bluuebunny/crossref_metadata_2025 huggingface dataset:
Challenges in nucleosynthesis of trans-iron elements
Authors: Rauscher T.
Published: March 2014

Nucleosynthesis beyond Fe poses additional challenges not encountered when studying astrophysical processes involving light nuclei. Astrophysical sites and conditions are not well known for some of the processes involved. On the nuclear physics side, different approaches are required, both in theory and experiment. The main differences and most important considerations are presented for a selection of nucleosynthesis processes and reactions, specifically the s-, r-, γ-, and νp-processes. Among the discussed issues are uncertainties in sites and production conditions, the difference between laboratory and stellar rates, reaction mechanisms, important transitions, thermal population of excited states, and uncertainty estimates for stellar rates. The utility and limitations of indirect experimental approaches are also addressed. The presentation should not be viewed as confining the discussed problems to the specific processes. The intention is to generally introduce the concepts and possible pitfalls along with some examples. Similar problems may apply to further astrophysical processes involving nuclei from the Fe region upward and/or at high plasma temperatures. The framework and strategies presented here are intended to aid the conception of future experimental and theoretical approaches.
The value of improved pastures to Brazilian beef production
Authors: Jank Liana , Barrios Sanzio C. , do Valle Cacilda B. , Simeão Rosangela M. , Alves Geovani F.
Published: March 2014

Brazil is an agricultural country, with 190 Mha of pastures sustaining 209 million cattle. Fewer than 10% of the cattle are fattened in feedlots, whereas cattle reared on pastures have a competitive advantage for export, eliminating the risks presented by the mad cow disease (bovine spongiform encephalopathy) and considerations related to animal welfare. Brazil has been the world’s largest exporter of beef since 2004 and has the largest commercial herd in the world. In 2011, 16.5% of its production was exported, and the livestock sector contributed 30.4% of the gross national product from agribusiness and 6.73% of the total GNP. Many forage breeding programs, mainly at Embrapa, have contributed to the development of improved pastures, and cultivars of Brachiaria brizantha, B. decumbens, B. humidicola and Panicum maximum are the main pastures used in the country. All have apomictic reproduction, which means there are few cultivars occupying very large, continuous areas, thus suggesting a risk to the productive system. Such is the case of B. brizantha cv. Marandu, which occupies around 50 Mha. The Brazilian tropical forage seed industry is also important, and Brazil is the main seed exporter, supplying all Latin American countries. Due to pasture degradation, around 8 Mha is renovated or recovered each year. Forages are also used and planted each year in integrated crop–livestock and integrated crop–livestock–forest systems. Nowadays, these systems occupy 4 Mha. Improved pastures are thus a major asset in Brazil not only for the beef production chain but also for the dairy industry.
Investors prefer entrepreneurial ventures pitched by attractive men
Authors: Brooks Alison Wood , Huang Laura , Kearney Sarah Wood , Murray Fiona E.
Published: March 2014

Significance

We identify a profound and consistent gender gap in entrepreneurship, a central path to job creation, economic growth, and prosperity. Across a field setting (three entrepreneurial pitch competitions in the United States) and two controlled experiments, we find that investors prefer entrepreneurial pitches presented by male entrepreneurs compared with pitches presented by female entrepreneurs, even when the content of the pitch is the same. This effect is moderated by male physical attractiveness: attractive males are particularly persuasive, whereas physical attractiveness does not matter among female entrepreneurs. These findings fundamentally advance the science related to gender, physical attractiveness, psychological persuasion, bias, role expectations, and entrepreneurship.
Testing Turing’s theory of morphogenesis in chemical cells
Authors: Tompkins Nathan , Li Ning , Girabawe Camille , Heymann Michael , Ermentrout G. Bard , Epstein Irving R. , Fraden Seth
Published: March 2014

Significance

Turing proposed that intercellular reaction-diffusion of molecules is responsible for morphogenesis. The impact of this paradigm has been profound. We exploit an abiological experimental system of emulsion drops containing the Belousov–Zhabotinsky reactants ideally suited to test Turing’s theory. Our experiments verify Turing’s thesis of the chemical basis of morphogenesis and reveal a pattern, not previously predicted by theory, which we explain by extending Turing’s model to include heterogeneity. Quantitative experimental results obtained using this artificial cellular system establish the strengths and weaknesses of the Turing model, applicable to biology and materials science alike, and pinpoint which directions are required for improvement.
Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens
Authors: Franceschini Andrea , Meier Roger , Casanova Alain , Kreibich Saskia , Daga Neha , Andritschke Daniel , Dilling Sabrina , Rämö Pauli , Emmenlauer Mario , Kaufmann Andreas , Conde-Álvarez Raquel , Low Shyan Huey , Pelkmans Lucas , Helenius Ari , Hardt Wolf-Dietrich , Dehio Christoph , von Mering Christian
Published: March 2014

Significance

Pathogens can enter into human cells using a variety of specific mechanisms, often hitchhiking on naturally existing transport pathways. To uncover parts of the host machinery that are required for entry, scientists conduct infection screens in cultured cells. In these screens, human genes are systematically inactivated by short RNA oligos, designed to bind and inactivate mRNA molecules. Here, we show that many of these oligos additionally bind unintended mRNA targets as well, and that this effect overall dominates and complicates such screens. Focusing on the strong “off-target” signal, we design novel oligos that no longer bind any one gene specifically but nevertheless strongly and reproducibly block pathogen entry—pointing to pathogen/host interactions at a higher-order, pathway level.
Chapter 4. Figuratively speaking – number in Kharia
Authors: Peterson John
Published: March 2014

The present study deals with number in Kharia, a South Munda language of eastern-central India. Kharia possesses three grammatical categories which may be loosely termed number – singular, dual and plural. While the singular is unmarked, the dual and plural are expressed by enclitic proforms. In addition to expressing two or more than two entities, however, these forms also fulfill a number of other, “figurative” functions such as deference, associativity and approximation, which are the main emphasis of the present discussion. Here we will make use of the concept of “n (+1) indexicality” (Silverstein 2003) as well as a version of the so-called “NP hierarchy” or “reference hierarchy” deriving from the original, binary feature-based version of this hierarchy in Silverstein (1976), as opposed to other versions of the hierarchy.
Chapter 5. Number in Kambaata
Authors: Treis Yvonne
Published: March 2014

The Cushitic language Kambaata (South Ethiopia) is a head-final and suffixing language with a rich nominal and verbal morphology. Number is marked on nouns and pronouns, and traces of number agreement are found on modifiers and verbs. This chapter concentrates on number marking on common nouns, thereby focusing on the interaction of number marking with lexical semantics. It demonstrates that in this language, number is a category between inflection and derivation.
Chapter 9. Number in Dinka
Authors: Andersen Torben
Published: March 2014

In Dinka, a Western Nilotic language, nouns are inflected for number and distinguish between singular and plural. The number inflection is not expressed by affixation, but by phonological alternations in the root and in such a way that the number is not directly observable, but only detectable through agreement. With simple native nouns, which are typically monosyllables, the number inflection is unpredictable and irregular, but some fairly common singular-plural patterns can be established, as seen in the Agar dialect. There is strong internal and external evidence that originally, many nouns had a marked singular and an unmarked plural. Synchronically, however, the singular is arguably the basic member of the number category as revealed by the use of the two numbers. In addition, some nouns have a collective form, which is grammatically singular. Number also plays a role in the derivational morphology of verbs.
Chapter 10. Counting chickens in Luwo
Authors: Storch Anne
Published: March 2014

This contribution treats the number marking of nouns, numerals and the way these are used in counting in Luwo. This Western Nilotic language of South Sudan exhibits interesting patterns in the pluralisation of nouns, which have to do with the grammatical marking of nominal aspect. Moreover, Luwo uses different number systems for different word classes, whereas number-inflection of nouns is semantically supercharged, while verbs and adjectives exhibit a semantically basic number-marking system. The semantics of nominal plurals, and the relevance of nominal aspect for a diachronic analysis of the nominal classifiers that seem to be underlying in the complex number-marking patterns of Western Nilotic languages, are investigated in detail in this paper.
Chapter 11. Number in South-Bauchi West languages (Chadic, Nigeria)
Authors: Caron Bernard
Published: March 2014

South-Bauchi West (SBW) languages build a dialect continuum spoken in Northern Nigeria that has been classified as West-Chadic B. Their internal classification reveals a split between two subgroups: the northern subgroup (Geji, Polci) and the southern subgroup (Zeem, Dass, Saya). This genetic split is completed by a grammatical heterogeneity that surfaces in the morphological complexity of the Saya cluster, a subset of the Southern sub-group. The aim of this paper is twofold: (i) see if these differences are corroborated by the study of number; (ii) shed new lights on the genesis of SBW. To that effect, the first section presents an overview of SBW grammatical structure and genetic classification. The following two sections study number in Noun Phrases (noun plurals, modifiers), and in Verb Phrases (imperatives, pluractionals, and plural suffixes). The last section examines the relationship in SBW between number and related categories such as honorifics, associatives and singulatives. The conclusion introduces some nuances in this vision of a division between the northern and southern sub-groups, with the Dass cluster (e.g. ZoÉ—i) behaving like the Northern languages in that they share the same absence of nominal and adjectival plurals and pluractional derivation. The presence of those plurals in the other members of the southern sub-group (i.e. the Zeem and Saya clusters) seems to be an innovation departing from a situation where number is expressed only by the personal pronouns, the modifiers within the nominal system, and the imperative. Pluractionals, although they are widespread in many Chadic languages, seem to be an innovation of Zeem and Saya as well. These innovative features may have developed through the influence of plateau languages. The innovation has gone one step further in the Zaar language with the optional marking of number on noun modifiers. Finally, a marginal case of subject-verb plural agreement on the right periphery has appeared in four languages (Zaranda, Geji, Pelu and Diir), first in the 2nd plural, and then has spread to the 3rd plural in one of the languages (Pelu).
The kinesin-8 Kip3 scales anaphase spindle length by suppression of midzone microtubule polymerization
Authors: Rizk Rania S. , DiScipio Katherine A. , Proudfoot Kathleen G. , Gupta Mohan L.
Published: March 2014

Mitotic spindle function is critical for cell division and genomic stability. During anaphase, the elongating spindle physically segregates the sister chromatids. However, the molecular mechanisms that determine the extent of anaphase spindle elongation remain largely unclear. In a screen of yeast mutants with altered spindle length, we identified the kinesin-8 Kip3 as essential to scale spindle length with cell size. Kip3 is a multifunctional motor protein with microtubule depolymerase, plus-end motility, and antiparallel sliding activities. Here we demonstrate that the depolymerase activity is indispensable to control spindle length, whereas the motility and sliding activities are not sufficient. Furthermore, the microtubule-destabilizing activity is required to counteract Stu2/XMAP215-mediated microtubule polymerization so that spindle elongation terminates once spindles reach the appropriate final length. Our data support a model where Kip3 directly suppresses spindle microtubule polymerization, limiting midzone length. As a result, sliding forces within the midzone cannot buckle spindle microtubules, which allows the cell boundary to define the extent of spindle elongation.
Settlement length and temporal settlement patterns of juvenile cod (Gadus morhua), haddock (Melanogrammus aeglefinus), and whiting (Merlangius merlangus) in a northern North Sea coastal nursery area
Authors: Bastrikin Dorota K. , Gallego Alejandro , Millar Colin P. , Priede Imants G. , Jones Emma G.
Published: March 2014

Knowledge of settlement timing and duration, which has been identified as an important milestone for demersal fish, is critical to understanding population connectivity, relevant to the development of spatially—and temporally—resolved conservation measures, and recruitment variability, as important density-dependent dynamics may take place at this stage. To study the settlement ecology of cod haddock, and whiting, sampling was conducted over spring and summer 2004–2006 at the northern North Sea nursery area. Over 4000 0-group juveniles were collected. Settlement was associated with clear and progressive changes in the prey composition of these juveniles. The size of fish that could be considered settled was estimated as 49 (±3) mm for cod, 78 (±4) mm for haddock, and 85 (±6) mm for whiting. Clear differences in temporal settlement patterns were also apparent. Cod settled in a single pulse lasting about a month (mid-May to mid-June) and initially occupied shallower, inshore waters, whereas haddock settled in one pulse, lasting ∼2 weeks (second half of May), favouring deeper, farther offshore locations. Whiting settled much later in the season and over a more protracted period (early June to early August), and their depth preferences also changed over time and with increasing length.
Galaxy and Mass Assembly (GAMA): fine filaments of galaxies detected within voids
Authors: Alpaslan Mehmet , Robotham Aaron S. G. , Obreschkow Danail , Penny Samantha , Driver Simon , Norberg Peder , Brough Sarah , Brown Michael , Cluver Michelle , Holwerda Benne , Hopkins Andrew M. , van Kampen Eelco , Kelvin Lee S. , Lara-Lopez Maritza A. , Liske Jochen , Loveday Jon , Mahajan Smriti , Pimbblet Kevin
Published: March 2014

Based on data from the Galaxy and Mass Assembly (GAMA) survey, we report on the discovery of structures that we refer to as ‘tendrils’ of galaxies: coherent, thin chains of galaxies that are rooted in filaments and terminate in neighbouring filaments or voids. On average, tendrils contain six galaxies and span 10 h−1 Mpc. We use the so-called line correlation function to prove that tendrils represent real structures rather than accidental alignments. We show that voids found in the Sloan Digital Sky Survey, 7th data release survey that overlap with GAMA regions contain a large number of galaxies, primarily belonging to tendrils. This implies that void sizes are strongly dependent on the number density and sensitivity limits of a survey. We caution that galaxies in low-density regions, which may be defined as ‘void galaxies,’ will have local galaxy number densities that depend on such observational limits and are likely higher than those can be directly measured.
The effect of helium accretion efficiency on rates of Type Ia supernovae: double detonations in accreting binaries
Authors: Ruiter A. J. , Belczynski K. , Sim S. A. , Seitenzahl I. R. , Kwiatkowski D.
Published: March 2014

The double-detonation explosion scenario of Type Ia supernovae (SNe Ia) has gained increased support from the SN Ia community as a viable progenitor model, making it a promising candidate alongside the well-known single degenerate and double degenerate scenarios. We present delay times of double-detonation SNe, in which a sub-Chandrasekhar mass carbon–oxygen white dwarf (WD) accretes non-dynamically from a helium-rich companion. One of the main uncertainties in quantifying SN rates from double detonations is the (assumed) retention efficiency of He-rich matter. Therefore, we implement a new prescription for the treatment of accretion/accumulation of He-rich matter on WDs. In addition, we test how the results change depending on which criteria are assumed to lead to a detonation in the helium shell. In comparing the results to our standard case (Ruiter et al.), we find that regardless of the adopted He accretion prescription, the SN rates are reduced by only ∼25 per cent if low-mass He shells (≲0.05 M⊙) are sufficient to trigger the detonations. If more massive (0.1 M⊙) shells are needed, the rates decrease by 85 per cent and the delay time distribution is significantly changed in the new accretion model – only SNe with prompt (<500 Myr) delay times are produced. Since theoretical arguments favour low-mass He shells for normal double-detonation SNe, we conclude that the rates from double detonations are likely to be high, and should not critically depend on the adopted prescription for accretion of He.
Mid-infrared period–luminosity relations of RR Lyrae stars derived from the AllWISE Data Release
Authors: Klein C. R. , Richards J. W. , Butler N. R. , Bloom J. S.
Published: March 2014

We use photometry from the recent AllWISE Data Release of the Wide-field Infrared Survey Explorer (WISE) of 129 calibration stars, combined with prior distances obtained from the established MV–[Fe/H] relation and Hubble Space Telescope trigonometric parallax, to derive mid-infrared period–luminosity relations for RR Lyrae pulsating variable stars. We derive relations in the W1, W2 and W3 wavebands (3.4, 4.6 and 12 μm, respectively), and for each of the two main RR Lyrae sub-types (RRab and RRc). We report an error on the period–luminosity relation slope for RRab stars of 0.2. We also fit posterior distances for the calibration catalogue and find a median fractional distance error of 0.8 per cent.
A Novel Porcine Model of Ventilator-associated Pneumonia Caused by Oropharyngeal Challenge with Pseudomonas aeruginosa
Authors: Li Bassi Gianluigi , Rigol Montserrat , Marti Joan-Daniel , Saucedo Lina , Ranzani Otavio T. , Roca Ignasi , Cabanas Maria , Muñoz Laura , Giunta Valeria , Luque Nestor , Rinaudo Mariano , Esperatti Mariano , Fernandez-Barat Laia , Ferrer Miquel , Vila Jordi , Ramirez Jose , Torres Antoni
Published: March 2014

Background:

Animal models of ventilator-associated pneumonia (VAP) in primates, sheep, and pigs differ in the underlying pulmonary injury, etiology, bacterial inoculation methods, and time to onset. The most common ovine and porcine models do not reproduce the primary pathogenic mechanism of the disease, through the aspiration of oropharyngeal pathogens, or the most prevalent human etiology. Herein the authors characterize a novel porcine model of VAP due to aspiration of oropharyngeal secretions colonized by Pseudomonas aeruginosa.

Methods:

Ten healthy pigs were intubated, positioned in anti-Trendelenburg, and mechanically ventilated for 72 h. Three animals did not receive bacterial challenge, whereas in seven animals, a P. aeruginosa suspension was instilled into the oropharynx. Tracheal aspirates were cultured and respiratory mechanics were recorded. On autopsy, lobar samples were obtained to corroborate VAP through microbiological and histological studies.

Results:

In animals not challenged, diverse bacterial colonization of the airways was found and monolobar VAP rarely developed. In animals with P. aeruginosa challenge, colonization of tracheal secretion increased up to 6.39 ± 0.34 log colony-forming unit (cfu)/ml (P < 0.001). VAP was confirmed in six of seven pigs, in 78% of the cases developed in the dependent lung segments (right medium and lower lobes, P = 0.032). The static respiratory system elastance worsened to 41.5 ± 5.8 cm H2O/l (P = 0.001).

Conclusions:

The authors devised a VAP model caused by aspiration of oropharyngeal P. aeruginosa, a frequent causative pathogen of human VAP. The model also overcomes the practical and legislative limitations associated with the use of primates. The authors’ model could be employed to study pathophysiologic mechanisms, as well as novel diagnostic/preventive strategies.
Sex and boldness explain individual differences in spatial learning in a lizard
Authors: Carazo Pau , Noble Daniel W. A. , Chandrasoma Dani , Whiting Martin J.
Published: March 2014

Understanding individual differences in cognitive performance is a major challenge to animal behaviour and cognition studies. We used the Eastern water skink (
Eulamprus quoyii
) to examine associations between exploration, boldness and individual variability in spatial learning, a dimension of lizard cognition with important bearing on fitness. We show that males perform better than females in a biologically relevant spatial learning task. This is the first evidence for sex differences in learning in a reptile, and we argue that it is probably owing to sex-specific selective pressures that may be widespread in lizards. Across the sexes, we found a clear association between boldness after a simulated predatory attack and the probability of learning the spatial task. In contrast to previous studies, we found a nonlinear association between boldness and learning: both ‘bold’ and ‘shy’ behavioural types were more successful learners than intermediate males. Our results do not fit with recent predictions suggesting that individual differences in learning may be linked with behavioural types via high–low-risk/reward trade-offs. We suggest the possibility that differences in spatial cognitive performance may arise in lizards as a consequence of the distinct environmental variability and complexity experienced by individuals as a result of their sex and social tactics.
Migration and the evolution of duetting in songbirds
Authors: Logue David M. , Hall Michelle L.
Published: March 2014

Many groups of animals defend shared resources with coordinated signals. The best-studied of these signals are the vocal duets produced by mated pairs of birds. Duets are believed to be more common among tropical-breeding species, but a comprehensive test of this hypothesis is lacking, and the mechanisms that generate latitudinal patterns in duetting are not known. We used a stratified sample of 372 songbird species to conduct the first broad-scale, phylogenetically explicit analysis of duet evolution. We found that duetting evolves in association with the absence of migration, but not with sexual monochromatism or tropical breeding. We conclude that the evolution of migration exerts a major influence on the evolution of duetting. The perceived association between tropical breeding and duetting may be a by-product of the migration–duetting relationship. Migration reduces the average duration of partnerships, potentially reducing the benefits of cooperative behaviour, including duetting. Ultimately, the evolution of coordinated resource-defence signals in songbirds may be driven by ecological conditions that favour sedentary lifestyles and social stability.
Interface electronic structures of reversible double-docking self-assembled monolayers on an Au(111) surface
Authors: Zhang Tian , Ma Zhongyun , Wang Linjun , Xi Jinyang , Shuai Zhigang
Published: March 2014

Double-docking self-assembled monolayers (DDSAMs), namely self-assembled monolayers (SAMs) formed by molecules possessing two docking groups, provide great flexibility to tune the work function of metal electrodes and the tunnelling barrier between metal electrodes and the SAMs, and thus offer promising applications in both organic and molecular electronics. Based on the dispersion-corrected density functional theory (DFT) in comparison with conventional DFT, we carry out a systematic investigation on the dual configurations of a series of DDSAMs on an Au(111) surface. Through analysing the interface electronic structures, we obtain the relationship between single molecular properties and the SAM-induced work-function modification as well as the level alignment between the metal Fermi level and molecular frontier states. The two possible conformations of one type of DDSAM on a metal surface reveal a strong difference in the work-function modification and the electron/hole tunnelling barriers. Fermi-level pinning is found to be a key factor to understand the interface electronic properties.
Hannaella pagnoccae sp. nov., a tremellaceous yeast species isolated from plants and soil
Authors: Landell Melissa Fontes , Brandão Luciana R. , Barbosa Anne C. , Ramos Jesus P. , Safar Silvana V. B. , Gomes Fatima C. O. , Sousa Francisca M. P. , Morais Paula B. , Broetto Leonardo , Leoncini Orílio , Ribeiro José Roberto , Fungsin Bundit , Takashima Masako , Nakase Takashi , Lee Ching-Fu , Vainstein Marilene H. , Fell Jack W. , Scorzetti Gloria , Vishniac Helen S. , Rosa Carlos A. , Valente Patricia
Published: March 2014

Several independent surveys of yeasts associated with different plant materials and soil led to the proposal of a novel yeast species belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences of the D1/D2 domains and internal transcribed spacer region of the large subunit of the rRNA gene suggested affinity to a phylogenetic lineage that includes Hannaella coprosmaensis, Hannaella oryzae and Hannaella sinensis. Thirty-two isolates were obtained from different sources, including bromeliads, nectar of Heliconia psittacorum (Heliconiaceae), flowers of Pimenta dioica (Myrtaceae), roots and leaves of sugar cane (Saccharum spp.) in Brazil, leaves of Cratoxylum maingayi, Arundinaria pusilla and Vitis vinifera in Thailand, soil samples in Taiwan, and prairie soil in the USA. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from Hannaella coprosmaensis and Hannaella oryzae by 36 and 46 nt substitutions, respectively. A novel species is suggested to accommodate these isolates, for which the name Hannaella pagnoccae sp. nov. is proposed. The type strain is BI118T ( = CBS 11142T = ATCC MYA-4530T).
Bacillus tianshenii sp. nov., isolated from a marine sediment sample
Authors: Jiang Zhao , Zhang Dao-Feng , Khieu Thi-Nhan , Son Chu Ky , Zhang Xiao-Mei , Cheng Juan , Tian Xin-Peng , Zhang Si , Li Wen-Jun
Published: March 2014

A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235T, was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235T belonged to the genus

Bacillus

. The strain grew optimally at 30 °C, pH 7.0 and in the presence of 2–4 % (w/v) NaCl. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. Strain YIM M13235T exhibited a menaquinone system with MK-7, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown glycolipid. The major fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 1ω10c and summed feature 4 (anteiso-C17 : 1 and/or iso-C17 : 1). The genomic DNA G+C content was 42.1 mol%. The DNA–DNA relatedness values between strain YIM M13235T and its close relatives (16S rRNA gene sequence similarities >97 %) including

Bacillus halmapalus

DSM 8723T,

Bacillus horikoshii

DSM 8719T and

Bacillus zhanjiangensis

JSM 099021T were 41 %, 44 % and 44 %, respectively. On the basis of genotypic, phenotypic and DNA–DNA relatedness data, it is apparent that strain YIM M13235T represents a novel species of the genus

Bacillus

, for which the name Bacillus tianshenii sp. nov. is proposed. The type strain is YIM M13235T ( = DSM 25879T = KCTC 33044T).
CMO1 encodes a putative choline monooxygenase and is required for the utilization of choline as the sole nitrogen source in the yeast Scheffersomyces stipitis (syn. Pichia stipitis)
Authors: Linder Tomas
Published: March 2014

Sixteen yeasts with sequenced genomes belonging to the ascomycete subphyla Saccharomycotina and Taphrinomycotina were assayed for their ability to utilize a variety of primary, secondary, tertiary and quartenary aliphatic amines as nitrogen sources. The results support a previously proposed pathway of quaternary amine catabolism whereby glycine betaine is first converted into choline, which is then cleaved to release trimethylamine, followed by stepwise demethylation of trimethylamine to release free ammonia. There were only a few instances of utilization ofN-methylated glycine species (sarcosine andN,N-dimethylglycine), which suggests that this pathway is not intact in any of the species tested. The ability to utilize choline as a sole nitrogen source correlated strongly with the presence of a putative Rieske non-haem iron protein homologous to bacterial ring-hydroxylating oxygenases and plant choline monooxygenases. Deletion of the gene encoding the Rieske non-haem iron protein in the yeastScheffersomyces stipitisabolished its ability to utilize choline as the sole nitrogen source, but did not affect its ability to use methylamine, dimethylamine, trimethylamine, ethylamine, diethylamine, ethanolamine or glycine as nitrogen sources. The gene was namedCMO1for putative choline monooxygenase 1. A bioinformatic survey of eukaryotic genomes showed thatCMO1homologues are found throughout the eukaryotic domain.
Identification of a core sequence for the binding of BosR to the rpoS promoter region in Borrelia burgdorferi
Authors: Ouyang Zhiming , Zhou Jianli , Brautigam Chad A. , Deka Ranjit , Norgard Michael V.
Published: March 2014

The alternative sigma factor RpoS in Borrelia burgdorferi plays a central role in modulating host adaptive responses when spirochaetes cycle between ticks and mammals. The transcriptional activation of σ54-dependent rpoS requires a Fur homologue designated BosR. Previously, BosR was shown to directly activate rpoS transcription by binding to the rpoS promoter. However, many other DNA binding features of BosR have remained obscure. In particular, the precise DNA sequence targeted by BosR has not yet been completely elucidated. The prediction of a putative Per box within the rpoS promoter region has further confounded the identification of the BosR binding sequence. Herein, by using electrophoretic mobility shift assays, we demonstrate that the putative Per box predicted in the rpoS promoter region is not involved in the binding of BosR. Rather, a 13 bp palindromic sequence (ATTTAANTTAAAT) with dyad symmetry, which we denote as the ‘BosR box’, functions as the core sequence recognized by BosR in the rpoS promoter region of Borrelia burgdorferi. Similar to a Fur box and a Per box, the BosR box probably comprises a 6–1–6 inverted repeat composed of two hexamers (ATTTAA) in a head-to-tail orientation. Selected mutations in the BosR box prevented recombinant BosR from binding to rpoS. In addition, we found that sequences neighbouring the BosR box also are required for the formation of BosR–DNA complexes. Identification of the BosR box advances our understanding of how BosR recognizes its DNA target(s), and provides new insight into the mechanistic details behind the unique regulatory function of BosR.
Identifying genetic relatives without compromising privacy
Authors: He Dan , Furlotte Nicholas A. , Hormozdiari Farhad , Joo Jong Wha J. , Wadia Akshay , Ostrovsky Rafail , Sahai Amit , Eskin Eleazar
Published: March 2014

The development of high-throughput genomic technologies has impacted many areas of genetic research. While many applications of these technologies focus on the discovery of genes involved in disease from population samples, applications of genomic technologies to an individual’s genome or personal genomics have recently gained much interest. One such application is the identification of relatives from genetic data. In this application, genetic information from a set of individuals is collected in a database, and each pair of individuals is compared in order to identify genetic relatives. An inherent issue that arises in the identification of relatives is privacy. In this article, we propose a method for identifying genetic relatives without compromising privacy by taking advantage of novel cryptographic techniques customized for secure and private comparison of genetic information. We demonstrate the utility of these techniques by allowing a pair of individuals to discover whether or not they are related without compromising their genetic information or revealing it to a third party. The idea is that individuals only share enough special-purpose cryptographically protected information with each other to identify whether or not they are relatives, but not enough to expose any information about their genomes. We show in HapMap and 1000 Genomes data that our method can recover first- and second-order genetic relationships and, through simulations, show that our method can identify relationships as distant as third cousins while preserving privacy.
ArabidopsisCAM7 and HY5 Physically Interact and Directly Bind to theHY5Promoter to Regulate Its Expression and Thereby Promote Photomorphogenesis
Authors: Abbas Nazia , Maurya Jay P. , Senapati Dhirodatta , Gangappa Sreeramaiah N. , Chattopadhyay Sudip
Published: March 2014

Arabidopsis thaliana CALMODULIN7 (CAM7), a unique member of the calmodulin gene family, plays a crucial role as a transcriptional regulator in seedling development. The elongated HYPOCOTYL5 (HY5) bZIP protein, an integrator of multiple signaling pathways, also plays an important role in photomorphogenic growth and light-regulated gene expression. CAM7 acts synergistically with HY5 to promote photomorphogenesis at various wavelengths of light. Although the genetic relationships between CAM7 and HY5 in light-mediated seedling development have been demonstrated, the molecular connectivity between CAM7 and HY5 is unknown. Furthermore, whereas HY5-mediated gene regulation has been fairly well investigated, the transcriptional regulation of HY5 is largely unknown. Here, we report that HY5 expression is regulated by HY5 and CAM7 at various wavelengths of light and also at various stages of development. In vitro and in vivo DNA–protein interaction studies suggest that HY5 and CAM7 bind to closely located T/G- and E-box cis-acting elements present in the HY5 promoter, respectively. Furthermore, CAM7 and HY5 physically interact and regulate the expression of HY5 in a concerted manner. Taken together, these results demonstrate that CAM7 and HY5 directly interact with the HY5 promoter to mediate the transcriptional activity of HY5 during Arabidopsis seedling development.
Strigolactone Promotes Degradation of DWARF14, an α/β Hydrolase Essential for Strigolactone Signaling inArabidopsis
Authors: Chevalier Florian , Nieminen Kaisa , Sánchez-Ferrero Juan Carlos , Rodríguez María Luisa , Chagoyen Mónica , Hardtke Christian S. , Cubas Pilar
Published: March 2014

Strigolactones (SLs) are phytohormones that play a central role in regulating shoot branching. SL perception and signaling involves the F-box protein MAX2 and the hydrolase DWARF14 (D14), proposed to act as an SL receptor. We used strong loss-of-function alleles of the Arabidopsis thaliana D14 gene to characterize D14 function from early axillary bud development through to lateral shoot outgrowth and demonstrated a role of this gene in the control of flowering time. Our data show that D14 distribution in vivo overlaps with that reported for MAX2 at both the tissue and subcellular levels, allowing physical interactions between these proteins. Our grafting studies indicate that neither D14 mRNA nor the protein move over a long range upwards in the plant. Like MAX2, D14 is required locally in the aerial part of the plant to suppress shoot branching. We also identified a mechanism of SL-induced, MAX2-dependent proteasome-mediated degradation of D14. This negative feedback loop would cause a substantial drop in SL perception, which would effectively limit SL signaling duration and intensity.
(Z)-3-[2-(2,4-Dinitrophenyl)hydrazin-1-ylidene]isobenzofuran-1(3H)-one dichloromethane hemisolvate
Authors: Agarwal Palak , Mishra Pragati , Gupta Nikita , Neelam  , Sahoo Priyaranjan , Kumar Satish
Published: March 2014

In the title compound, 2C14H8N4O6·CH2Cl2, the dichloromethane solvent molecule resides on a crystallographic twofold axis. The mean plane of the phthalisoimide ring is oriented at a dihedral angle of 32.93 (12)° with respect to the nitro-substituted benzene ring. An intramolecular N—H...O hydrogen bond occurs. The crystal packing features a short Cl...O halogen-bond interaction [3.093 (3) Å].
Polyhedra, complexes, nets and symmetry
Authors: Schulte Egon
Published: March 2014

Skeletal polyhedra and polygonal complexes in ordinary Euclidean 3-space are finite or infinite 3-periodic structures with interesting geometric, combinatorial and algebraic properties. They can be viewed as finite or infinite 3-periodic graphs (nets) equipped with additional structure imposed by the faces, allowed to be skew, zigzag or helical. A polyhedron or complex isregularif its geometric symmetry group is transitive on the flags (incident vertex–edge–face triples). There are 48 regular polyhedra (18 finite polyhedra and 30 infinite apeirohedra), as well as 25 regular polygonal complexes, all infinite, which are not polyhedra. Their edge graphs are nets well known to crystallographers and they are identified explicitly. There are also six infinite families ofchiralapeirohedra, which have two orbits on the flags such that adjacent flags lie in different orbits.
A complex network of interactions controls coexistence and relative abundances in Patagonian grass‐shrub steppes
Authors: Cipriotti Pablo A. , Aguiar Martín R. , Wiegand Thorsten , Paruelo José M.
Published: March 2014

The coexistence of shrubs and grasses has intrigued ecologists for the past century, and the conundrum of shrub–grass coexistence is at the core of debates on the functioning of semi‐arid ecosystems. Here, we explored how the interplay of root competition and facilitation between life‐forms at different life stages and demographic bottlenecks controls the long‐term coexistence of multiple shrub and grass species in semi‐arid Patagonian steppes.

We used the spatially explicit and individual‐based simulation model DINVEG that integrates the abundant information on the semi‐arid Patagonian grass–shrub steppes to test six competing hypotheses on the mechanisms that govern the coexistence and relative abundances of several grass and shrub species. The structurally realistic model allows for a direct comparison of model outputs with a wide range of previously collected field data.

We formulate three competing hypotheses on vertical root overlap between grasses and shrubs (no overlap, partial overlap, full overlap) that were crosses with two hypotheses on asymmetric shrub–grass facilitation (with and without). Each of the six variants of DINVEG were tested in their ability to generate dynamics in accordance with detailed field data, and we performed global sensitivity analyses to reveal demographic bottlenecks and controls.

The hypothesis combining partial vertical root overlap with no facilitation was the most likely hypothesis given the data. It created demographic bottlenecks in recruitment and emergence that controlled grass and shrub abundances, respectively, and only this hypothesis generated a situation where grasses controlled shrub abundances (by limiting shrub recruitment), but where grass abundance was only weakly controlled by shrubs. Internal water dynamics generated reduced competition of shrubs to neighboured grasses that was sufficient to produce the observed ring of grasses around shrubs, and most of the parameterizations that approximated the observed species‐specific abundances were able to reproduce the observed equilibrated spatial patterns of the mature community.

Synthesis. We found a complex network of mechanisms that controlled growth‐form coexistence and relative abundances in the Patagonian grass‐shrub steppe where both, demographic bottlenecks and species interactions across life‐forms, species and life stages were important. Our study points to alternative mechanisms of shrub–grass coexistence that may play an important role in dry grasslands and steppes where fire and herbivory are not key drivers and provide an avenue to detect them.
A Schematic View of Crisis Threat Assessment
Authors: Yin Shoujun , Jing Runtian
Published: March 2014

Given the short time available for decision‐making during a crisis, a schema is considered useful to organizations both for making sense of crisis situations and for developing an effective crisis plan. As an effort to bridge the existing ‘objective’ and ‘subjective’ approaches in crisis classification, a schematic view of assessing crisis threats is elaborated in this study and a new instrument for empirical measurement is further developed. The study is based on a triangulated research design. Based on inductive research and a questionnaire survey, we developed a schematic framework using a measuring instrument for assessing crisis threats that has four dimensions: command incompetence, environmental pressure, information ambiguity, and coordination difficulties. Then, a comparative case study was used to justify the schematic framework.
Blast Injury and the Human Skeleton: An Important Emerging Aspect of Conflict‐Related Trauma
Authors: Dussault Marie Christine , Smith Martin , Osselton David
Published: March 2014

Recent decades have seen an accelerating trend in warfare whereby a growing proportion of conflict‐related deaths have been caused by explosions. Analysis of blast injury features little in anthropological literature. We present a review of clinical literature that includes prevalence of injury to anatomical regions and potential indicators of blast injury which can be used by forensic anthropologists. This includes high prevalence of extremity (22.8–91.2%) and facial (19.6–40%) injury in combat contexts, lower limb fractures (19–74.3%) in suicide bombing, traumatic amputation (3–43%) and diffuse fracture patterns in terrorist bombings. Potential indicators of blast trauma include blowout fractures in sinus cavities from blast overpressure, transverse mandibular fractures, and visceral surface rib fractures. Ability to recognize blast trauma and distinguish it in the skeleton is of importance in investigations and judicial proceedings relating to war crimes, terrorism, and human rights violations and likely to become increasingly crucial to forensic anthropology knowledge.
Concentrations of remifentanil, propofol, fentanyl, and midazolam during rewarming from therapeutic hypothermia
Authors: BJELLAND T. W. , KLEPSTAD P. , HAUGEN B. O. , NILSEN T. , SALVESEN Ø. , DALE O.
Published: March 2014

Background

The clearance of sedatives and analgesics may be reduced by therapeutic hypothermia. However, little is known about the concentrations of such drugs during rewarming. The aim of this study was to describe the serum concentrations of sedatives and analgesics during rewarming from therapeutic hypothermia.

Methods

Blood samples were collected for quantification of drug concentrations in 22 patients given analgesia/sedation with either remifentanil/propofol or fentanyl/midazolam during rewarming from therapeutic hypothermia (33–34°C) after cardiac arrest. Samples for were drawn before (−2 h) and during rewarming (0–8 h). Linear mixed effects models were used to describe serum concentrations and adjust for rates of infusion during rewarming from therapeutic hypothermia.

Results

Subjects with samples analyzed were remifentanil (n = 8), propofol (n = 14), fentanyl (n = 8), and midazolam (n = 8). Age, body mass index, and simplified acute physiology score II [mean (standard deviation)] were 64 (14.2) years, 27.3 (3.7) kg/m2, and 69 (13.2), respectively. While the concentration of fentanyl was not significantly affected by temperature, concentrations of remifentanil, propofol, and midazolam decreased with core temperature by 16%, 12%, and 11% (mean values) from 33°C to 37°C after adjusting for rates of infusion, respectively.

Conclusion

Concentrations of remifentanil, propofol, and midazolam decreased during rewarming from therapeutic hypothermia when adjusting for rates of infusion. No changes were demonstrated for fentanyl.
Bruch′s membrane thickness in high myopia
Authors: Jonas Jost B. , Holbach Leonard , Panda‐Jonas Songhomitra
Published: March 2014

Purpose

To measure the thickness of Bruch′s membrane (BM) and assess its associations with axial length.

Methods

Using a light microscope, we measured the thickness of Bruch′s membrane, choroid and sclera on horizontal anterior‐posterior histological sections of enucleated human globes.

Results

The study included 54 eyes (42 with glaucomatous optic nerve damage; 23 globes with axial length ≥26.5 mm) with a mean axial length of 26.6 ± 3.3 mm (range: 21.0–34.0 mm). In the non‐highly myopic eyes, BM was significantly thicker at the pars plana region (6.6 ± 1.1 μm) than at the equator (4.1 ± 1.5 μm; p < 0.001), the midpoint between equator and posterior pole (4.1 ± 1.5 μm; p < 0.001), the parapapillary region (4.5 ± 1.0 μm; p = 0.006) or the posterior pole (4.4 ± 1.7 μm; p = 0.001). At any measurement location at or behind the ora serrata, BM thickness did not differ significantly (all p ≥ 0.40) between the non‐glaucomatous non‐highly myopic group and the glaucomatous non‐highly myopic group, or between the non‐highly myopic group and the highly myopic group. BM thickness at any location was not significantly (all p > 0.45) related to axial length. The ratio of scleral thickness to BM thickness and the ratio of choroidal thickness to BM thickness significantly decreased with longer axial length for measurements taken behind the equator.

Conclusions

BM is physiologically thickest in the pars plana, with no major thickness differences between locations at or behind the ora serrata. In contrast to choroidal and scleral thickness, BM thickness is not significantly related to axial length. Axially elongated eyes have a normal BM thickness, despite a thinned choroid and sclera.