bluuebunny/crossref_metadata_2025 huggingface dataset:
Governing the Environment: Three Motivating Factors
Authors: Park Susan
Published: December 2015

Governance arrangements have become increasingly complex over time, such that today everything from the Internet to medicine and warfare is subject to some form of governance at the global level. Notably, these changes in global governance can come slowly or quickly, depending on circumstances. For example, evolutionary change is evident in the establishment of new treaties and protocols on regulating the various aspects of war and its aftermath—an area where the list of agreements is long and growing. But change can also happen very quickly as new mechanisms—for example, for coordinating states’ responses during pandemics—are established during crises.
The Ethics of Arming Rebels
Authors: Pattison James
Published: December 2015

Despite the popularity of arming rebels as a foreign policy option, there is very little, if any, detailed engagement with the ethical issues surrounding the practice. There is a growing literature on the ethical issues surrounding civil wars and, more specifically, the conditions for engaging in just rebellion; but the focus of this literature is largely on the question of the justifiability of the rebels themselves in engaging in civil war and their conduct when doing so, rather than the permissibility of the arming of rebels by other agents. It is precisely this issue that I want to address here. Overall, I argue that the process should be generally eschewed. More specifically, this article seeks to establish that arming rebels is generally impermissible and only exceptionally morally permissible (even, as I will argue, when rebels are engaged in unjust wars). The former, far more restrictive claim will be established in the first part of the article. The latter, more permissive claim will be established in the second part of the article.
Parliamentary Report
Authors: Cranmer Frank
Published: December 2015

In the Parliamentary report for February to May I wrote that Lord Falconer's Assisted Dying Bill, reintroduced under the new ballot procedure for private Peers' bills, had little chance of becoming law in the current session. As it turned out, that judgment was a little premature, because Rob Marris came first in the Commons ballot for private Members' bills and decided to introduce an Assisted Dying (No 2) Bill in similar terms to Lord Falconer's. In the event, however, when his Bill had its second reading debate on 11 September – the first occasion on which the Commons had had an opportunity to debate the matter since 1997 – it was decisively defeated, by 330 votes to 118.
Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines
Authors: Ngugi David Kamanda , Blom Jochen , Stepanauskas Ramunas , Stingl Ulrich
Published: December 2015

Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine–seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.
Excitons in poly(para phenylene vinylene): a quantum-chemical perspective based on high-level ab initio calculations
Authors: Mewes Stefanie A. , Mewes Jan-Michael , Dreuw Andreas , Plasser Felix
Published: December 2015

Exciton analyses of high-level quantum-chemical computations for poly(paraphenylene vinylene) reveal the nature of the excitonic bands in PPV oligomers.
Symmetry-breaking in the H2@C60 endofullerene revealed by inelastic neutron scattering at low temperature
Authors: Mamone Salvatore , Johnson Mark R. , Ollivier Jacques , Rols Stéphane , Levitt Malcolm H. , Horsewill Anthony J.
Published: December 2015

The fine structure of the rotational ground state of molecular ortho-hydrogen confined inside the fullerene cage C60 is investigated by inelastic neutron scattering (INS).
Gold-catalyzed transformations of α-diazocarbonyl compounds: selectivity and diversity
Authors: Liu Lu , Zhang Junliang
Published: December 2015

Gold-catalyzed diazo transformations display very unique reactivity and selectivity compared to other noble metals. This review will summarize gold-catalyzed transformations of α-diazocarbonyl compounds.
The relative importance of tailpipe and non-tailpipe emissions on the oxidative potential of ambient particles in Los Angeles, CA
Authors: Shirmohammadi Farimah , Hasheminassab Sina , Wang Dongbin , Schauer James J. , Shafer Martin M. , Delfino Ralph J. , Sioutas Constantinos
Published: December 2015

This study examines the associations between the oxidative potential of ambient PM2.5and PM0.18, measured by means of the dithiothreitol (DTT) assay, and their chemical constituents and modeled sources. Particulate matter (PM) samples were collected from 2012–2013 in Central Los Angeles (LA) and 2013–2014 in Anaheim, California, USA. Detailed chemical analyses of the PM samples, including carbonaceous species, inorganic elements and water-soluble ions, were conducted. Univariate analysis indicated a high correlation (R> 0.60) between the DTT activity and the concentrations of carbonaceous species at both sites. The strongest correlations were observed between DTT and organic tracers of primary vehicle tailpipe emissions including polycyclic aromatic hydrocarbons (PAHs) and hopanes as well as EC, with higher correlations for PM0.18versusPM2.5components. Moreover, metals and trace elements (e.g., Ba, Cu, Fe, Mn, Pb and Sb) in both size ranges were also associated with DTT activity. Multiple linear regression (MLR) analysis was performed on DTT activity and PM sources identified by a Molecular Marker-Chemical Mass Balance (MM-CMB) model (i.e.major carbonaceous sources: vehicle tailpipe emissions, wood smoke, primary biogenic and secondary organic carbon) together with other typical sources of ambient PM (i.e.crustal material, vehicular abrasion, secondary ions and sea salt). Overall, our findings illustrate the relative importance of different traffic sources on the oxidative potential of ambient PM. Despite major reductions of tailpipe emissions, the lack of similar reductions (and possibly an increase) in non-tailpipe emissions makes them an important source of traffic-related PM in Los Angeles and their increasing role in the overall PM toxicity raises concerns for public health.
Protein intrinsic disorder within the Potyvirus genus: from proteome-wide analysis to functional annotation
Authors: Charon Justine , Theil Sébastien , Nicaise Valérie , Michon Thierry
Published: December 2015

The first proteome-wide analysis of intrinsic disorder in a major plant virus genus.
Antibodies as stratagems against cancer
Authors: Papageorgiou Louis , Cuong Nguyen Tien , Vlachakis Dimitrios
Published: December 2015

Antibodies have been in the frontline of anticancer research during the last few decades, since a number of different ways have been discovered to utilize them as parts or main components of anticancer drugs.
A time-course analysis of changes in cerebral metal levels following a controlled cortical impact
Authors: Portbury Stuart D. , Hare Dominic J. , Sgambelloni Charlotte , Finkelstein David I. , Adlard Paul A.
Published: December 2015

A LA-ICP-MS time course study of changing metal concentrations following traumatic brain injury in mice.
DABCO-catalyzed unusual [4 + 2] cycloaddition reaction: non-substituted allenoate acts as a four-carbon synthon and facile synthesis of spirooxindoles
Authors: Liu Yufen , Du Yanlong , Yu Aimin , Mu Haifeng , Meng Xiangtai
Published: December 2015

The first example of a non-substituted allenoate to act as a four-carbon synthon in a DABCO-catalyzed domino reaction is reported.
Synthesis of some quaternary ammonium gemini surfactants and evaluation of their performance as corrosion inhibitors for carbon steel in oil well formation water containing sulfide ions
Authors: Migahed M. A. , Shaban M. M. , Fadda A. A. , Ali Tamer Awad , Negm N. A.
Published: December 2015

Three quaternary ammonium gemini surfactants were synthesized, characterized, and evaluated as corrosion inhibitors for carbon steel in oil well formation water containing sulfide ions.
Total chemical synthesis of photoactivatable proteins for light-controlled manipulation of antigen–antibody interactions
Authors: Tang Shan , Wan Zhengpeng , Gao Yiren , Zheng Ji-Shen , Wang Jing , Si Yan-Yan , Chen Xin , Qi Hai , Liu Lei , Liu Wanli
Published: December 2015

We report the chemical synthesis of the first photo-activatable protein antigen that can be used to study antigen–antibody interaction mediated responses in B cells.
Quantum coherence in a processable vanadyl complex: new tools for the search of molecular spin qubits
Authors: Tesi Lorenzo , Lucaccini Eva , Cimatti Irene , Perfetti Mauro , Mannini Matteo , Atzori Matteo , Morra Elena , Chiesa Mario , Caneschi Andrea , Sorace Lorenzo , Sessoli Roberta
Published: December 2015

A multitechnique investigation of an evaporable vanadyl spin system with long-lived quantum coherence that self-assembles on gold.
Trends and disparities in sepsis hospitalisations in Victoria, Australia
Authors: Ore Timothy
Published: December 2015

Objective The aim of the present study was to determine the clinical and epidemiological characteristics of patients with sepsis admitted to hospitals in Victoria, Australia, during the period 2004–14. The data include incidence, severity and mortality. Methods In all, 44 222 sepsis hospitalisations were identified between 2004–05 and 2013–14 from the Victorian Admitted Episodes Dataset. The dataset contains clinical and demographic information on all admissions to acute public and private hospitals. Using the International Classification of Diseases (10th Revision) Australian Modification codes, incidence rates, severity of disease and mortality were calculated. Results Sepsis hospitalisation rates per 10 000 population increased significantly (P < 0.01) over the period, from 6.9 (95% confidence interval (CI) 5.6–7.8) to 10.0 (95% CI 9.1–11.1), an annual growth rate of 3.8%. The age-standardised in-hospital death rates per 100 000 population grew significantly (P < 0.01) from 9.2 (95% CI 7.8–10.4) in 2004–05 to 13.0 (95% CI 11.7–14.6) in 2013–14, an annual growth rate of 3.1%. Among people under 45 years of age, the 0–4 years age group had the highest hospitalisation rate (3.0 per 10 000 population; 95% CI 2.7–3.4). Nearly half (46.2%) of all sepsis hospitalisations were among patients born overseas, with a rate of 14.5 per 10 000 population (95% CI 12.4–16.2) in that group compared with a rate of 5.9 per 10 000 population (95% CI 5.3–6.7) for patients born in Australia. The age-standardised sepsis hospitalisation rate was 2.6-fold greater in the lowest compared with highest socioeconomic areas (12.7 per 10 000 population (95% CI 11.2–13.8) vs 4.8 per 10 000 population (95% CI 4.1–5.7), respectively). Conclusion This paper shows a significant upward trend in both sepsis separation rates and in-hospital death rates over the period; unlike sepsis, in-hospital death rates from all diagnoses fell over the same period. The results can be used to stimulate review of clinical practice. Greater understanding of the epidemiology of sepsis could improve care quality and outcomes. What is known about the topic? Sepsis is associated with high mortality rates and severe sepsis is the most common cause of death in intensive care units (ICU). The last published study of sepsis in Victoria (in 2005) showed a gradual rise in rates; since then, there is little information as to whether there has been any significant improvement in treatment outcomes. What does this paper add? This paper provides new information by analysing trends and variations in sepsis hospitalisations in Victoria by several demographic groups from 2004–05 to 2013–14. What are the implications for practitioners? Patients with severe sepsis consume approximately half the ICU resources. Reliable and recent data on the growth of this disease are important for prevention, allocation of resources and to track the effectiveness of care. A key area for intervention is promoting greater adherence to clinical guidelines.
Relationship between the concentration of bone morphogenetic protein-15 (BMP-15) and growth differentiation factor-9 (GDF-9) in pre-ovulatory follicles, ovarian cysts and serum in sows
Authors: Stankiewicz Tomasz , Błaszczyk Barbara
Published: December 2015

The aim of the study was to compare and assess the relationship between peripheral and ovarian bone morphogenetic protein-15 (BMP-15) and growth differentiation factor-9 (GDF-9) concentration in cysts-bearing and non-cysts-bearing sows. The research involved multiparous sows (cysts-bearing sows, n = 20; non-cysts-bearing sows, n = 26). Serum, cystic follicular fluid or fluid from the ovulatory follicles was collected from each of the sows at the time of the slaughter. The collected serum and cystic/follicular fluid samples were tested for BMP-15 and GDF-9 concentrations. BMP-15 and GDF-9 concentrations in fluid from ovarian cysts were significantly higher than in the follicular fluid (P < 0.01). The concentration of BMP-15 and GDF-9 in the serum of sows with cysts was also higher than in ovulating sows (P < 0.05 and P < 0.01, respectively). The concentration of BMP-15 in serum was positively correlated with the concentration of said protein in pre-ovulatory follicles and cysts (r = 0.70; P < 0.01 and r = 0.50; P < 0.05, respectively). A positive correlation was also found between the concentration of serum GDF-9 and cyst GDF-9 (r = 0.55; P < 0.05). Moreover, another positive correlation was detected between the BMP-15 and GDF-9 concentrations, with the highest correlation coefficient recorded in the cyst fluid (r = 0.87; P < 0.01). This study for the first time demonstrates the presence of BMP-15 and GDF-9 in the cyst fluid in sows and determines a positive correlation between the concentration of the above factors in the follicular/cystic fluid and serum. Therefore, it is possible that the determination of BMP-15 and GDF-9 serum concentration may assist diagnosing ovarian cysts in sows. However, it is suggested that further studies involving a more in-depth analysis of the role of BMP-15 and GDF-9 in the pathogenesis of ovarian cysts in pigs are needed.
Tangled up in mood
Authors: Bardagil-Mas Bernat
Published: December 2015

The two primary goals of this article are to present data concerning the mood-based alignment split that can be observed in Panará pronominal clitics and to put forward a tentative formal analysis that can capture the motivations of such phenomena in the grammar. This paper aims to explore an approach to mood from a simple syntactic perspective, in which different sets of features active in the narrow syntax suffice to derive the case marking phenomena that are correlated with mood in Panará.
Three types of suffixes in French
Authors: Don Jan , Sleeman Petra , Westveer Thom
Published: December 2015

Traditionally a two-way distinction is made in French between learned and non-learned suffixes, based on etymology. However, this distinction does not account for all suffixes. Furthermore, suffixes are traditionally considered as categorial heads, but some suffixes derive words of multiple categories. This paper proposes an alternative analysis of French suffixes, distinguishing three instead of two types, using a theory by Creemers et al. (2015) proposed for Dutch. In their analysis in the framework of Distributed Morphology, Creemers et al. distinguish three instead of two types of suffixes, proposing an alternative to Lowenstamm (2010). Starting from their proposal, we show that it is possible to distinguish three types of suffixes in French as well, accounting for the categorial flexibility of some suffixes, without resorting to the vague distinction between learned and non-learned.
Prepositional object gaps in British English
Authors: Griffiths James , Sailor Craig
Published: December 2015

In British English (BrE), a subset of pronominal objects of prepositions in have/with possessives may be optionally realised asprepositional object gaps(POGs). In this short paper, we introduce three core properties of this previously unreported phenomenon, and then outline a preliminary syntactic analysis to straightforwardly capture them. These properties are: POGs are only observed in BrE, POGs are only observed in have/with possessives, and POGs are only observed in structurally simplex complements of possessivehaveandwith. We show that these properties are straightforwardly captured by an analysis that treats POGs as arising from A-movement of the possessor. We claim that the locus of variation between dialects that permit POGs and dialects that do not is the feature specification of a single syntactic head, which either induces or precludes A-movement. This proposal accords with current Minimalist approaches to microparametric variation, in which all variation stems from the lexicon.
‘A relieved Obama’ won’t last long
Authors: de Hoop Helen , Kemperman Erica
Published: December 2015

Indefinite articles are generally used to introduce new or unfamiliar entities to the discourse. However, in noun phrases such as een opgeluchte Obama ‘a relieved Obama’, the proper noun denotes a familiar individual who does not even have to be new in the discourse. Yet, an indefinite article is used in this construction. We have conducted a corpus study in written Dutch and a production experiment in order to find out the characteristics of this construction as well as its definite counterpart. We will show that the denotation of the adjective plays a crucial role in the semantic composition of the construction, and that preferences for either a definite or an indefinite article correlate with differences in the duration of the state denoted by the adjective. We will use semantic type-theory to account for these findings.
Crossover restrictions, A-bar pronouns and discourse antecedents
Authors: van Kampen Jacqueline
Published: December 2015

The difference between weak crossovers and weakest crossovers is usually derived from a distinction between quantifiers and non-quantifiers (Lasnik & Stowell 1991). In this paper I will derive crossover restrictions from a new example set, long movement constructions with Dutch A-bar pronouns. Besides question wh-pronouns and relative pronouns, the set of Dutch A-bar pronouns includes topic d-pronouns not available in English. I will argue that A-bar pronouns constitute a uniform set of quantifiers, be it quantifiers with a discourse antecedent. To explain the present analysis, I take Safir (2004) and Ruys (2004) as a starting point. A major difference between these approaches and my own is that my analysis will make a distinction between strong crossovers as binding failures versus weak and weakest crossovers as a matter of discourse dependency, whereas it is more usual to see a related explanation for strong and weak crossovers versus weakest crossovers.
Distributive, collective and “everything” in between
Authors: Rouweler Liset , Hollebrandse Bart
Published: December 2015

In this paper we studied the interpretation of sentences with the Dutch universal quantifiers alle (all) and elke (each) in collective, distributive and cumulative situations. In the first experiment, 25 adults and 30 children from 5 and 6 years old performed a truth-value judgement task. Adults and children show similar interpretations for collective and distributive, but perform different for cumulative. As a follow-up we performed a preference task. Participants gave their preferences for the three situations for both quantifiers. Children, regardless of the quantifier, prefer the distributive situation. Adults have a strong preference for distributive for elke, showing a wider range of interpretation for alle. These data clearly indicate that Dutch children do not yet have acquired the full range of restrictions for the quantifiers alle and elke.
No Association Observed Between Blood Pressure Variability During the Acute Phase of Ischemic Stroke and In-Hospital Outcomes
Authors: Tziomalos Konstantinos , Giampatzis Vasilios , Bouziana Stella D. , Spanou Marianna , Kostaki Stavroula , Papadopoulou Maria , Angelopoulou Stella-Maria , Tsopozidi Maria , Savopoulos Christos , Hatzitolios Apostolos I.
Published: December 2015

BACKGROUND

Recent data suggest that blood pressure (BP) variability confers increased cardiovascular risk independently of BP. We aimed to evaluate the association between BP variability during the acute phase of ischemic stroke and the in-hospital outcome.

METHODS

We prospectively studied 608 consecutive patients admitted with acute ischemic stroke (39.5% males, age: 79.1±6.6 years). Variability in BP was assessed with the SD and with the coefficient of variation of systolic (SBP) and diastolic BP (DBP) during the first 2 and the first 3 days of hospitalization. The outcome was assessed with dependency rates at discharge and with in-hospital mortality.

RESULTS

Patients who were dependent at discharge did not differ from patients who were independent in any index of BP variability. Independent predictors of dependency at discharge were age (relative risk (RR) 1.17, 95% confidence interval (CI) 1.09–1.25, P < 0.001), history of prior ischemic stroke (RR 2.08, 95% CI 1.02–4.24, P = 0.04), and National Institutes of Health Stroke Scale (NIHSS) at admission (RR 1.64, 95% CI 1.44–1.86, P < 0.001). Patients who died during hospitalization did not differ in any index of BP variability from patients who were discharged. DBP at admission was independently and directly associated with in-hospital mortality (RR 1.06, 95% CI 1.03–1.09, P < 0.001). Other independent predictors of in-hospital mortality were history of atrial fibrillation (RR 3.30, 95% CI 1.46–7.49, P = 0.004) and NIHSS at admission (RR 1.18, 95% CI 1.13–1.23, P < 0.001).

CONCLUSIONS

Our data do not support the hypothesis of an association between BP variability and in-hospital outcomes among patients admitted for ischemic stroke.
CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes
Authors: Wolf Thomas , Shelest Vladimir , Nath Neetika , Shelest Ekaterina
Published: December 2015

Motivation: Secondary metabolites (SM) are structurally diverse natural products of high pharmaceutical importance. Genes involved in their biosynthesis are often organized in clusters, i.e., are co-localized and co-expressed. In silico cluster prediction in eukaryotic genomes remains problematic mainly due to the high variability of the clusters’ content and lack of other distinguishing sequence features.

Results: We present Cluster Assignment by Islands of Sites (CASSIS), a method for SM cluster prediction in eukaryotic genomes, and Secondary Metabolites by InterProScan (SMIPS), a tool for genome-wide detection of SM key enzymes (‘anchor’ genes): polyketide synthases, non-ribosomal peptide synthetases and dimethylallyl tryptophan synthases. Unlike other tools based on protein similarity, CASSIS exploits the idea of co-regulation of the cluster genes, which assumes the existence of common regulatory patterns in the cluster promoters. The method searches for ‘islands’ of enriched cluster-specific motifs in the vicinity of anchor genes. It was validated in a series of cross-validation experiments and showed high sensitivity and specificity.

Availability and implementation: CASSIS and SMIPS are freely available at https://sbi.hki-jena.de/cassis.

Contact:  thomas.wolf@leibniz-hki.de or ekaterina.shelest@leibniz-hki.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Sequence database versioning for command line and Galaxy bioinformatics servers
Authors: Dooley Damion M. , Petkau Aaron J. , Van Domselaar Gary , Hsiao William W.L.
Published: December 2015

Motivation: There are various reasons for rerunning bioinformatics tools and pipelines on sequencing data, including reproducing a past result, validation of a new tool or workflow using a known dataset, or tracking the impact of database changes. For identical results to be achieved, regularly updated reference sequence databases must be versioned and archived. Database administrators have tried to fill the requirements by supplying users with one-off versions of databases, but these are time consuming to set up and are inconsistent across resources. Disk storage and data backup performance has also discouraged maintaining multiple versions of databases since databases such as NCBI nr can consume 50 Gb or more disk space per version, with growth rates that parallel Moore's law.

Results: Our end-to-end solution combines our own Kipper software package—a simple key-value large file versioning system—with BioMAJ (software for downloading sequence databases), and Galaxy (a web-based bioinformatics data processing platform). Available versions of databases can be recalled and used by command-line and Galaxy users. The Kipper data store format makes publishing curated FASTA databases convenient since in most cases it can store a range of versions into a file marginally larger than the size of the latest version.

Availability and implementation: Kipper v1.0.0 and the Galaxy Versioned Data tool are written in Python and released as free and open source software available at https://github.com/Public-Health-Bioinformatics/kipper and https://github.com/Public-Health-Bioinformatics/versioned_data, respectively; detailed setup instructions can be found at https://github.com/Public-Health-Bioinformatics/versioned_data/blob/master/doc/setup.md

Contact: Damion.Dooley@Bccdc.Ca or William.Hsiao@Bccdc.Ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
INSECT 2.0: a web-server for genome-wide cis-regulatory modules prediction
Authors: Parra R. Gonzalo , Rohr Cristian O. , Koile Daniel , Perez-Castro Carolina , Yankilevich Patricio
Published: December 2015

INSECT is a user-friendly web server to predict the occurrence of Cis-Regulatory Modules (CRMs), which control gene expression. Here, we present a new release of INSECT which includes several new features, such as whole genome analysis, nucleosome occupancy predictions, and which provides additional links to third-party functional tools that complement user capabilities, CRM analysis and hypothesis construction. Improvements in the core implementation have led to a faster and more efficient tool. In addition, this new release introduces a new interface designed for a more integrative and dynamic user experience.

Availability and implementation:  http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT2

Contact:  pyankilevich@ibioba-mpsp-conicet.gov.ar
Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes
Authors: Oren Aharon , da Costa Milton S. , Garrity George M. , Rainey Fred A. , Rosselló-Móra Ramon , Schink Bernhard , Sutcliffe Iain , Trujillo Martha E. , Whitman William B.
Published: December 2015

The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.
Expression, crystallization and structure elucidation of γ-terpinene synthase fromThymus vulgaris
Authors: Rudolph Kristin , Parthier Christoph , Egerer-Sieber Claudia , Geiger Daniel , Muller Yves A. , Kreis Wolfgang , Müller-Uri Frieder
Published: December 2015

The biosynthesis of γ-terpinene, a precursor of the phenolic isomers thymol and carvacrol found in the essential oil fromThymussp., is attributed to the activitiy of γ-terpinene synthase (TPS). Purified γ-terpinene synthase fromT. vulgaris(TvTPS), theThymusspecies that is the most widely spread and of the greatest economical importance, is able to catalyze the enzymatic conversion of geranyl diphosphate (GPP) to γ-terpinene. The crystal structure of recombinantly expressed and purifiedTvTPS is reported at 1.65 Å resolution, confirming the dimeric structure of the enzyme. The putative active site ofTvTPS is deduced from its pronounced structural similarity to enzymes from other species of the Lamiaceae family involved in terpenoid biosynthesis: to (+)-bornyl diphosphate synthase and 1,8-cineole synthase fromSalviasp. and to (4S)-limonene synthase fromMentha spicata.
Structure of a thermostable serralysin fromSerratiasp. FS14 at 1.1 Å resolution
Authors: Wu Dongxia , Ran Tinting , Wang Weiwu , Xu Dongqing
Published: December 2015

Serralysin is a well studied metalloprotease, and typical serralysins are not thermostable. The serralysin isolated fromSerratiasp. FS14 was found to be thermostable, and in order to reveal the mechanism responsible for its thermostability, the crystal structure of serralysin fromSerratiasp. FS14 was solved to a crystallographicRfactor of 0.1619 at 1.10 Å resolution. Similar to its homologues, it mainly consists of two domains: an N-terminal catalytic domain and a `parallel β-roll' C-terminal domain. Comparative studies show that the shape of the catalytic active-site cavity is more open owing to the 189–198 loop, with a short 310-helix protruding further from the molecular surface, and that the β-sheets comprising the `parallel β-roll' are longer than those in its homologues. The formation of hydrogen bonds from one of the nonconserved residues (Asn200) to Lys27 may contribute to the thermostability.
Purification, crystallization and structural elucidation ofD-galactaro-1,4-lactone cycloisomerase fromAgrobacterium tumefaciensinvolved in pectin degradation
Authors: Vetting Matthew W. , Bouvier Jason T. , Gerlt John A. , Almo Steven C.
Published: December 2015

Pectin is found in the cell wall of plants and is often discarded as waste. A number of research groups are interested in redirecting this biomass waste stream for the production of fuel and bulk chemicals. The primary monomeric subunit of this polysaccharide is D-galacturonate, a six-carbon acid sugar that is degraded in a five-step pathway to central metabolic intermediates by some bacteria, includingAgrobacterium tumefaciens. In the third step of the pathway, D-galactaro-1,4-lactone is converted to 2-keto-3-deoxy-L-threo-hexarate by a member of the mandelate racemase subgroup of the enolase superfamily with a novel activity for the superfamily. The 1.6 Å resolution structure of this enzyme was determined, revealing an overall modified (β/α)7β TIM-barrel domain, a hallmark of the superfamily. D-Galactaro-1,4-lactone was manually docked into the active site located at the interface between the N-terminal lid domain and the C-terminal barrel domain. On the basis of the position of the lactone in the active site, Lys166 is predicted to be the active-site base responsible for abstraction of the α proton. His296 on the opposite side of the active site is predicted to be the general acid that donates a proton to the β carbon as the lactone ring opens. The lactone ring appears to be oriented within the active site by stacking interactions with Trp298.
Crystal structure of HINT fromHelicobacter pylori
Authors: Tarique K. F. , Devi S. , Abdul Rehman S. A. , Gourinath S.
Published: December 2015

Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which also have the ability to bind and inhibit protein kinase C. The structure of HINT, which exists as a homodimer, is highly conserved from humans to bacteria and shares homology with the product of fragile histidine triad protein (FHit), a tumour suppressor gene of this superfamily. Here, the structure of HINT fromHelicobacter pylori(HpHINT) in complex with AMP is reported at a resolution of 3 Å. The final model hasRandRfreevalues of 26 and 28%, respectively, with good electron density. Structural comparison with previously reported homologues and phylogenetic analysis showsH. pyloriHINT to be the smallest among them, and suggests that it branched out separately during the course of evolution. Overall, this structure has contributed to a better understanding of this protein across the animal kingdom.
Crystal structure of 8-iodoquinolinium tetrachloridoaurate(III)
Authors: Onserio Benard O. , Tamang Sem Raj , Hoefelmeyer James D.
Published: December 2015

The structure of the title salt, (C9H7IN)[AuCl4], is comprised of planar 8-iodoquinolinium cations (r.m.s. deviation = 0.05 Å) and square-planar tetrachloridoaurate(III) anions. The asymmetric unit contains one 8-iodoquinolinium cation and two halfs of [AuCl4]−anions, in each case with the central AuIIIatom located on an inversion center. Intermolecular halogen–halogen contacts were found between centrosymmetric pairs of I [3.6178 (4) Å] and Cl atoms [3.1484 (11), 3.3762 (13), and 3.4935 (12) Å]. Intermolecular N—H...Cl and C—H...Cl hydrogen bonding is also found in the structure. These interactions lead to the formation of a three-dimensional network. Additionally, there is an intramolecular N—H...I hydrogen bond between the aromatic iminium and iodine. There are no aurophilic interactions or short contacts between I and Au atoms, and there are no notable π-stacking interactions between the aromatic cations.
Crystal structure of (E)-(benzylidene)(pyridin-2-ylmethyl)amine
Authors: Harrypersad Shane , Foucher Daniel , Lough Alan J.
Published: December 2015

In the title molecule, C13H12N2, all non-H atoms, except for those of the pyridine ring, are essentially coplanar, with an r.m.s. deviation of 0.025 Å. The mean plane of these atoms forms a dihedral angle of 80.98 (4)° with the pyridine ring. In the crystal, weak C—H...π interactions link the molecules, forming a three-dimensional network.
Crystal structure ofN-[3-(dimethylamino)propyl]-N′,N′,N′′,N′′-tetramethyl-N-(N,N,N′,N′-tetramethylformamidiniumyl)guanidinium bis(tetraphenylborate)
Authors: Tiritiris Ioannis , Kantlehner Willi
Published: December 2015

In the title salt, C15H36N62+·2C24H20B−, the three N—C bond lengths in the central C3N unit of the bisamidinium ion range between 1.388 (3) and 1.506 (3) Å, indicating single- and double-bond character. Furthermore, four C—N bonds have double-bond character. Here, the bond lengths range from 1.319 (3) to 1.333 (3) Å. Delocalization of the positive charges occurs in the N/C/N and C/N/C planes. The dihedral angle between both N/C/N planes is 70.5 (2)°. In the crystal, C—H...π interactions between H atoms of the cation and the benzene rings of both tetraphenylborate ions are present. The benzene rings form aromatic pockets, in which the bisamidinium ion is embedded. This leads to the formation of a two-dimensional supramolecular pattern along theabplane.
Crystal structure of 1-mesityl-3-methyl-4-phenyl-1H-1,2,3-triazol-3-ium iodide
Authors: Canseco-González Daniel , García Juventino J. , Flores-Alamo Marcos
Published: December 2015

In the cation of the title salt, C18H20N3+·I−, the mesityl and phenyl rings are inclined to the central triazolium ring by 61.39 (16) and 30.99 (16)°, respectively, and to one another by 37.75 (15)°. In the crystal, molecules are linkedviaC—H...I hydrogen bonds, forming slabs parallel to theabplane. Within the slabs there are weak π–π interactions present involving the mesityl and phenyl rings [inter-centroid distances are 3.8663 (18) and 3.8141 (18) Å].
Crystal structure of dimethyl-1κ2C-bis(μ-4-methylphenolato-1:2κ2O:O)(N,N,N′,N′-tetramethylethylenediamine-2κ2N,N′)indium(III)lithium(I)
Authors: Briand Glen G. , Decken Andreas , Hoey Marshall R.
Published: December 2015

The mixed bimetallic title compound, [InLi(CH3)2(C7H7O)2(C6H16N2)] or [(tmeda)Li-μ-(4-MeC6H4O)2InMe2] (tmeda isN,N,N′,N′-tetramethylethylenediamine), exhibits a four-membered LiO2In ring coreviabridging 4-methylphenolate groups. The Li and In atoms are in distorted tetrahedral N2O2and C2O2bonding environments, respectively. The Li atom is further chelated by a tmeda group, yielding a spirocyclic structure.
Crystal structure of {bis[(1H-benzimidazol-2-yl-κN3)methyl]sulfane}dichloridomercury(II)
Authors: Bouchouit Mehdi , Benzerka Saida , Bouraiou Abdelmalek , Merazig Hocine , Belfaitah Ali , Bouacida Sofiane
Published: December 2015

In the asymmetric unit of the title compound, [HgCl2(C16H14N4S)], the HgIIcation is linked to two Cl atoms and two imidazole N atoms of the chelating bis[(1H-benzimidazol-2-yl)methyl]sulfane ligand, forming a slightly distorted tetrahedral environment. The substitued imidazole rings of the ligand are almost perfectly planar [with maximum deviations of 0.017 (3) and 0.012 (3) Å] and form a dihedral angle of 42.51 (5)°. The crystal packing can be described as alternating layers parallel to (010). In this arrangement, N—H...Cl hydrogen bonds between the N—H groups of the benzimidazole moieties and chloride ligands are responsible for the formation of the chain-like packing pattern along [010] exhibiting aC(6) graph-set motif.
Rolling out lean production systems: a knowledge-based perspective
Authors: Secchi Raffaele , Camuffo Arnaldo
Published: December 2015

Purpose

– Adopting a knowledge-based perspective, the purpose of this paper is to investigate the roll-out process of lean production systems and explores the dimensions that might enhance or hinder its performance. It develops a framework to understand and design lean roll-out processes, identifying the research dimensions/design variables to classify and interpret such processes.

Design/methodology/approach

– This exploratory multiple case study analyses seven lean roll-out processes in multinational companies’ plants. An original data set, developed on the basis of a purposely design research protocol, was built through two rounds of plant visits and structured interviews. The cross-case analysis compares and contrasts the lean roll-out processes according to the research dimensions constituting the framework.

Findings

– The effectiveness and the efficiency of the lean roll-out processes: first, negatively co-vary with the degree of lean knowledge codification; second, positively co-vary with the degree of autonomy of the plant; third, positively co-vary with the degree of contextual ambidexterity. Moreover, lean roll-out processes characterized by principles-based knowledge replication strategy, plant autonomy and contextual ambidexterity are comparatively more effective and efficient.

Research limitations/implications

– This is an exploratory qualitative study that develops propositions potentially testable in larger scale, more analytical research.

Practical implications

– This study provides a tentative roadmap to successfully approach the roll-out of lean production systems in complex organizations.

Originality/value

– This study challenges the current theory and practice which implicitly assumes that lean roll-outs take place linearly, cascading a set of predefined lean operations practices. Instead, the authors show that a less codified, more decentralized and contextually ambidextrous approach might be more effective.
Sustainable supply management as a purchasing capability
Authors: Dabhilkar Mandar , Bengtsson Lars , Lakemond Nicolette
Published: December 2015

Purpose

– The purpose of this paper is to use the relative power and total interdependence concepts as an intervening theoretical lens to explain why and how sustainable supply management (SSM) initiatives by manufacturing firms differ across the Kraljic matrix according to purchasing capability.

Design/methodology/approach

– Tested hypotheses by subjecting survey data from 338 manufacturers on buyer-supplier relationships in Europe and North America to regression analysis.

Findings

– Shows three situations where relative power and total interdependence determine the effectiveness of purchasing capabilities. First, sustainability programs impact supplier compliance in all Kraljic categories but bottleneck items. Second, there are significant trade-offs between lower cost and higher social and environmental supplier compliance for noncritical components. Third, strategic alignment of sustainability objectives between corporate and supply function levels only leads to improved financial performance for strategic components.

Research limitations/implications

– Further research could take power and dependence into account to explain when and how purchasing capabilities focussed on sustainability can be achieved.

Practical implications

– Shows how supply strategists could devise-tailored approaches for different purchasing categories with respect to power and dependence when pursuing economic, social and environmental objectives in combination – the triple bottom line – along their supply chains.

Originality/value

– Illustrates and provides a theoretical explanation for why SSM is a purchasing capability that must vary across purchasing categories defined by different situations of power and dependence.
Borrowing tools from the public library
Authors: Söderholm Jonas
Published: December 2015

Purpose

– The purpose of this paper is to investigate tool lending library patrons’ perception of their tool borrowing, in order to explore the role of a public lending service in the context of their lives. It addresses the research question, why do patrons borrow tools from the library?

Design/methodology/approach

– A case study was conducted, consisting of semi-structured interviews with patrons of a tool lending library. Led by a phenomenographic approach, the interviews focused on participants’ recounted experiences. Transcripts were structured into major categories and underlying themes. Findings were discussed from a perspective taking departure in Wiegand’s notion of “the library in the life of the user,” and summarized with regards to sustainable community development.

Findings

– Participants are found to talk about their tool borrowing from two main viewpoints. First, reasons for making the decision. This involves weighing practical considerations, e.g., cost, storage, access, and frequency of use. It also includes ideological motivations, and sympathy with the concept. Second, effects of their borrowing, interpreted as how it enables them. This enablement includes inspiration, learning, support to self-employment, and strengthening of community. Patrons focus on local aspects of social and economic development, rather than global or environmental motivations.

Research limitations/implications

– A single and in part unique setting was studied. The findings provide foundation for a developed discussion on the societal role of public libraries providing “non-traditional” materials such as tools, with particular regards to community settings and sustainability.

Originality/value

– Addresses knowledge gaps on borrowing and tool lending libraries.
Third-party classification
Authors: Klimaszewski Cheryl
Published: December 2015

Purpose

– The purpose of this paper is to foreground the ways in which material objects emerged as a kind of classificatory force during a visit to a local museum in rural Romania. It considers ways in which classification both influences and is influenced by the spatio-temporal assemblages of things.

Design/methodology/approach

– Visual and textual ethnographic field data collected to document the museum tour are interpreted using a phenomenological approach. Jane Bennett’s agency of assemblage is used to contextualize these instants of interruption within the space/time arrangements of objects within the museum.

Findings

– The “marginal” category of translator commentary emerged during data coding to reveal “instants of interruption.” These instants exhibited classificatory tendencies that revealed relationships between seemingly disparate elements. As such, the translator acted as a kind of third-party classificatory force that illuminated how relationships between physical assemblages of things in the world can act as a force for new knowledge production.

Originality/value

– This paper contributes to the literature on social classification and document theory by revealing how alternative approaches to classification can open up additional avenues for research and knowledge discovery.
Transgender information behaviour
Authors: Pohjanen Aira Maria , Kortelainen Terttu Anna Maarit
Published: December 2015

Purpose

– The purpose of this paper is to explore information behaviour and the information barriers transgendered people encounter. This study produces new information about the information needs in the construction of the transgendered identity, the changing of the information needs during this phase, utilized information sources, information sharing and barriers encountered in the information behaviour displayed by transgendered people.

Design/methodology/approach

– Semi-structured interviews were used to explore the information behaviour of 12 transgendered participants. This study represents a phenomenological-hermeneutic approach. A qualitative content analysis was used in analysing the data with categories derived from previous research and research questions.

Findings

– Serendipity played an important role at the beginning of the participants’ information seeking phase: the young individual would not have terms corresponding to his or her experience because of the invisibility of the transgender phenomenon in the culture. The barriers to seeking information were psychological, demographic, role-related or interpersonal, environmental or source characteristic. Fear was apparent as a barrier in the surrounding culture often caused by expectations, attitudes in the family environment and people around. Source characteristic barriers were related to the lack of terms and vocabulary required to seek information and also the lack of the information itself. Information about transgender and gender minorities was essential in building up a clear gender identity, and the most relevant information sources of this sort of information this were other transgendered people and the experience-based information they had shared.

Originality/value

– The information behaviour of transgendered people has not been previously studied. In this study a model of information behaviour and information barriers was made. The model includes individual’s information practices, sources of information and also the barriers affecting information behaviour.