bluuebunny/crossref_metadata_2025 huggingface dataset:
Feature metathesis and the change of PIE *du̯ to Classical Armenian -rk-*
Authors: DeLisi Jessica
Published: February 2014

This paper reexamines the correspondence of Classical Armenian -rk- with Proto-Indo-European *du̯ and attempts to explain the change in a phonologically plausible way without recourse to illicit clusters or ad hoc rules not otherwise operational in the language. Instead, the change of *du̯ to -rk- is analyzed in Optimality framework as an instantiation of the Armenian sonority-based metathesis. Instead of the expected segment metathesis, however, I argue that this cluster underwent metathesis only of the feature [±continuant]. The need for feature metathesis rather than segment metathesis for this sequence was motivated by a TETU effect (The Emergence of The Unmarked) due to the markedness of the segment [w] in Classical Armenian. The markedness of [w] in Classical Armenian is supported by the later glide fortition seen in forms such as gini “wine”, from PIE *u̯oinii̯o-.
Ainsi
Authors: Molinier Christian
Published: February 2014

This article studies the adverb ainsi in its twin functions of manner adverb modifying a given verb, and of sentence adverb — here a connective. This dual functioning is characteristic of a number of adverbs, and as with them, all the characteristic properties of each of these types are verified. In both cases, the basic meaning of ainsi is that of ‘conformity’ — conformity of a manner of doing or being with another manner of doing or being, and conformity of the content of an utterance with a previously evoked state of affairs. For each of these two uses, we study the particular order of words, on occasion in relation to their character, and show that manner adverb ainsi is unique within its category in setting itself apart from other adverbial form types allowing “subject inversion”.
bwtool: a tool for bigWig files
Authors: Pohl Andy , Beato Miguel
Published: February 2014

BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth). bwtool is a tool designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Additionally, the tool enables the conversion of the positions of signal data from one genome assembly to another, also known as ‘lifting’. We believe bwtool can be useful for the analyst frequently working with bigWig data, which is becoming a standard format to represent functional signals along genomes. The article includes supplementary examples of running the software.

Availability and implementation: The C source code is freely available under the GNU public license v3 at http://cromatina.crg.eu/bwtool.

Contact:  andrew.pohl@crg.eu, andypohl@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.
CoNtRol: an open source framework for the analysis of chemical reaction networks
Authors: Donnell Pete , Banaji Murad , Marginean Anca , Pantea Casian
Published: February 2014

Summary: We introduce CoNtRol, a web-based framework for analysis of chemical reaction networks (CRNs). It is designed to be both extensible and simple to use, complementing existing CRN-related tools. CoNtRol currently implements a number of necessary and/or sufficient structural tests for multiple equilibria, stable periodic orbits, convergence to equilibria and persistence, with the potential for incorporation of further tests.

Availability and implementation: Reference implementation: reaction-networks.net/control/. Source code and binaries, released under the GPLv3: reaction-networks.net/control/download/. Documentation: reaction-networks.net/wiki/CoNtRol.

Contact:  pete.donnell@port.ac.uk
Successful Gastrostomy Tube Weaning Program Using an Intensive Multidisciplinary Team Approach
Authors: Brown Jessica , Kim Cindy , Lim Audrey , Brown Shonda , Desai Hema , Volker Leigh , Katz Mitchell
Published: February 2014

Objectives:

The present study evaluated the effectiveness of a multidisciplinary intensive inpatient model for gastrostomy tube (GT) weaning.

Methods:

A retrospective chart review was completed on 30 GT‐dependent children, ages 3.9 (±1.4) years, admitted to the inpatient feeding program (length of stay 19 days) from May 2009 to December 2011. Administered GT calories were decreased on admission by an average of 73% from home regimen. Patients were offered 3 meals and 2 to 3 snacks/day, including 3 intensive feeding therapy sessions (Monday to Friday), along with psychosocial support, nutrition guidance, and behavioral therapy. Daily calorie counts and weights were recorded. Patients returned for a postdischarge feeding evaluation at an average of 4 months and a clinic visit at 1 year. Data were analyzed using paired samples t tests.

Results:

Before admission, patients received 69% (±25) of goal calories by GT and 22% (±19) of goal calories orally. During admission, average caloric intake by mouth as a percentage of goal increased during the course of weeks 1, 2, and 3 (68%, 77%, and 82%, respectively), with a statistically significant increase between weeks 1 and 2 (P = 0.001) and 1 and 3 (P = 0.011). At discharge, 90% had discontinued GT feedings. Average percent weight change during admission was 0.2% (±4). At 1 year follow‐up, 83% remained successfully off GT feedings.

Conclusions:

Children who are GT dependent can be weaned off GT feedings during a 3‐week admission using a multidisciplinary feeding model. The therapeutic gains were maintained at 1 year postdischarge.
The Coordination of C4 Photosynthesis and the CO2-Concentrating Mechanism in Maize and Miscanthus × giganteus in Response to Transient Changes in Light Quality
Authors: Sun Wei , Ubierna Nerea , Ma Jian-Ying , Walker Berkley J. , Kramer David M. , Cousins Asaph B.
Published: February 2014

Unequal absorption of photons between photosystems I and II, and between bundle-sheath and mesophyll cells, are likely to affect the efficiency of the CO2-concentrating mechanism in C4 plants. Under steady-state conditions, it is expected that the biochemical distribution of energy (ATP and NADPH) and photosynthetic metabolite concentrations will adjust to maintain the efficiency of C4 photosynthesis through the coordination of the C3 (Calvin-Benson-Bassham) and C4 (CO2 pump) cycles. However, under transient conditions, changes in light quality will likely alter the coordination of the C3 and C4 cycles, influencing rates of CO2 assimilation and decreasing the efficiency of the CO2-concentrating mechanism. To test these hypotheses, we measured leaf gas exchange, leaf discrimination, chlorophyll fluorescence, electrochromatic shift, photosynthetic metabolite pools, and chloroplast movement in maize (Zea mays) and Miscanthus × giganteus following transitional changes in light quality. In both species, the rate of net CO2 assimilation responded quickly to changes in light treatments, with lower rates of net CO2 assimilation under blue light compared with red, green, and blue light, red light, and green light. Under steady state, the efficiency of CO2-concentrating mechanisms was similar; however, transient changes affected the coordination of C3 and C4 cycles in M. giganteus but to a lesser extent in maize. The species differences in the ability to coordinate the activities of C3 and C4 cycles appear to be related to differences in the response of cyclic electron flux around photosystem I and potentially chloroplast rearrangement in response to changes in light quality.
(3R,4S)-3-Methyl-4-phenyl-2-[(R)-1-phenylethyl]-3,4-dihydroisoquinolin-2-ium tetrafluoridoborate
Authors: Ben Ali Karim , Retailleau Pascal
Published: February 2014

The title salt, C24H24N+·BF4−, is one of two possible diastereoisomers having a different configuration of the asymmetric centre in the α-phenylethyl substituent, whose absolute configuration was established to beR. The two phenyl substituents of the cation have a cofacial orientation, albeit with a long centroid–centroid separation of 4.129 (3) Å. The crystal structure exhibits numerous C—H...F contacts between counter-ions, with the tetrafluoridoborate anion surrounded by five iminium cations.
2-(4-Chlorophenyl)-4-oxo-4-phenylbutanenitrile
Authors: Ma Ben , Zhou Hongyan , Yang Jingya
Published: February 2014

The title molecule, C16H12ClNO, has a V-shaped conformation and the dihedral angle between the planes of the phenyl and benzene rings of 64.6 (1)°. No directional intermolecular interactions could be identified in the crystal.
5-(4-Fluorophenyl)-2-(4-methylphenyl)-3-methylsulfanyl-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: February 2014

The asymmetric unit of the title compound, C22H17FOS, contains two independent molecules (AandB). The dihedral angles between the benzofuran ring systems [r.m.s. deviations of 0.026 (1), 0.004 (1) and 0.003 (1) Å, respectively, for moleculeA, and 0.002 (1), 0.004 (1) and 0.005 (1) Å forB] and the pendant 4-fluorophenyl and 4-methylphenyl rings are 39.48 (4) and 30.86 (5)°, respectively, for moleculeA, and 33.34 (6) and 20.99 (8)° forB. In the crystal, molecules are linked by weak C—H...F and C—H...π interactions, resulting in a three-dimensional network.
Bis(6-nitro-1,10-phenanthrolin-1-ium) 2,5-dicarboxyterephthalate
Authors: Zhong Kai-Long , Ni Chao
Published: February 2014

In the structure of the title 2:1 proton-transfer compound, 2C12H8N3O2+·C10H4O82−, the 6-nitro-1,10-phenanthroline molecules act as proton sponges, accepting protons from pyromellitic acid. The –NO2group of one of the 6-nitro-1,10-phenanthrolin-1-ium cations is disordered and was refined with a site-occupancy ratio of 0.624 (15):0.376 (15). Two –COOH(–COO−) groups of the 2,5-dicarboxyterephthalate dianion are disordered and were refined with site-occupancy ratios of 0.769 (4):0.231 (4) and 0.766 (5):0.234 (5). The –NO2group of the second cation is also disordered about a pseudo-twofold rotation axis and was refined with a site-occupancy ratio of 0.903 (3):0.097 (3). There is an intramolecular O—H...O hydrogen bond in the anion. The phenanthroline rings of the two cations are inclined to one another by 31.3 (1)°. In the anions, considering the major components only, the carboxylic acid groups (–COOH) are inclined to the benzene ring by 17.3 (2) and 22.3 (3)°. The carboxylate groups (–COO−) are twisted by 9.3 (2) and 13.6 (6)° with respect to the benzene ring. In the crystal, adjacent 2,5-dicarboxyterephthalate anions are linkedviaO—H...O hydrogen bonds, forming chains propagating along [010]. The cations are attached to the chain of anions by N—H...O hydrogen bonds.
(E)-Benzyl(4-{[1-(prop-2-en-1-yl)-1H-1,2,3-triazol-4-yl]methoxy}benzylidene)amine
Authors: Akkurt Mehmet , Jarrahpour Aliasghar , Chermahini Mehdi Mohammadi , Shiri Pezhman , Özdemir Namık
Published: February 2014

The triazole ring of the title compound, C20H20N4O, is normal to the central benzene ring, making a dihedral angle of 90.0 (3)°, and forms a dihedral angle of 69.2 (3)° with the terminal phenyl ring. The dihedral angle between the phenyl and benzene rings is 88.2 (3)°. The atoms of the terminal propenyl group are disordered over two sets of sites, with a site-occupancy ratio of 0.663 (13):0.337 (13). In the crystal, C—H...N contacts lead to the formation of a layer structure extending parallel to (011). Two weak C—H...π interactions are also observed.
Fluoren-9-one oxime
Authors: Bugenhagen Bernhard , Al Jasem Yosef , Al-Azani Mariam , Thiemann Thies
Published: February 2014

In the title molecule, C13H9NO, the fluorene system and the oxime group non-H atoms are essentially coplanar, with a maximum deviation from the fluorene mean plane of 0.079 (2) Å for the oxime O atom. A short intramolecular C—H...O generates anS(6) ring. In the crystal, molecules related by a twofold screw axis are connected by O—H...N hydrogen bonds, forming [100] chains Within these chains, molecules related by a unit translation along [100] show π–π stacking interactions between their fluorene ring systems with an interplanar distance of 3.347 (2) Å. The dihedral angle between the fluorene units of adjacent molecules along the helix is 88.40 (2)°. There is a short C—H...π contact between the fluorene groups belonging to neighbouring chains.
In-house and synchrotron X-ray diffraction studies of 2-phenyl-1,10-phenanthroline, protonated salts, complexes with gold(III) and copper(II), and an orthometallation product with palladium(II)
Authors: Krause Jeanette A. , Zhao Daoli , Chatterjee Sayandev , Falcon Roland , Stoltz Kristen , Warren John C. , Wiswell Sara E. , Connick William B. , Collins Sibrina N.
Published: February 2014

Different salts of the 2-phenyl-1,10-phenanthrolin-1-ium cation, (pnpH)+, are obtained by reacting 2-phenyl-1,10-phenanthroline (pnp), C18H12N2, (I), with a variety of anions, such as hexafluoridophosphate, C18H13N2+·PF6−, (II), trifluoromethanesulfonate, C18H13N2+·CF3SO3−, (III), tetrachloridoaurate, (C18H13N2)[AuCl4], (IV), and bromide (as the dihydrate), C18H13N2+·Br−·2H2O, (V). Compound (I) crystallizes withZ′ = 2, with both independent molecules adopting a coplanar conformation. In (II)–(IV), a hydrogen bond exists between the cation and anion, while one of the lattice water molecules serves as a hydrogen-bonded bridge between the cation and anion in (V). Reaction of (I) with HAuCl4gives the salt complex (IV); however, reaction with KAuCl4produces the monodentate complex trichlorido(2-phenyl-1,10-phenanthroline-κN10)gold(III), [AuCl3(C18H12N2)], (VI). Dichlorido(2-phenyl-1,10-phenanthroline-κ2N,N′)copper(II), [CuCl2(C18H12N2)], (VII), results from the reaction of CuCl2·2H2O and (I), in which the CuIIcenter adopts a tetrahedrally distorted square-planar geometry. The pendent phenyl ring twists to a bisecting position relative to the phenanthroline plane. The square-planar PdIIcomplex, bromido[2-(phenanthrolin-2-yl)phenyl-κ3C1,N,N′]palladium(II), [PdBr(C18H11N2)], (VIII), is obtained from the reaction of (I) with [PdCl2(cycloocta-1,5-diene)], followed by addition of bromine. A coplanar geometry for the pendent ring is adopted as a result of the tridentate bonding motif.
Cobalt(II) chloride complexes with 1,1′-dimethyl-4,4′-bipyrazole featuring first- and second-sphere coordination of the ligand
Authors: Domasevitch Konstantin V.
Published: February 2014

Incatena-poly[[dichloridocobalt(II)]-μ-(1,1′-dimethyl-4,4′-bipyrazole-κ2N2:N2′)], [CoCl2(C8H10N4)]n, (1), two independent bipyrazole ligands (Me2bpz) are situated across centres of inversion and in tetraaquabis(1,1′-dimethyl-4,4′-bipyrazole-κN2)cobalt(II) dichloride–1,1′-dimethyl-4,4′-bipyrazole–water (1/2/2), [Co(C8H10N4)2(H2O)4]Cl2·2C8H10N4·2H2O, (2), the Co2+cation lies on an inversion centre and two noncoordinated Me2bpz molecules are also situated across centres of inversion. The compounds are the first complexes involvingN,N′-disubstituted 4,4′-bipyrazole tectons. They reveal a relatively poor coordination ability of the ligand, resulting in a Co–pyrazole coordination ratio of only 1:2. Compound (1) adopts a zigzag chain structure with bitopic Me2bpz links between tetrahedral CoIIions. Interchain interactions occur by means of very weak C—H...Cl hydrogen bonding. Complex (2) comprises discrete octahedraltrans-[Co(Me2bpz)2(H2O)4]2+cations formed by monodentate Me2bpz ligands. Two equivalents of additional noncoordinated Me2bpz tectons are important as `second-sphere ligands' connecting the cations by means of relatively strong O—H...N hydrogen bonding with generation of doubly interpenetratedpcu(α-Po) frameworks. Noncoordinated chloride anions and solvent water molecules afford hydrogen-bonded [(Cl−)2(H2O)2] rhombs, which establish topological links between the above frameworks, producing a rare eight-coordinated uninodal net of {424.5.63} (ilc) topology.
A new one-dimensional nickel metal–organic framework:catena-poly[[[diaquabis(4-{[(1-phenyl-1H-tetrazol-5-yl)sulfanyl]methyl}benzoato-κO)nickel(II)]-μ-4,4′-bipyridine-κ2N:N′] monohydrate]
Authors: Geng Aijing , Zhang Qingfu , Wang Jiajia , Zhang Haina , Sun Dezhi
Published: February 2014

The title complex, {[Ni(C15H11N4O2S)2(C10H8N2)(H2O)2]·H2O}n, was synthesized by the reaction of nickel chloride, 4-{[(1-phenyl-1H-tetrazol-5-yl)sulfanyl]methyl}benzoic acid (HL) and 4,4′-bipyridine (bpy) under hydrothermal conditions. The asymmetric unit contains two half NiIIions, each located on an inversion centre, twoL−ligands, one bpy ligand, two coordinated water molecules and one unligated water molecule. Each NiIIcentre is six-coordinated by two monodentate carboxylate O atoms from two differentL−ligands, two pyridine N atoms from two different bpy ligands and two terminal water molecules, displaying a nearly ideal octahedral geometry. The NiIIions are bridged by 4,4′-bipyridine ligands to afford a linear array, with an Ni...Ni separation of 11.361 (1) Å, which is further decorated by two monodentateL−ligandstransto each other, resulting in a one-dimensional fishbone-like chain structure. These one-dimensional fishbone-like chains are further linked by O—H...O, O—H...N and C—H...O hydrogen bonds and π–π stacking interactions to form a three-dimensional supramolecular architecture. The thermal stability of the title complex was investigatedviathermogravimetric analysis.
Life span in the wild: the role of activity and climate in natural populations of bees
Authors: Straka Jakub , Černá Kateřina , Macháčková Lenka , Zemenová Monika , Keil Petr
Published: February 2014

Animal life span is constrained by ecology and physiology. The latter has been studied under controlled conditions, but little is known about determinants of life span under natural conditions.

We studied the relationships between length of adult life, magnitude of foraging activity, and environmental abiotic conditions in two bee species: a pollen specialist Andrena vaga (Andrenidae) and a pollen generalist Anthophora plumipes (Apidae).

Our research indicates that life span is driven both directly by climate and indirectly through climate‐dependent activity patterns. We found a negative relationship between proportion of active days and length of life; in contrast, a high activity rate within the active days had no negative effect on longevity.

Individuals active during warm and/or wet days lived longer, with precipitation being a more important determinant of life span than temperature.

Timing of the first appearance at the site was also an important predictor of bee life span. Individuals that first appeared closer to the end of season (critical time horizon) lived a shorter time than individuals observed earlier. The first observed active day in the season was also correlated with seasonal temperature and precipitation.

We demonstrate that life span and activity patterns of wild populations of insects are regulated by a tractable interplay of ecological (mostly climatic) variables that were previously studied only in isolation or in vitro.
Fine needle aspiration cytology of lymphoproliferative lesions of the oral cavity
Authors: Cozzolino I. , Vigliar E. , Todaro P. , Peluso A. L. , Picardi M. , Sosa Fernandez L. V. , Mignogna M. D. , Tuccari G. , Selleri C. , Zeppa P.
Published: February 2014

Objective

Oral cavity non‐Hodgkin lymphoma (OCL) is a rare condition that may be clinically and radiologically indistinguishable from other pathologies of the mouth. A complete excision or adequate biopsy of the OCL may be difficult. Fine needle aspiration (FNA) cytology has been successfully utilized in the pre‐operative diagnosis of oral masses and in lymphoma involving other anatomical areas. Our experience with FNA pre‐operative cytological diagnosis of 16 OCLs is reported herein.

Methods

The results of FNA cytology on 16 consecutive lymphoproliferative lesions of the oral cavity collected over an 8‐year period in three institutions were retrieved. Sampled lesions were submucosal masses of different sizes bulging into the oral cavity. Rapid on‐site evaluation (ROSE) and routine cytological staining were performed. Immunocytochemistry (ICC), flow cytometry (FC) and polymerase chain reaction (PCR) of the IGH (immunoglobulin heavy) locus were performed on additional passes according to ROSE.

Results

Fourteen OCLs, one myeloma and one florid reactive lymphoid hyperplasia (FRLH) were diagnosed by FNA. OCLs were diagnosed as large B‐cell (eight cases) and small B‐cell (six cases) lymphomas. Histology revealed eight diffuse large B‐cell lymphomas (DLBCL), four lymphomas of mucosa‐associated lymphoid tissue (MALT), two follicular lymphomas and one FRLH; no false‐negative or false‐positive results were diagnosed, but accurate subclassification was obtained in four cases only.

Conclusions

FNA diagnosis of OCLs may be hampered by the rare incidence, anatomical context and difficulties in obtaining a sufficient amount of cells. Ancillary techniques should be used according to ROSE; a pre‐operative FNA cytology diagnosis can avoid unnecessary extensive surgery and speed up the institution of therapeutic procedures.
Crystal structures of two tetrameric β‐carbonic anhydrases from the filamentous ascomycete Sordaria macrospora
Authors: Lehneck Ronny , Neumann Piotr , Vullo Daniela , Elleuche Skander , Supuran Claudiu T. , Ficner Ralf , Pöggeler Stefanie
Published: February 2014

Carbonic anhydrases (CAs) are metalloenzymes catalyzing the reversible hydration of carbon dioxide to bicarbonate (hydrogen carbonate) and protons. CAs have been identified in archaea, bacteria and eukaryotes and can be classified into five groups (α, β, γ, δ, ζ) that are unrelated in sequence and structure. The fungal β‐class has only recently attracted attention. In the present study, we investigated the structure and function of the plant‐like β‐CA proteins CAS1 and CAS2 from the filamentous ascomycete Sordaria macrospora. We demonstrated that both proteins can substitute for the Saccharomyces cerevisiae β‐CA Nce103 and exhibit an in vitro CO2 hydration activity (kcat/Km of CAS1: 1.30 × 106 m−1·s−1; CAS2: 1.21 × 106 m−1·s−1). To further investigate the structural properties of CAS1 and CAS2, we determined their crystal structures to a resolution of 2.7 Å and 1.8 Å, respectively. The oligomeric state of both proteins is tetrameric. With the exception of the active site composition, no further major differences have been found. In both enzymes, the Zn2+ ‐ion is tetrahedrally coordinated; in CAS1 by Cys45, His101 and Cys104 and a water molecule and in CAS2 by the side chains of four residues (Cys56, His112, Cys115 and Asp58). Both CAs are only weakly inhibited by anions, making them good candidates for industrial applications.

Structured digital abstract

CAS1 and CAS2 bind by x-ray crystallography (View interaction)

Database

Structural data have been deposited in the Protein Data Bank database under accession numbers 4O1J for CAS1 and 4O1K for CAS2.
Soil nutrient budgets following projected corn stover harvest for biofuel production in the conterminous United States
Authors: Tan Zhengxi , Liu Shuguang
Published: February 2014

Increasing demand for food and biofuel feedstocks may substantially affect soil nutrient budgets, especially in the United States where there is great potential for corn (Zea mays L) stover as a biofuel feedstock. This study was designed to evaluate impacts of projected stover harvest scenarios on budgets of soil nitrogen (N), phosphorus (P), and potassium (K) currently and in the future across the conterminous United States. The required and removed N, P, and K amounts under each scenario were estimated on the basis of both their average contents in grain and stover and from an empirical model. Our analyses indicate a small depletion of soil N (−4 ± 35 kg ha−1) and K (−6 ± 36 kg ha−1) and a moderate surplus of P (37 ± 21 kg ha−1) currently on the national average, but with a noticeable variation from state to state. After harvesting both grain and projected stover, the deficits of soil N, P, and K were estimated at 114–127, 26–27, and 36–53 kg ha−1 yr−1, respectively, in 2006–2010; 131–173, 29–32, and 41–96 kg ha−1 yr−1, respectively, in 2020; and 161–207, 35–39, and 51–111 kg ha−1 yr−1, respectively, in 2050. This study indicates that the harvestable stover amount derived from the minimum stover requirement for maintaining soil organic carbon level scenarios under current fertilization rates can be sustainable for soil nutrient supply and corn production at present, but the deficit of P and K at the national scale would become larger in the future.
Comparative Analysis of Low‐Cycle Fatigue Behavior of 2D‐Cf‐PyC/SiC Composites in Different Environments
Authors: Zhang Yani , Cheng Laifei , Zhang Litong , Luan Xingang
Published: February 2014

A carbon fiber‐reinforced silicon carbide matrix composite with pyrolytic carbon interface (Cf‐PyC/SiC) and a protective coating was prepared by isothermal low pressure chemical vapor infiltration. Low‐cycle fatigue behavior of this material system was investigated at high temperatures up to 1800°C in a combustion environment and at room temperature in air, respectively. The combustion environment includes thermal mechanical loading, high temperatures, and oxidizing atmosphere. Low‐cycle fatigue tests were conducted at a maximum stress level of 180 MPa but at various temperatures and fatigue cycles. The residual strength variation of fatigue‐survived samples was due to different damage mechanisms in different environments.
Population genomics of eusocial insects: the costs of a vertebrate‐like effective population size
Authors: Romiguier J. , Lourenco J. , Gayral P. , Faivre N. , Weinert L. A. , Ravel S. , Ballenghien M. , Cahais V. , Bernard A. , Loire E. , Keller L. , Galtier N.
Published: February 2014

The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life‐history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome‐wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA‐seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes – a marker of the effective population size – in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels.
Comparing omeprazole with fluoxetine for treatment of patients with heartburn and normal endoscopy who failed once daily proton pump inhibitors: Double‐blind placebo‐controlled trial
Authors: Ostovaneh M. R. , Saeidi B. , Hajifathalian K. , Farrokhi‐Khajeh‐Pasha Y. , Fotouhi A. , Mirbagheri S. S. , Emami H. , Barzin G. , Mirbagheri S. A.
Published: February 2014

Background

Patients with heartburn but without esophageal erosion respond less well to proton pump inhibitors (PPIs). There is a growing body of evidence implicating the role of psychological comorbidities in producing reflux symptoms. Pain modulators improve symptoms in patients with other functional gastrointestinal disorders. We aimed to compare the efficacy of fluoxetine with omeprazole and placebo to achieve symptomatic relief in patients with heartburn and normal endoscopy who failed once daily PPIs.

Methods

Endoscopy‐negative patients with heartburn who failed once daily PPIs were randomly allocated to receive 6 weeks treatment of fluoxetine, omeprazole, or placebo. Random allocation was stratified according to ambulatory pH monitoring study. Percentage of heartburn‐free days and symptom severity was assessed.

Key Results

Sixty patients with abnormal and 84 patients with normal pH test were randomized. Subjects receiving fluoxetine experienced more improvement in percentage of heartburn‐free days (median 35.7, IQR 21.4–57.1) than those on omeprazole (median 7.14, IQR 0–50, p < 0.001) or placebo (median 7.14, IQR 0–33.6, p < 0.001). In normal pH subgroup, fluoxetine was superior to both omeprazole and placebo regarding percentage of heartburn‐free days (median improvement, 57.1, IQR 35.7–57.1 vs 13.9, IQR, 0–45.6 and 7.14, 0–23.8, respectively, p < 0.001), but no significant difference was observed between medications in abnormal pH subgroup.

Conclusions & Inferences

Fluoxetine was superior to omeprazole for improving the symptoms of patients with heartburn and normal endoscopy who failed once daily PPIs. The superiority of fluoxetine was mostly attributed to those with normal esophageal pH rather than those with abnormal pH (ClinicalTrials.gov, number NCT01269788).
Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage‐specific whole‐genome duplications
Authors: Jourda Cyril , Cardi Céline , Mbéguié‐A‐Mbéguié Didier , Bocs Stéphanie , Garsmeur Olivier , D'Hont Angélique , Yahiaoui Nabila
Published: February 2014

Whole‐genome duplications (WGDs) are widespread in plants, and three lineage‐specific WGDs occurred in the banana (Musa acuminata) genome. Here, we analysed the impact of WGDs on the evolution of banana gene families involved in ethylene biosynthesis and signalling, a key pathway for banana fruit ripening.

Banana ethylene pathway genes were identified using comparative genomics approaches and their duplication modes and expression profiles were analysed.

Seven out of 10 banana ethylene gene families evolved through WGD and four of them (1‐aminocyclopropane‐1‐carboxylate synthase (ACS), ethylene‐insensitive 3‐like (EIL), ethylene‐insensitive 3‐binding F‐box (EBF) and ethylene response factor (ERF)) were preferentially retained. Banana orthologues of AtEIN3 and AtEIL1, two major genes for ethylene signalling in Arabidopsis, were particularly expanded. This expansion was paralleled by that of EBF genes which are responsible for control of EIL protein levels. Gene expression profiles in banana fruits suggested functional redundancy for several MaEBF and MaEIL genes derived from WGD and subfunctionalization for some of them.

We propose that EIL and EBF genes were co‐retained after WGD in banana to maintain balanced control of EIL protein levels and thus avoid detrimental effects of constitutive ethylene signalling. In the course of evolution, subfunctionalization was favoured to promote finer control of ethylene signalling.
Hematopoietic stem cell transplantation effects on spinal cord compression in Hurler
Authors: Ferrara Giovanna , Maximova Natalia , Zennaro Floriana , Gregori Massimo , Tamaro Paolo
Published: February 2014

Hurler syndrome type 1 (MPS‐1) is an autosomal recessive lysosomal disorder due to the deficiency of the enzyme alpha‐L‐iduronidase which is necessary for the degradation of dermatan and heparan sulfate. It is characterized by deposit of glycosaminoglycans in tissues, progressive multisystem dysfunction, and early death. HSCT for children with MPS‐I is effective, resulting in increased life expectancy and improvement of clinical parameters. The spinal MRI performed on a female 10 yr old undergoing HSCT at the age of 18 months and receiving ERT revealed a considerable decrease in soft tissue around the tip of odontoid causing a significant reduction in spinal cord compression. In light of this result, we suppose that combined ERT and HSCT are successful in Hurler I disease.
Regulation of potassium transport in plants under hostile conditions: implications for abiotic and biotic stress tolerance
Authors: Shabala Sergey , Pottosin Igor
Published: February 2014

Intracellular potassium homeostasis is a prerequisite for the optimal operation of plant metabolic machinery and plant's overall performance. It is controlled by K+ uptake, efflux and intracellular and long‐distance relocation, mediated by a large number of K+‐selective and non‐selective channels and transporters located at both plasma and vacuolar membranes. All abiotic and biotic stresses result in a significant disturbance to intracellular potassium homeostasis. In this work, we discuss molecular mechanisms and messengers mediating potassium transport and homeostasis focusing on four major environmental stresses: salinity, drought, flooding and biotic factors. We argue that cytosolic K+ content may be considered as one of the ‘master switches’ enabling plant transition from the normal metabolism to ‘hibernated state’ during first hours after the stress exposure and then to a recovery phase. We show that all these stresses trigger substantial disturbance to K+ homeostasis and provoke a feedback control on K+ channels and transporters expression and post‐translational regulation of their activity, optimizing K+ absorption and usage, and, at the extreme end, assisting the programmed cell death. We discuss specific modes of regulation of the activity of K+ channels and transporters by membrane voltage, intracellular Ca2+, reactive oxygen species, polyamines, phytohormones and gasotransmitters, and link this regulation with plant‐adaptive responses to hostile environments.
Signaling by small metabolites in systemic acquired resistance
Authors: Shah Jyoti , Chaturvedi Ratnesh , Chowdhury Zulkarnain , Venables Barney , Petros Robby A.
Published: February 2014

Plants can retain the memory of a prior encounter with a pest. This memory confers upon a plant the ability to subsequently activate defenses more robustly when challenged by a pest. In plants that have retained the memory of a prior, localized, foliar infection by a pathogen, the pathogen‐free distal organs develop immunity against subsequent infections by a broad‐spectrum of pathogens. The long‐term immunity conferred by this mechanism, which is termed systemic acquired resistance (SAR), is inheritable over a few generations. Signaling mediated by the phenolic metabolite salicylic acid (SA) is critical for the manifestation of SAR. Recent studies have described the involvement of additional small metabolites in SAR signaling, including methyl salicylate, the abietane diterpenoid dehydroabietinal, the lysine catabolite pipecolic acid, a glycerol‐3‐phosphate‐dependent factor and the dicarboxylic acid azelaic acid. Many of these metabolites can be systemically transported through the plant and probably facilitate communication by the primary infected tissue with the distal tissues, which is essential for the activation of SAR. Some of these metabolites have been implicated in the SAR‐associated rapid activation of defenses in response to subsequent exposure to the pathogen, a mechanism termed priming. Here, we summarize the role of these signaling metabolites in SAR, and the relationship between them and SA signaling in SAR.
Electromagnetic Compatibility Between DCS and Switchboard
Authors: Zhang Hao , Hou Yousheng , Che Junxia , Zhang Liqiang , Jiang Tao , Zhou Chuangbin
Published: February 2014

This paper describes EMC problems and solution in China Nuclear power plant engineering. EMP from switchboard interrupts DCS control system and causes nuclear safety actuation failure when command on commission. Adapting solutions are introduced to improve EMC on site. But the best solution is to archive EMC in factory with a joint test.
A Study of GOTHIC 8.0 Code Application to AP1000 Containment Response
Authors: Wang Guodong , Wang Zhe
Published: February 2014

The AP1000 containment model has been developed by using WGOTHIC version 4.2 code. Condensation heat and mass transfer from the volumes to the containment shell, conduction through the shell, and evaporation from the shell to the riser were all calculated by using the special CLIMEs model. In this paper, the latest GOTHIC version 8.0 code is used to model both condensation and evaporation heat and mass transfer process. An improved heat and mass transfer model, the diffusion layer model (DLM), is adopted to model the condensation on the inside wall of containment. The Film heat transfer coefficient option is used to model the evaporation on the outside wall of containment. As a preliminary code consolidation effort, it is possible to use GOTHIC 8.0 code as a tool to analysis the AP1000 containment response.
Analysis of Steam Blocking in a Low Pressure Heating System
Authors: Chen Jinbo , Gong Haiguang , Tong Lili
Published: February 2014

An analytic investigation of the steam blocking in low pressure heating channels was conducted. In this paper, the dynamic model of the vapor-liquid interface is established through the basic conservation equations, and the rupture time of the vapor-liquid interface is predicted based on the Rayleigh-Taylor instability. Subsequently, the steam blocking model considering the steam accumulation and the vapor-liquid interface rupture in geysering flow is established. On these bases, the relative volume and relative pressure of the accumulated steam, the relative acceleration and perturbation intensity of the vapor-liquid interface, the time-varying behavior of the ratio of resistance and buoyancy are obtained. It is found that the accumulated steam basically increases linearly with the time going; The oscillation of the pressure and velocity, which is very large at the beginning time of the steam accumulation, decreases gradually with the continuous steam accumulation; The Reynolds number of the liquid within the rising section is very small at the stagnation state since there is no forced circulation flow, and finally a blockage is engendered in the pipeline with the steam accumulated. The theoretical results are in good agreements with the results obtained by a small-scale experiment. The mechanism model is able to predict the steam blocking property during the geysering flow in heating channels well, and can also establish a theoretical basis for the later analysis of the steam blocking elimination.
Fluid-Structure Coupling Analysis for the Flow Distribution Device of Nuclear Reactor Internals
Authors: Zhang Mingqian , Duan Yuangang , Ran Xiaobing , Liu Yanwu
Published: February 2014

In order to better understand the stresses to which the flow distribution device (FDD) is subjected for the pressure fluctuation, we need to improve our knowledge of the fluid flow inside the reactor pressure vessel (RPV). The flow field of the reactor lower plenum which is associated with a typical pressurized water reactor (PWR) is simulated by using ANSYS CFX code. Calculations have been carried out from reactor pressure vessel inlet to the core outlet. Grid sizes of million nodes with the k-epsilon turbulent model have been used with a porous zone approach for the reactor core space. Predictions of the steady-state pressure and velocity field have been made. The results are compared with the scaled experiment data in order to verify the accurate description of the fluid flow. Based on this verified turbulent model, a sub-domain is extracted from the lower plenum for the transient two-way Fluid-Structure Interaction (FSI) simulation which is limited by the computer capability and computing time. This transient analysis of fluid-structure coupling system is conducted by using CFX and ANSYS in numeric calculation of flow field and structure, with an exchanging platform MFX-ANSYS/CFX which can transfer fluid pressure and structure displacement between computational fluid dynamics (CFD) and computational structure dynamics (CSD) grid systems. The loose coupling method is used to investigate the transient dynamic response of the flow distribution device which is immerged in the bottom plenum. Dynamic stress and strain of the flow distribution device are given and discussed. This analysis practice can be guidance for the optimization design of reactor and improve our understanding of reactor components flow induced vibration phenomena.
Behavior of the Spent Fuel Pool and Dose Rate Calculations for the CPR1000 Reactor Under Severe Accident Conditions Using the Integral Code MELCOR
Authors: Mueller Klaus , Yeung Moses , Byard Justin , Peng Zhen Xun , Tao Jun , Liao Yehong , Duan Cheng Jie , Yang Zhi Fei , Xie Xiao Fei
Published: February 2014

The behavior of the spent fuel pool and the fission product release and transport for the CPR1000 reactor under severe accident conditions was analyzed using the integral severe accident code MELCOR. In the investigated accident scenario a total failure of the pump of the spent fuel cooling system was assumed. Furthermore, it is assumed that accident management fails to bring water into the spent fuel pool using mobile pumps or due to the non-recovery of the cooling pump. The grace time available for measures in order to avoid significant fission product release to the environment is determined. The calculated hydrogen mass flow rate due to clad oxidation and the steam flow rate from the spent fuel pool to the compartment above the spent fuel pool serve as boundary conditions for the three dimensional fluid dynamics code GASFLOW to assess possible hydrogen combustion or detonation in the compartment. Using this spent fuel pool MELCOR model the dose submerged in air or water can be determined.

The calculated gamma dose rate in a specific compartment can be used for equipment qualification and compartment accessibility assessment. It was found that after four days the fuel assemblies are significantly heated-up and ten hours later the fission products are released as well as a significant amount of hydrogen is produced. A preliminary GASFLOW analysis shows by assuming an air atmosphere in the fuel building, that the risk of a hydrogen combustion or detonation is high. In late state of the accident a convection flow of pure hydrogen is established in spent fuel pool region. It was shown, that the flow conditions strongly influence the fission product transport behavior and consequently the dose rates in the compartment above the spent fuel pool.
Thermal-Hydraulic Evaluation of an LBE Cooled 19-Pin Bundle in the Frame of TRACE Validation
Authors: Jaeger Wadim , Boettcher Micheal , Sánchez Espinoza Victor Hugo
Published: February 2014

In the frame of the validation and verification of the thermal hydraulic system code TRACE for lead alloy cooled systems, a 19 pin bundle is analyzed, in particular, the influence of the spacers. TRACE is updated and improved in order to be used for the analyses of liquid metal cooled reactors. For the present investigation, isothermal hydraulic experiments, carried out at the Karlsruhe Lead Laboratory, are used to validate the pressure losses related to wall friction and spacers. In this experimental set-up, a 19 rod bundle, cooled by liquid lead-bismuth eutectics (LBE) is used. In addition, thermal analyses are performed in order to evaluate the axial temperature profile of coolant and cladding and to validate the chosen heat transfer models. Since the thermal experiments have not been performed yet, the validation is done by comparing TRACE results to CFD results following a unique approach for the turbulent Prandtl number. Special emphasize is paid to the validation of the models to account for heat transfer enhancement at and in the vicinity of spacers due to increased turbulences.
Experimental and Numerical Study of the Movement Mechanism and Characteristics of the Quasi-Static Pebble Flow
Authors: Jia Xinlong , Gui Nan , Yang Xingtuan , Tu Jiyuan , Jiang Shengyao
Published: February 2014

Quasi-static pebble flow, or so-called the very slow pebble flow, in a pebble bed reactor, with evident randomicity and dispersibility, is extremely complex. Improving the knowledge of the movement mechanism of quasi-static pebble flow can be beneficial to the safety of the pebble bed reactor. This study utilizes a phenomenological method and a discrete element method to investigate the interface features of two regions composed of differently colored pebbles. A pseudo-two dimensional experimental setup is established to facilitate the observation of movement of pebble. Then, the DEM simulation is carried out to analyze the further details of particle movement mechanism. To some extent, the two methods are closely related and mutually confirmed. In this study, some special phenomena are observed, such as the non-uniformity, mixing zone, stagnant zones, the propagation of voids, slow flow zone, etc. Moreover, some basic issues on the movement mechanism and characteristics of quasi-static pebble flow are discussed, e.g. the interpretation of force analysis inside the pebble packing, propagation and distribution of voids, formation of equilibrium arches, the effects of stagnant zone on the flow field, and so on. These characteristics of the quasi-static pebble flow are very different from the continuous flow, and the understanding of these characteristics is very helpful for the design and analysis of pebble bed reactors.
Evaluation of Interaction Effects on Part-Through Cracks in Steam Generator Tubes
Authors: Kang Yong-Seok , Kim Hong-Deok , Lee Kuk-Hee , Park Jai-Hak
Published: February 2014

Degraded steam generator tubing can affect its safety functions. Therefore, its integrity should be maintained for each degradation form and all detected degradation must be assessed to verify that if adequate integrity is retained. Determination of tube integrity limits includes identifying acceptable structural parameters such as flaw length, depth, and amplitude of signals. If we consider just single-cracked tubes, short and deep flaws are not likely to threaten structural integrity of tubes. But if it has multiple-cracks, we have to consider interaction effects of multiple adjacent cracks on its burst pressure. Because adjacent multiple cracks can be merged due to the crack growth then it can challenge against the structural performance limit. There are some studies on the interaction effects of adjacent cracks. However, existing works on the interaction effect consider only through-wall cracks. No study has been carried out on the interaction effects of part-through cracks. Most cracks existing in real steam generator tubing are not through-wall cracks but part-through cracks. Hence, integrity of part-through cracks is more practical issue than that of through-wall cracks.

This paper presents experimental burst test results with steam generator tubing for evaluation of interaction effects with axial oriented two collinear and parallel part-through cracks. The interaction effect between two adjacent cracks disappeared when the distance exceeds about 2 mm.