralogs of PDX1 (PDX1.1 and PDX1.3) producing the vitamin at comparable rates. Since single mutants are viable but the pdx1.1 pdx1.3 double mutant is lethal, the corresponding enzymes seem redundant. However, the single mutants exhibit substantial phenotypic differences, particularly at the level of root development, with pdx1.3 being more impaired than pdx1.1. Here, we investigate the differential regulation of PDX1.1 and PDX1.3 by identifying factors involved in their disparate phenotypes. Swapped-promoter experiments clarify the presence of distinct regulatory elements in the upstream regions of both genes. Exogenous sucrose (Suc) triggers impaired ethylene production in both mutants but is more severe in pdx1.3 than in pdx1.1. Interestingly, Suc specifically represses PDX1.1 expression, accounting for the stronger vitamin B6 deficit in pdx1.3 compared with pdx1.1. Surprisingly, Suc enhances auxin levels in pdx1.1, whereas the levels are diminished in pdx1.3. In the case of pdx1.3, the previously reported reduced meristem activity combined with the impaired ethylene and auxin levels manifest the specific root developmental defects. Moreover, it is the deficit in ethylene production and/or signaling that triggers this outcome. On the other hand, we hypothesize that it is the increased auxin content of pdx1.1 that is responsible for the root developmental defects observed therein. We conclude that PDX1.1 and PDX1.3 play partially nonredundant roles and are differentially regulated as manifested in disparate root growth impairment morphologies.
Coordination of bis(pyrazol-1-yl)amine to palladium(II): influence of the co-ligands and counter-ions on the molecular and crystal structures
Authors: Mendoza María de los Angeles , Bernès Sylvain , Mendoza-Díaz Guillermo
Published: December 2014

The structures of a series of complexes with general formulan[Pd(pza)X]Y·mH2O (n= 1, 2;X= Cl, Br, I, N3, NCS;Y= NO3, I, N3, [Pd(SCN)4];m= 0, 0.5, 1) have been determined, where pza is the tridentate ligand bis[2-(3,5-dimethylpyrazol-1-yl)ethyl]amine, C14H23N5. In all complexes, {bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}chloridopalladium nitrate, [Pd(pza)Cl]NO3, (1), {bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}bromidopalladium nitrate, [Pd(pza)Br]NO3, (2), {bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}iodidopalladium iodide hemihydrate, [Pd(pza)I]I·0.5H2O, (3), azido{bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}palladium azide monohydrate, [Pd(pza)N3]N3·H2O, (4), and bis[{bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}(thiocyanato-κN)palladium] tetrakis(thiocyanato-κS)palladate, [Pd(pza)NCS]2[Pd(SCN)4], (5), the [Pd(pza)X]+complex cation displays a square-planar coordination geometry, and the pza ligand is twisted, approximating twofold rotation symmetry. Although the pza ligand is found with the same conformation along the series, the dihedral angle between pyrazole rings depends on the co-ligandX. This angle span the range 79.0 (3)–88.6 (1)° for the studied complexes. In (3), two complex cations, two I−anions and one water molecule of crystallization are present in the asymmetric unit. In (5), the central amine group of pza is disordered over two positions [occupancy ratio 0.770 (18):0.230 (18)]. The complex [Pd(SCN)4]2−anion of this compound exhibits inversion symmetry and shows the Pd2+transition metal cation likewise in a square-planar coordination environment. Compound (5) is also a rare occurrence of a non-polymeric compound in which the pseudohalide ligand NCS−behaves both as thiocyanate and isothiocyanate,i.e.is coordinating either through the N atom (in the cation) or the S atom (in the anion).
Crystal structure of 1,7,8,9-tetrachloro-4-(2-fluorobenzyl)-10,10-dimethoxy-4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5-dione
Authors: Zhong Jia-liang , Hou Jia-wei , Liu Li-hong , Liu He
Published: December 2014

In the title compound, C17H12Cl4FNO4, the configuration of the cycloalkene skeleton isendo,cis. The benzene ring is twisted by 71.01 (11)° from the attached pyrrolidine ring. In the crystal, one of the methine groups of the fused-ring system forms a weak C—H...O hydrogen bond. The other methine groups participates in a C—H...F interaction to the same adjacent molecule. Together, these generate [010] chains.
Crystal structure of 3-(morpholin-4-yl)-1-phenyl-3-(pyridin-2-yl)propan-1-one
Authors: Ahamed F. M. Mashood , Padusha M. Syed Ali , Gunasekaran B.
Published: December 2014

In the title compound C18H20N2O2, the morpholine ring adopts a chair conformation with the exocyclic N—C bond in an equatorial orientation. The N atom of the morpholine ring and the C atom of the carbonyl group are in ananticonformation about the central C—C bond [torsion angle = −162.92 (11)°] and the dihedral angle between the planes of the benzene ring and the pyridine ring is 83.30 (5)°. In the crystal, pairs of very weak C—H...π interactions link the molecules into inversion dimers.
Crystal structure of (Z)-2-[(E)-2-benzylidenehydrazin-1-ylidene]-1,2-diphenylethanone
Authors: Bouchama Abdelaziz , Yahiaoui Messaoud , Chiter Chaabane , Setifi Zouaoui , Simpson Jim
Published: December 2014

The title compound, C21H16N2O, has an almost planar (r.m.s. deviation = 0.0074 Å) 1,2-dibenzylidenehydrazine backbone with an approximately orthogonal almost planar (r.m.s. deviation = 0.0368 Å) phenylethanone substituent on one of the imine C atoms. The dihedral angle between the two mean planes is 76.99 (4)°. In the crystal, molecules are linkedviaC—H...O hydrogen bonds and C—H...π contacts, forming a three-dimensional structure with molecules stacked along thea-axis direction.
Crystal structure of 3-bromo-4-dimethylamino-1-methyl-1,2,4-triazol-5(4H)-one
Authors: Laus Gerhard , Gelbrich Thomas , Wurst Klaus , Schottenberger Herwig
Published: December 2014

The title compound, C5H9BrN4O, was obtained as a minor by-product in the synthesis of 4-dimethylamino-1-methyl-1,2,4-triazolin-5-one. Except for the methyl groups of the 4-dimethylamino moiety, all the non-H atoms lie on a crystallographic mirror plane." In the crystal, the molecules are linked by C—Br...O=C interactions [Br...O = 2.877 (2) Å, C—Br...O = 174.6 (1)°] into infinite chains in thec-axis direction.
Crystal structure of 3-carbamothioylpyridinium thiocyanate
Authors: Bouchareb Hasna , Boudraa Mhamed , Bouacida Sofiane , Merazig Hocine , Chtoun El Hossain
Published: December 2014

In the cation of the title salt, C6H7N2S+·SCN−, the C=S bond is orientedtranswith respect to the C—C=N fragment in the pyridine ring. The planes of the aromatic ring and the thioamide fragment of the cation make a dihedral angle of 38.31 (4)°. In the crystal, the components are linked by N—H...S and N—H...N, hydrogen bonds, forming a two-dimensional network parallel to (10-1).
A novel pathway for the synthesis of inositol phospholipids uses cytidine diphosphate (CDP)‐inositol as donor of the polar head group
Authors: Jorge Carla D. , Borges Nuno , Santos Helena
Published: December 2014

We describe a novel biosynthetic pathway for glycerophosphoinositides in Rhodothermus marinus in which inositol is activated by cytidine triphosphate (CTP); this is unlike all known pathways that involve activation of the lipid group instead. This work was motivated by the detection in the R. marinus genome of a gene with high similarity to CTP:L‐myo‐inositol‐1‐phosphate cytidylyltransferase, the enzyme that synthesizes cytidine diphosphate (CDP)‐inositol, a metabolite only known in the synthesis of di‐myo‐inositol phosphate. However, this solute is absent in R. marinus. The fate of radiolabelled CDP‐inositol was investigated in cell extracts to reveal that radioactive inositol was incorporated into the chloroform‐soluble fraction. Mass spectrometry showed that the major lipid product has a molecular mass of 810 Da and contains inositol phosphate and alkyl chains attached to glycerol by ether bonds. The occurrence of ether‐linked lipids is rare in bacteria and has not been described previously in R. marinus. The relevant synthase was identified by functional expression of the candidate gene in Escherichia coli. The enzyme catalyses the transfer of L‐myo‐inositol‐1‐phosphate from CDP‐inositol to dialkylether glycerol yielding dialkylether glycerophosphoinositol. Database searching showed homologous proteins in two bacterial classes, Sphingobacteria and Alphaproteobacteria. This is the first report of the involvement of CDP‐inositol in phospholipid synthesis.
Risk assessment for preeclampsia in nulliparous women at 11–13 weeks gestational age: prospective evaluation of two algorithms
Authors: Skråstad RB , Hov GG , Blaas H‐GK , Romundstad PR , Salvesen KÅ
Published: December 2014

Objective

To evaluate two algorithms for prediction of preeclampsia in a population of nulliparous women in Norway.

Design

Prospective screening study.

Setting

National Centre for Fetal Medicine in Trondheim, Norway.

Population

Five hundred and forty‐one nulliparous women.

Methods

The women were examined between 11+0 and 13+6 weeks with interviews for maternal characteristics and measurements of mean arterial pressure, uterine artery pulsatility index, pregnancy‐associated plasma protein A and placental growth factor. The First Trimester Screening Program version 2.8 by The Fetal Medicine Foundation (FMF) was compared with the Preeclampsia Predictor TM version 1 revision 2 by Perkin Elmer (PREDICTOR).

Main outcome measures

Prediction of preeclampsia requiring delivery before 37 weeks, before 42 weeks and late preeclampsia (delivery after 34 weeks).

Results

The performance of the two algorithms was similar, but quite poor, for prediction of preeclampsia requiring delivery before 42 weeks with an area under the curve of 0.77 (0.67–0.87) and sensitivity 40% (95% CI 19.1–63.9) at a fixed 10% false positive rate for FMF and 0.74 (0.63–0.84) and sensitivity 30% (95% CI 11.9–54.3) at a fixed 10% false positive rate for PREDICTOR. The FMF algorithm for preeclampsia requiring delivery <37 weeks had an area under the curve of 0.94 (0.86–1.0) and sensitivity of 80% (95% CI 28.4–99.5) at a 10% fixed false positive rate.

Conclusions

Fetal Medicine Foundation and PREDICTOR algorithms had similar and only modest performance in predicting preeclampsia. The results indicate that the FMF algorithm is suitable for prediction of preterm preeclampsia.
Temporal dynamics of active Archaea in oxygen‐depleted zones of two deep lakes
Authors: Hugoni Mylène , Domaizon Isabelle , Taib Najwa , Biderre‐Petit Corinne , Agogué Hélène , Galand Pierre E. , Debroas Didier , Mary Isabelle
Published: December 2014

Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.
The exopolysaccharide Psl–eDNA interaction enables the formation of a biofilm skeleton in Pseudomonas aeruginosa
Authors: Wang Shiwei , Liu Xi , Liu Hongsheng , Zhang Li , Guo Yuan , Yu Shan , Wozniak Daniel J. , Ma Luyan Z.
Published: December 2014

A hallmark of bacterial biofilms is a self‐produced extracellular matrix of exopolysaccharide, extracellular DNA (eDNA) and proteins that hold bacterial cells together in the community. However, interactions among matrix components and how the interactions contribute to the formation of matrix remain unclear. Here, we show the physical interaction between exopolysaccharide Psl and eDNA, the two key biofilm matrix components of the opportunistic pathogen Pseudomonas aeruginosa. The interaction allows the two components to combine to form a web of eDNA–Psl fibres, which resembles a biofilm skeleton in the centre of pellicles to give bacteria structural support and capability against agents targeted on one matrix component. The web of eDNA–Psl fibres was also found in flow‐cell biofilms at microcolonies initiation stage. The colocalization of eDNA or Psl fibres with bacterial cell membrane stain suggests that fibre‐like eDNA is likely derived from the lysis of dead bacteria in biofilms. Psl can interact with DNA from diverse sources, suggesting that P. aeruginosa has the ability to use DNA of other organisms (such as human neutrophils and other bacterial species) to form its own communities, which might increase the survival of P. aeruginosa in multispecies biofilms or within a human host.
Low frequency of endospore‐specific genes in subseafloor sedimentary metagenomes
Authors: Kawai Mikihiko , Uchiyama Ikuo , Takami Hideto , Inagaki Fumio
Published: December 2014

Spore formation is considered to be one of the microbial strategies for long‐term survival in subseafloor sedimentary habitats. However, our knowledge of the genetic and physiological characteristics of subseafloor microbes is limited. Here, we studied the distribution and frequency of genes that are related to endospore formation in 10 subseafloor sedimentary metagenomes from Site C9001 off Japan and Site 1229 off Peru. None or very low frequencies of endospore‐specific genes (e.g. dpaA, dpaB, sspA, spo0A, spoIIGA, spoIIM, spoIIIAB, spoIVA, spoIVB, yabP, yunB, spoVM) were observed in the subseafloor metagenomes. Based on the number of universally conserved single copy genes, the frequency ratio of putative endospore‐formers was estimated to be < 10%, which is consistent with the frequency of Clostridia‐derived genomes (2–4%) but is lower than previous estimates based on the concentration of dipicolinic acid. Conceivable explanations for this discrepancy are as follows: the efficiency of lysis and DNA extraction of subseafloor endospore cells may have been lower than those of vegetative cells, conversion factor of dipicolinic acid content per cell may differ, and/or sporulation‐related genes and other functional strategies for long‐term survival in the deep subseafloor biosphere are evolutionarily distinct from known spore‐forming gene repertoires.
Empowerment and satisfaction in a multinational study of routine clinical practice
Authors: Clarke E. , Puschner B. , Jordan H. , Williams P. , Konrad J. , Kawohl W. , Bär A. , Rössler W. , Del Vecchio V. , Sampogna G. , Nagy M. , Süveges A. , Krogsgaard Bording M. , Slade M.
Published: December 2014

Objective

Decision‐making between mental health clinicians and patients is under‐researched. We tested whether mental health patients are more satisfied with a decision made (i) using their preferred decision‐making style and (ii) with a clinician with the same decision‐making style preference.

Method

As part of the CEDAR Study (ISRCTN75841675), a convenience sample of 445 patients with severe mental illness from six European countries were assessed for desired clinical decision‐making style (rated by patients and paired clinicians), decision‐specific experienced style and satisfaction.

Results

Patients who experienced more involvement in decision‐making than they desired rated higher satisfaction (OR = 2.47, P = 0.005, 95% CI 1.32–4.63). Decisions made with clinicians whose decision‐making style preference was for more active involvement than the patient preference were rated with higher satisfaction (OR = 3.17, P = 0.003, 95% CI 1.48–6.82).

Conclusion

More active involvement in decision‐making than the patient stated as desired was associated with higher satisfaction. A clinical orientation towards empowering, rather than shared, decision‐making may maximise satisfaction.