bluuebunny/crossref_metadata_2025 huggingface dataset:
A quantitative metabolomics study of high sodium response in Clostridium acetobutylicum ATCC 824 acetone-butanol-ethanol (ABE) fermentation
Authors: Zhao Xinhe , Condruz Stefan , Chen Jingkui , Jolicoeur Mario
Published: June 2016

Hemicellulose hydrolysates, sugar-rich feedstocks used in biobutanol refinery, are normally obtained by adding sodium hydroxide in the hydrolyze process. However, the resulting high sodium concentration in the hydrolysate inhibits ABE (acetone-butanol-ethanol) fermentation, and thus limits the use of these low-cost feedstocks. We have thus studied the effect of high sodium on the metabolic behavior of Clostridium acetobutyricum ATCC 824, with xylose as the carbon source. At a threshold sodium concentration of 200 mM, a decrease of the maximum cell dry weight (−19.50 ± 0.85%) and of ABE yield (−35.14 ± 3.50% acetone, −33.37 ± 0.74% butanol, −22.95 ± 1.81% ethanol) were observed compared to control culture. However, solvents specific productivities were not affected by supplementing sodium. The main effects of high sodium on cell metabolism were observed in acidogenesis, during which we observed the accumulation of ATP and NADH, and the inhibition of the pentose phosphate (PPP) and the glycolytic pathways with up to 80.73 ± 1.47% and 68.84 ± 3.42% decrease of the associated metabolic intermediates, respectively. However, the NADP+-to-NADPH ratio was constant for the whole culture duration, a phenomenon explaining the robustness of solvents specific productivities. Therefore, high sodium, which inhibited biomass growth through coordinated metabolic effects, interestingly triggered cell robustness on solvents specific productivity.
Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome
Authors: Miyazato Paola , Katsuya Hiroo , Fukuda Asami , Uchiyama Yoshikazu , Matsuo Misaki , Tokunaga Michiyo , Hino Shinjiro , Nakao Mitsuyoshi , Satou Yorifumi
Published: June 2016

The recent development and advancement of next-generation sequencing (NGS) technologies have enabled the characterization of the human genome at extremely high resolution. In the retrovirology field, NGS technologies have been applied to integration-site analysis and deep sequencing of viral genomes in combination with PCR amplification using virus-specific primers. However, virus-specific primers are not available for some epigenetic analyses, like chromatin immunoprecipitation sequencing (ChIP-seq) assays. Viral sequences are poorly detected without specific PCR amplification because proviral DNA is very scarce compared to human genomic DNA. Here, we have developed and evaluated the use of biotinylated DNA probes for the capture of viral genetic fragments from a library prepared for NGS. Our results demonstrated that viral sequence detection was hundreds or thousands of times more sensitive after enrichment, enabling us to reduce the economic burden that arises when attempting to analyze the epigenetic landscape of proviruses by NGS. In addition, the method is versatile enough to analyze proviruses that have mismatches compared to the DNA probes. Taken together, we propose that this approach is a powerful tool to clarify the mechanisms of transcriptional and epigenetic regulation of retroviral proviruses that have, until now, remained elusive.
Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes
Authors: Li Erna , Wei Xiao , Ma Yanyan , Yin Zhe , Li Huan , Lin Weishi , Wang Xuesong , Li Chao , Shen Zhiqiang , Zhao Ruixiang , Yang Huiying , Jiang Aimin , Yang Wenhui , Yuan Jing , Zhao Xiangna
Published: June 2016

Enterobacter aerogenes (Enterobacteriaceae) is an important opportunistic pathogen that causes hospital-acquired pneumonia, bacteremia, and urinary tract infections. Recently, multidrug-resistant E. aerogenes have been a public health problem. To develop an effective antimicrobial agent, bacteriophage phiEap-2 was isolated from sewage and its genome was sequenced because of its ability to lyse the multidrug-resistant clinical E. aerogenes strain 3-SP. Morphological observations suggested that the phage belongs to the Siphoviridae family. Comparative genome analysis revealed that phage phiEap-2 is related to the Salmonella phage FSL SP-031 (KC139518). All of the structural gene products (except capsid protein) encoded by phiEap-2 had orthologous gene products in FSL SP-031 and Serratia phage Eta (KC460990). Here, we report the complete genome sequence of phiEap-2 and major findings from the genomic analysis. Knowledge of this phage might be helpful for developing therapeutic strategies against E. aerogenes.
Honeybee economics: optimisation of foraging in a variable world
Authors: Stabentheiner Anton , Kovac Helmut
Published: June 2016

In honeybees fast and efficient exploitation of nectar and pollen sources is achieved by persistent endothermy throughout the foraging cycle, which means extremely high energy costs. The need for food promotes maximisation of the intake rate and the high costs call for energetic optimisation. Experiments on how honeybees resolve this conflict have to consider that foraging takes place in a variable environment concerning microclimate and food quality and availability. Here we report, in simultaneous measurements of energy costs, gains and intake rate and efficiency, how honeybee foragers manage this challenge in their highly variable environment. If possible, during unlimited sucrose flow, they follow an ‘investment-guided’ (‘time is honey’) economic strategy promising increased returns. They maximise net intake rate by investing both own heat production and solar heat to increase body temperature to a level which guarantees a high suction velocity. They switch to an ‘economizing’ (‘save the honey’) optimisation of energetic efficiency if the intake rate is restricted by the food source when an increased body temperature would not guarantee a high intake rate. With this flexible and graded change between economic strategies honeybees can do both maximise colony intake rate and optimise foraging efficiency in reaction to environmental variation.
The hexagonal shape of the honeycomb cells depends on the construction behavior of bees
Authors: Nazzi Francesco
Published: June 2016

The hexagonal shape of the honey bee cells has attracted the attention of humans for centuries. It is now accepted that bees build cylindrical cells that later transform into hexagonal prisms through a process that it is still debated. The early explanations involving the geometers’ skills of bees have been abandoned in favor of new hypotheses involving the action of physical forces, but recent data suggest that mechanical shaping by bees plays a role. However, the observed geometry can arise only if isodiametric cells are previously arranged in a way that each one is surrounded by six other similar cells; here I suggest that this is a consequence of the building program adopted by bees and propose a possible behavioral rule ultimately accounting for the hexagonal shape of bee cells.
Selection of reliable reference genes for RT-qPCR analysis during developmental stages and abiotic stress in Setaria viridis
Authors: Martins Polyana Kelly , Mafra Valéria , de Souza Wagner Rodrigo , Ribeiro Ana Paula , Vinecky Felipe , Basso Marcos Fernando , da Cunha Bárbara Andrade Dias Brito , Kobayashi Adilson Kenji , Molinari Hugo Bruno Correa
Published: June 2016

Real-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but reliable results depend on the use of stable reference genes for proper normalization. This study proposed to test the expression stability of 13 candidate reference genes in Setaria viridis, a monocot species recently proposed as a new C4 model plant. Gene expression stability of these genes was assayed across different tissues and developmental stages of Setaria and under drought or aluminum stress. In general, our results showed Protein Kinase, RNA Binding Protein and SDH as the most stable genes. Moreover, pairwise analysis showed that two reference genes were sufficient to normalize the gene expression data under each condition. By contrast, GAPDH and ACT were the least stably expressed genes tested. Validation of suitable reference genes was carried out to profile the expression of P5CS and GolS during abiotic stress. In addition, normalization of gene expression of SuSy, involved in sugar metabolism, was assayed in the developmental dataset. This study provides a list of reliable reference genes for transcript normalization in S. viridis in different tissues and stages of development and under abiotic stresses, which will facilitate genetic studies in this monocot model plant.
Rare coding TTN variants are associated with electrocardiographic QT interval in the general population
Authors: Kapoor Ashish , Bakshy Kiranmayee , Xu Linda , Nandakumar Priyanka , Lee Dongwon , Boerwinkle Eric , Grove Megan L. , Arking Dan E. , Chakravarti Aravinda
Published: June 2016

We have shown previously that noncoding variants mapping around a specific set of 170 genes encoding cardiomyocyte intercalated disc (ID) proteins are more enriched for associations with QT interval than observed for genome-wide comparisons. At a false discovery rate (FDR) of 5%, we had identified 28 such ID protein-encoding genes. Here, we assessed whether coding variants at these 28 genes affect QT interval in the general population as well. We used exome sequencing in 4,469 European American (EA) and 1,880 African American (AA) ancestry individuals from the population-based ARIC (Atherosclerosis Risk In Communities) Study cohort to focus on rare (allele frequency <1%) potentially deleterious (nonsynonymous, stop-gain, splice) variants (n = 2,398 for EA; n = 1,693 for AA) and tested their effects on standardized QT interval residuals. We identified 27 nonsynonymous variants associated with QT interval (FDR 5%), 22 of which were in TTN. Taken together with the mapping of a QT interval GWAS locus near TTN, our observation of rare deleterious coding variants in TTN associated with QT interval show that TTN plays a role in regulation of cardiac electrical conductance and coupling and is a risk factor for cardiac arrhythmias and sudden cardiac death.
Alpinetin attenuates inflammatory responses by suppressing TLR4 and NLRP3 signaling pathways in DSS-induced acute colitis
Authors: He Xuexiu , Wei Zhengkai , Wang Jingjing , Kou Jinhua , Liu Weijian , Fu Yunhe , Yang Zhengtao
Published: June 2016

Alpinetin, a composition of Alpinia katsumadai Hayata, has been reported to have a number of biological properties, such as antibacterial, antitumor and other important therapeutic activities. However, the effect of alpinetin on inflammatory bowel disease (IBD) has not yet been reported. The purpose of this study was to investigate the anti-inflammatory effect and mechanism of alpinetin on dextran sulfate sodium (DSS)-induced colitis in mice. In vivo, DSS-induced mice colitis model was established by giving mice drinking water containing 5% (w/v) DSS for 7 days. Alpinetin (25, 50 and 100 mg/kg) were administered once a day by intraperitoneal injection 3 days before DSS treatment. In vitro, phorbol myristate acetate (PMA)-differentiated monocytic THP-1 macrophages were treated with alpinetin and stimulated by lipopolysaccharide (LPS). The results showed that alpinetin significantly attenuated diarrhea, colonic shortening, histological injury, myeloperoxidase (MPO) activity and the expressions of tumor necrosis factor (TNF-α) and interleukin (IL-1β) production in mice. In vitro, alpinetin markedly inhibited LPS-induced TNF-α and IL-1β production, as well as Toll-like receptor 4 (TLR4) mediated nuclear transcription factor-kappaB (NF-κB) and NOD-like receptor protein 3 (NLRP3) inflammasome activation. In conclusion, this study demonstrated that alpinetin had protective effects on DSS-induced colitis and may be a promising therapeutic reagent for colitis treatment.
Identification of long non-coding RNAs involved in neuronal development and intellectual disability
Authors: D’haene Eva , Jacobs Eva Z. , Volders Pieter-Jan , De Meyer Tim , Menten Björn , Vergult Sarah
Published: June 2016

Recently, exome sequencing led to the identification of causal mutations in 16–31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies.
Transfer and amplification of chirality in Phe-based C3-symmetric non-ionic amphiphiles
Authors: Buendía Julia , García Fátima , Yélamos Belén , Sánchez Luis
Published: June 2016

The chiral features provided by the Phe fragment in amphiphiles 1 and 2 are transferred to the supramolecular level to yield enantiomerically enriched helices. Despite the very low degree of cooperativity, an amplification of chirality phenomenon is demonstrated by MR experiments.
Microstructures of negative and positive azeotropes
Authors: Shephard J. J. , Callear S. K. , Imberti S. , Evans J. S. O. , Salzmann C. G.
Published: June 2016

Azeotropes famously impose fundamental restrictions on distillation processes, yet their special thermodynamic properties make them highly desirable for a diverse range of industrial and technological applications. Using neutron diffraction, this study provides first insights into the microstructures of azeotropes.
Thermometry and up-conversion luminescence of Yb3+–Er3+ co-doped Na2Ln2Ti3O10 (Ln = Gd, La) phosphors
Authors: Zhang Zhiyu , Guo Chongfeng , Suo Hao , Zhao Xiaoqi , Zhang Niumiao , Li Ting
Published: June 2016

Yb3+/Er3+-ion co-doped Na2Ln2Ti3O10 (Ln = Gd, La) up-conversion phosphors were successfully synthesized by a sol–gel method, and their crystal structures were characterized by powder X-ray diffraction.
From information theory to quantitative description of steric effects
Authors: Alipour Mojtaba , Safari Zahra
Published: June 2016

In this study, further evidences of the efficiency of informational theory for a quantitative description of steric effects are showcased.
H3P⋯AgI: generation by laser-ablation and characterization by rotational spectroscopy and ab initio calculations
Authors: Stephens Susanna L. , Tew David P. , Walker Nicholas R. , Legon Anthony C.
Published: June 2016

The new compound H3P⋯AgI has been synthesized in the gas phase by means of the reaction of laser-ablated silver metal with a pulse of gas consisting of a dilute mixture of ICF3 and PH3 in argon.
Depolymerization of 1,4-polybutadiene by metathesis: high yield of large macrocyclic oligo(butadiene)s by ligand selectivity control
Authors: Dewaele Annelies , Renders Tom , Yu Baoyi , Verpoort Francis , Sels Bert F.
Published: June 2016

Herein, we demonstrate a practical high yield preparation of large macrocyclic oligo(butadiene)s, preferably the C16 to C44 fraction, from commercial 1,4-polybutadiene by exploring intramolecular backbiting using a series of commercially available Ru catalysts.
Influence of Ta substitution for Nb in Zn3Nb2O8and the impact on the crystal structure and microwave dielectric properties
Authors: Zhao Yonggui , Zhang Ping
Published: June 2016

Zn3(Nb1−xTax)2O8(x= 0.02–0.10) ceramics were preparedviaa solid-state reaction route and the dependence of their microwave dielectric properties on their structural characteristics were investigated.
In situ growth of ZIF-8 nanocrystals on layered double hydroxide nanosheets for enhanced CO2 capture
Authors: Liu Peng-Fei , Tao Kai , Li Guo-Chang , Wu Meng-Ke , Zhu Shuai-Ru , Yi Fei-Yan , Zhao Wen-Na , Han Lei
Published: June 2016

A hexagonal nanosheet LDH@ZIF-8 composite was fabricated by in situ growth of ZIF-8 on Zn–Al LDH and exhibited a CO2 adsorption capacity of 1.0 mmol g−1 at room temperature and 1 bar.
Multiplexing slanted spiral microchannels for ultra-fast blood plasma separation
Authors: Rafeie Mehdi , Zhang Jun , Asadnia Mohsen , Li Weihua , Warkiani Majid Ebrahimi
Published: June 2016

Blood and blood products are critical components of health care.
SOHPRED: a new bioinformatics tool for the characterization and prediction of human S-sulfenylation sites
Authors: Wang Xiaofeng , Yan Renxiang , Li Jinyan , Song Jiangning
Published: June 2016

SOHPRED is a new and competitive bioinformatics tool for characterizing and predicting human S-sulfenylation sites.
Ultrafast synthesis of silver nanoplates in ethanol at room temperature
Authors: Gao Xianhui , Li Dan , Chen Zhenhua , Mei Xifan , Wang Yan
Published: June 2016

The formation of silver nanoplates was obtained based on aged NaBH4 in the presence of NaBO2.
Aggregation-induced emission enhancement and cell imaging of a novel (carbazol-N-yl)triphenylamine–BODIPY
Authors: Li Qian , Qian Ying
Published: June 2016

The AIEE fluorogen BCPA–BODIPY emits strong red fluorescence and shows a good uptake by MCF-7 cells.
Chiral phosphoric acid-catalyzed asymmetric transfer hydrogenation of 3-trifluoromethylthioquinolines
Authors: Zhou Ji , Zhang Qian-Fan , Zhao Wei-Hao , Jiang Guo-Fang
Published: June 2016

A chiral phosphoric acid-catalyzed asymmetric transfer hydrogenation of 3-trifluoromethylthioquinolines was developed, providing chiral 2,3-disubstituted 1,2,3,4-tetrahydroquinoline derivatives containing a stereogenic trifluoromethylthio group with up to 99% enantioselectivity.
Synthesis of 2,6-trans- and 3,3,6-trisubstituted tetrahydropyran-4-ones from Maitland–Japp derived 2H-dihydropyran-4-ones: a total synthesis of diospongin B
Authors: Clarke Paul A. , Nasir Nadiah Mad , Sellars Philip B. , Peter Alejandra M. , Lawson Connor A. , Burroughs James L.
Published: June 2016

6-Substituted-2H-dihydropyran-4-ones can be transformed into 2,6-trans- and 3,3,6-trisubstituted tetrahydropyrans via conjugate addition and electrophilic trapping.
Redox-triggered crosslinking of a degradable polymer
Authors: Delle Chiaie Kayla R. , Yablon Lauren M. , Biernesser Ashley B. , Michalowski Gregory R. , Sudyn Alexander W. , Byers Jeffery A.
Published: June 2016

A unique redox-triggered crosslinking reaction is disclosed that capitalizes on the orthogonal reactivity of an iron-based catalyst for the ring opening polymerization of cyclic diesters and epoxides.
Hydrazone–palladium catalyzed annulation of 1-cinnamyloxy-2-ethynylbenzene derivatives
Authors: Watanabe Kohei , Mino Takashi , Ikematsu Tatsuya , Hatta Chikako , Yoshida Yasushi , Sakamoto Masami
Published: June 2016

The annulation of 1-cinnamyloxy-2-ethynylbenzene derivatives using a hydrazone–palladium catalyst system proceeded smoothly and gave the corresponding 2-substituted-3-cinnamylbenzofurans in good-to-excellent yields.
Organic vapor-modulated surface enhanced Raman scattering spectroscopy
Authors: Shin Dongha
Published: June 2016

It is reported that organic vapor such as ammonia can significantly alter the electronic structure of the nanostructure, resulting in modulation of the efficiency of surface enhanced Raman scattering spectroscopy (SERS).
Thiopropyl-containing ionic liquid based periodic mesoporous organosilica as a novel and efficient adsorbent for the removal of Hg(ii) and Pb(ii) ions from aqueous solutions
Authors: Elhamifar Dawood , Shojaeipoor Frood , Yari Omolbanin
Published: June 2016

In the present study, a novel thiol-functionalized ionic liquid based periodic mesoporous organosilica (PMO-IL-SH) is prepared, characterized and its efficiency for the removal of mercury and lead ions from aqueous solutions is investigated.
Electrochemical reduction of cationic Li+@C60 to neutral Li+@C60˙−: isolation and characterisation of endohedral [60]fulleride
Authors: Ueno Hiroshi , Aoyagi Shinobu , Yamazaki Yu , Ohkubo Kei , Ikuma Naohiko , Okada Hiroshi , Kato Tatsuhisa , Matsuo Yutaka , Fukuzumi Shunichi , Kokubo Ken
Published: June 2016

Li@C60 was synthesised by electrochemical reduction of ionic Li+@C60 salt. This is the first report of isolation and unambiguous characterisation of endohedral metallo[60]fullerene.
A P2-Na0.67Co0.5Mn0.5O2 cathode material with excellent rate capability and cycling stability for sodium ion batteries
Authors: Zhu Yuan-En , Qi Xingguo , Chen Xiaoqing , Zhou Xianlong , Zhang Xu , Wei Jinping , Hu Yongsheng , Zhou Zhen
Published: June 2016

This work presents P2-type layered Na0.67Co0.5Mn0.5O2 with a hierarchical architecture as a cathode material for sodium ion batteries. Owing to its superior structural flexibility, it delivered outstanding rate capability and long cyclic stability.
Glucose fuel cell based on carbon nanotube-supported pyrene–metalloporphyrin catalysts
Authors: Elouarzaki K. , Holzinger M. , Le Goff A. , Thery J. , Marks R. S. , Cosnier S.
Published: June 2016

We demonstrated that the performance of a fuel cell can be optimized by selecting a suitable grafting linker for the catalyst material.
Improved sodium-ion storage performance of TiO2nanotubes by Ni2+doping
Authors: Yan Dong , Yu Caiyan , Li Dongsheng , Zhang Xiaojie , Li Jiabao , Lu Ting , Pan Likun
Published: June 2016

Ni2+doped TiO2nanotubes, synthesized through a sol–gel process, hydrothermal process and thermal treatment, exhibit excellent electrochemical performance as an anode for sodium-ion batteries.
Tuning stiffness of cell-laden hydrogel via host–guest interactions
Authors: Shih Han , Lin Chien-Chi
Published: June 2016

We report a dynamic hydrogel system with on-demand tunable matrix stiffness.
Single-step synthesis of hyperbranched, luminescent Mn2+-doped ZnSe1−xSx nanocrystals using dichalcogenide precursors
Authors: Yazdanparast Mohammad S. , Webb Matthew T. , McLaurin Emily J.
Published: June 2016

Taking advantage of dichalcogenide precursors, a simple, single-step heat-up method for obtaining Mn2+-doped ZnSe1−xSx nanocrystals (NCs) is presented.
Synthesis of colloidal MnSb nanoparticles: consequences of size and surface characteristics on magnetic properties
Authors: Hettiarachchi Malsha A. , Abdelhamid Ehab , Nadgorny Boris , Brock Stephanie L.
Published: June 2016

A solution phase methodology was developed to synthesize superparamagnetic MnSb nanoparticles, ca. 14 nm in diameter, with low polydispersity.
Star-shaped D–π–A oligothiophenes with a tris(2-methoxyphenyl)amine core and alkyldicyanovinyl groups: synthesis and physical and photovoltaic properties
Authors: Luponosov Yuriy N. , Min Jie , Solodukhin Alexander N. , Bakirov Artem V. , Dmitryakov Petr V. , Shcherbina Maxim A. , Peregudova Svetlana M. , Cherkaev Georgiy V. , Chvalun Sergei N. , Brabec Christoph J. , Ponomarenko Sergei A.
Published: June 2016

We report a series of D–π–A star-shaped oligomers with a tris(2-methoxyphenyl)amine core and alkyldicyanovinyl groups.
UV light-switchable transparent polymer films and invisible luminescent inks based on carbon dots and lanthanide complexes
Authors: Wang Yu , Čépe Klára , Zbořil Radek
Published: June 2016

We present a simple approach for the preparation of UV light-switchable transparent composite polymer films and invisible luminescent inks based on the combination of carbon dots (CDs) and trisdipicolinate lanthanide complexes.
Excitonic recombination dynamics mediated by polymorph transformation in cadmium sulfide nanocrystals
Authors: Wang Pan , Li Zhifang , Yang Tianye , Wang Zhiyang , Zhu Pinwen , Zhang Mingzhe
Published: June 2016

The excitonic recombination dynamics could be mediated by the different bandgaps and wave function overlaps in polymorphic CdS nanocrystals.
Multiple stressors associated with acid sulfate soil effluent influence mud crab Scylla serrata predation on Sydney rock oysters Saccostrea glomerata
Authors: Glaspie Cassandra N. , Seitz Rochelle D.
Published: June 2016

Studies of long-term exposure to multiple stressors on predator–prey interactions are necessary to determine the effect of coastal degradation on organisms that have had generations to adapt and acclimate to change. In New South Wales, Australia, a natural gradient of multiple stressors produced by acid sulfate soil effluent was used to determine the impact of exposure to multiple stressors on predator–prey dynamics between mud crabs Scylla serrata and Sydney rock oysters Saccostrea glomerata. Wild oysters were collected from two polluted and two reference sites that varied in their distance away from a flood gate that acted as a point source of water with low salinity, low pH and low alkalinity. Oysters from sites affected by multiple stressors and those from reference sites were offered to mud crabs in 48-h laboratory no-choice feeding trials. Oysters from affected sites had lower mortality than those from a reference site that was farthest from the source of polluted water. Linear models containing distance from flood gate best explained oyster mortality. Differences in rates of mortality were due to the decreased time crabs spent foraging on affected oysters. Long-term exposure to acid sulfate soil effluent alters trophic dynamics between predators and prey, which may have consequences for coastal food webs.
Population genetic structure of the goby Stiphodon rutilaureus (Gobiidae) in the New Georgia Group, Solomon Islands
Authors: Boseto David T. , Furiness Magnuson Sharon J. , Pezold Frank L.
Published: June 2016

In this study, we use eight microsatellite loci and a mitochondrial locus to investigate the population structure of the amphidromous goby species Stiphodon rutilaureus in the New Georgia Group, Solomon Islands. In total, 206 specimens were collected between June 2010 and August of 2012 on three different trips. The AMOVA results from both types of loci reveal that >95% of variation is contained within populations. Pairwise comparisons reveal non-significant differences between three different regions for the mitochondrial analysis but a significant difference between the west and central regions for the microsatellites. The findings in this study concur with results from previous studies, indicating low or no population structure among populations of amphidromous sicydiine goby species on different islands within an archipelago. This study can provide suggestions for management and conservation of fragile aquatic species.
Cadmium toxicity and soil biological index under potato (Solanum tuberosum L.) cultivation
Authors: Hassan Waseem , Bano Rizwana , Bashir Safdar , Aslam Zubair
Published: June 2016

Increasing cadmium (Cd) pollution in soil is of great concern. A pot experiment was conducted with the aim of assessing the effect of Cd on soil biological indices under potato cultivation. Cadmium was added to 10 kg soil in each pot (6 seeds pot–1) as Cd(NO3)2 at 0, 15, 30, 45 and 60 mg kg–1 with three replications. All soil and plant parameters decreased with all Cd treatments; however, high levels of Cd had a significant (P < 0.05) suppressive effect. The highest Cd level significantly (P < 0.05) decreased microbial biomass carbon (2.16-fold), nitrogen (11.37-fold) and phosphorus (10.3-fold), as well as enzyme activities of dehydrogenase (4.36-fold), phosphatase (9.23-fold), and urease (9.61-fold). The highest Cd level also decreased pH (1.46-fold), potato shoot (3.55-fold) and root (7.43-fold) length, root (10.9-fold) and shoot (6.04-fold) fresh weight, root (7.51-fold) and shoot (13.7-fold) dry weight, chlorophyll content (27.0-fold), carotenoid content (4.08-fold), and plant macronutrient and micronutrient uptake in potato root and shoots. Conversely, the highest level of Cd significantly (P < 0.05) increased the biomass C : N (5.27-fold) and C : P (4.77-fold) ratios, soil extractable Cd (5.38-fold), and Cd uptake in potato root (5.05-fold) and shoot (4.82-fold) at the end of the experiment (day 60). Cadmium contamination substantially affected soil biological indices and growth of potato, and the Cd threshold was strongly associated with the extent of Cd concentration and duration to accumulate. Soil microbial biomass, enzymatic activities, pH and potato physiological parameters could be used as a sensitive indicators to reflect environmental stresses in soil ecosystems.
Mitigation of N2O emissions from surface-irrigated cropping systems using water management and the nitrification inhibitor DMPP
Authors: Jamali Hizbullah , Quayle Wendy , Scheer Clemens , Baldock Jeff
Published: June 2016

Soils under irrigated agriculture are a significant source of nitrous oxide (N2O) owing to high inputs of nitrogen (N) fertiliser and water. This study investigated the potential for N2O mitigation by manipulating the soil moisture deficit through irrigation scheduling in combination with, and in comparison to, using the nitrification inhibitor, 3,4-dimethylpyrazole phosphate (DMPP). Lysimeter cores planted with wheat were fitted with automated chambers for continuous measurements of N2O fluxes. Treatments included conventional irrigation (CONV), reduced deficit irrigation (RED), CONV-DMPP and RED-DMPP. The total seasonal volume of irrigation water applied was constant for all treatments but the timing and quantity in individual irrigation applications varied among treatments. 15N-labelled urea was used to track the source of N2O emissions and plant N uptake. The majority of N2O emissions occurred immediately after irrigations began on 1 September 2014. Applying RED and DMPP individually slightly decreased N2O emissions but when applied in combination (RED-DMPP) the greatest reductions in N2O emissions were observed. There was no effect of treatments on plant N uptake, 15N recovery or yield possibly because the system was not N limited. Half of the plant N and 53% to 87% of N2O was derived from non-fertiliser sources in soil, highlighting the opportunity to further exploit this valuable N pool.
Greenhouse gas (N2O and CH4) fluxes under nitrogen-fertilised dryland wheat and barley on subtropical Vertosols: risk, rainfall and alternatives
Authors: Schwenke Graeme D. , Herridge David F. , Scheer Clemens , Rowlings David W. , Haigh Bruce M. , McMullen K. Guy
Published: June 2016

The northern Australian grains industry relies on nitrogen (N) fertiliser to optimise yield and protein, but N fertiliser can increase soil fluxes of nitrous oxide (N2O) and methane (CH4). We measured soil N2O and CH4 fluxes associated with wheat (Triticum aestivum) and barley (Hordeum vulgare) using automated (Expts 1, 3) and manual chambers (Expts 2, 4, 5). Experiments were conducted on subtropical Vertosol soils fertilised with N rates of 0–160kgNha–1. In Expt 1 (2010), intense rainfall for a month before and after sowing elevated N2O emissions from N-fertilised (80kgNha–1) wheat, with 417gN2O-Nha–1 emitted compared with 80g N2O-Nha–1 for non-fertilised wheat. Once crop N uptake reduced soil mineral N, there was no further treatment difference in N2O. Expt 2 (2010) showed similar results, however, the reduced sampling frequency using manual chambers gave a lower cumulative N2O. By contrast, very low rainfall before and for several months after sowing Expt 3 (2011) resulted in no difference in N2O emissions between N-fertilised and non-fertilised barley. N2O emission factors were 0.42, 0.20 and –0.02 for Expts 1, 2 and 3, respectively. In Expts 4 and 5 (2011), N2O emissions increased with increasing rate of N fertiliser. Emissions were reduced by 45% when the N fertiliser was applied in a 50:50 split between sowing and mid-tillering, or by 70% when urea was applied with the nitrification inhibitor 3,4-dimethylpyrazole-phosphate. Methane fluxes were typically small and mostly negative in all experiments, especially in dry soils. Cumulative CH4 uptake ranged from 242 to 435g CH4-Cha–1year–1, with no effect of N fertiliser treatment. Considered in terms of CO2 equivalents, soil CH4 uptake offset 8–56% of soil N2O emissions, with larger offsets occurring in non-N-fertilised soils. The first few months from N fertiliser application to the period of rapid crop N uptake pose the main risk for N2O losses from rainfed cereal cropping on subtropical Vertosols, but the realisation of this risk is dependent on rainfall. Strategies that reduce the soil mineral N pool during this time can reduce the risk of N2O loss.
Fire spread in chaparral – a comparison of laboratory data and model predictions in burning live fuels
Authors: Weise David R. , Koo Eunmo , Zhou Xiangyang , Mahalingam Shankar , Morandini Frédéric , Balbi Jacques-Henri
Published: June 2016

Fire behaviour data from 240 laboratory fires in high-density live chaparral fuel beds were compared with model predictions. Logistic regression was used to develop a model to predict fire spread success in the fuel beds and linear regression was used to predict rate of spread. Predictions from the Rothermel equation and three proposed changes as well as two physically based models were compared with observed spread rates of spread. Flame length–fireline intensity relationships were compared with flame length data. Wind was the most important variable related to spread success. Air temperature, live fuel moisture content, slope angle and fuel bed bulk density were significantly related to spread rate. A flame length–fireline intensity model for Galician shrub fuels was similar to the chaparral data. The Rothermel model failed to predict fire spread in nearly all of the fires that spread using default values. Increasing the moisture of extinction marginally improved its performance. Modifications proposed by Cohen, Wilson and Catchpole also improved predictions. The models successfully predicted fire spread 49 to 69% of the time. Only the physical model predictions fell within a factor of two of actual rates. Mean bias of most models was close to zero. Physically based models generally performed better than empirical models and are recommended for further study.
美国留学生词语搭配的偏误分析及其对词语教学的启示
Authors: Li Shouji
Published: June 2016

Using both quantitative and qualitative approaches, this study investigates the collocational errors in compositions written for
the HSK (The Chinese language proficiency test) by American learners of Chinese. The results show that the vast majority of
collocational errors are “verb + noun” collocations, and most of these errors are caused by the use of incorrect verbs. The main
factors that caused these errors are also analyzed. The analysis shows that the misuse of synonyms, as well as orthographically
and phonologically similar words, is the leading cause of the errors. The negative transfer of the learners’ mother tongue is also
found to be a relatively important factor. Lastly, the study suggests that learners should be led by the teacher to notice
collocations in texts, and then learn to construct collocation patterns on the basis of the analysis of the semantic features of
most frequent words that collocate with the head words. The grasp of collocation patterns and the ability to generalize to more
abstract patterns are some useful strategies to improve the outcomes of the teaching of vocabulary.
Temporality in speech – Linear Unit Grammar
Authors: Mauranen Anna
Published: June 2016

Language is usually modelled through a predominantly synoptic perspective; even if the object of analysis is spoken language, we tend to look at extracts where the analysis of parts makes use of the whole. Holistic analyses can be very good for capturing realities of language in many respects, but in the case of modelling temporal aspects of processing they fall into the trap of unrealistic hindsight. The experience of speech is time-bound: a hearer will go on what he or she has heard at any given point, and will anticipate what may follow. The predictions will be either confirmed or rejected in rapid succession, as speech moves on. The time window for working memory is very brief, and processing focuses on continuously changing input. Models of this process must take into account this dynamism, and they need to take on board the fact that language must be continually processed even while utterances are still incomplete. Most models of language structure are based on completed units; this tends to lead to a hierarchical view of language, embodied in most grammars. The reality of temporally progressing speech is nevertheless fundamentally linear along the dimension of time.
Specificational there-clefts
Authors: Davidse Kristin , Kimps Ditte
Published: June 2016

In this article we present functional-structural and information structure arguments for recognizing specificationalthere-clefts, i.e. clefts that specify a value for a variable. We distinguish two types which hinge on whether the matrix is a listing or a canonical existential. Listingthere-clefts enumerate one or more instances as corresponding to the variable, e.g.You are quite right David, it was engineered, seems there’s only me and you who can see this.Quantifyingthere-clefts indicate the quantity of instantiation of the variable, e.g.Look at the shape of it. There’s only one thing that’s that shape.
Phasal dynamism and the unfolding of meaning as text
Authors: Bartlett Tom
Published: June 2016

In this paper I explore the etic category of textuality and the emic category of Theme arguing that while Theme in English may simultaneously signal the point of departure of a clause with respect to the preceding text and also the ‘aboutness’ of the clause in relation to the method of development of a text, this is not necessarily the case with other languages. In particular I consider the rich textual resources of Scottish Gaelic, a verb-initial language with no morphological marking for Theme, to problematise standard treatments of thematicity in languages other than English. I elaborate on Cloran’s (2010) account of Rhetorical Units to present as a hypothesis for further exploration the idea that, while Gaelic and English ground clauses in both space and time, Gaelic is a process-centred language while English is a Subject-centred language and that these differences in the respective characterology of the two languages have repercussions on the process of textualisation and the method of development in each language.
Theme in English and Spanish
Authors: Moyano Estela Inés
Published: June 2016

This article offers a comparative view of a Systemic Functional (SF) account of Theme in English and Spanish declarative clauses. It considers the lexicogrammatical realization of Theme in both languages and shows how Themes across the clauses construe the method of development of a phase of discourse in the respective languages, unmarked Themes scaffolding textual continuity and marked Themes scaffolding transitions between discourse phases. The paper reviews the concept of Theme in Systemic Functional Linguistics (SFL) and analyzes texts in both languages, taking into account a trinocular perspective (Matthiessen & Halliday 2009): from above, considering textual discourse functions related to the lexicogrammatical function of Theme; from roundabout, considering other textual functions in the clause as New; and from below, paying attention to the role that different ranks may play in the realization of the function under focus. In addition, the paper argues for a re-interpretation of previous SFL accounts of Spanish Theme, on the assumptions of SFL language typology. Based on the analysis of fragments of Research Articles, the paper shows how English and Spanish texts perform similar strategies to maintain the method of development of a text, through the interaction between lexical strings and reference chains with the function of Theme (Fries 1981; Martin 1992). It is shown, however, that the lexicogrammatical realization of unmarked Theme differs between these languages.
Speakingwithothers involves placing ourselves explicitly as authors in the research text
Authors: Crimmins Gail
Published: June 2016

Narrative researchers need to carefully consider if and how they represent the words and worlds of people/s who do not yet have the power to represent themselves. This paper explores the dialectic of speakingfororofOthers, and posits that making manifest the co-constructed nature of narrative research to both research participants and research audiences can address some of the ideological, political, and ethical considerations involved in re-presenting the narratives of Other/ed people. In particular, it identifies that artistic forms of communication enable the researcher to speakwithOther/ed research participants by making explicit the dialogic nature of narrative re-presentation, and can fully engage audiences in the content of narrative research so that the stories of Other/ed people get heard. Therefore, it’s posited that the form of academic communication is central to the debate about whether/how we might re-present Other/ed stories.
Long-term significance of immigration
Authors: Chaitin Julia , Sternberg Rotem
Published: June 2016

This qualitative study explored the long-term significance ofaliya(Jewish immigration) to Israel for 32 immigrants/refugees who settled along the Israeli-Gaza border. The participants shared their life stories and discussed life in this war-torn region. We found that the interviewees presented three major meanings ofaliya: (1) Zionist ideology, sustained throughout life; (2) the need for finding a safe haven, and seeing their region as such a place in spite of the rocket attacks; and (3) immigration as a forced choice, connected to feelings of discontent with how their lives evolved. We conclude that by better understanding the long-term psycho-social meaning of immigration for Israelis, we can also better understand why and how they continue to live in an area marked by ongoing political conflict, and use this knowledge to inform individual and community resilience and socio-political policy.
A sketch of Theodore R. Sarbin’s life
Authors: Scheibe Karl E. , Barrett Frank J.
Published: June 2016

Ted Sarbin was born on May 8, 1911 in Cleveland, Ohio. He died on August 31, 2005, in Carmel, California. He was born into a poor Jewish family from eastern Europe, and died at his home — beloved by his friends and family, and acclaimed by his professional colleagues as a psychologist of distinction. This article traces the course of his life — with special attention to the formative influences in his education as a psychologist. As a psychologist, he became a significant critical voice — arguing for a psychology that would embrace narrative as a principle of understanding human life, and contextualism, as opposed to mechanism, as a world view.
SUMOylation of DNA topoisomerase IIα regulates histone H3 kinase Haspin and H3 phosphorylation in mitosis
Authors: Yoshida Makoto M. , Ting Lily , Gygi Steven P. , Azuma Yoshiaki
Published: June 2016

DNA topoisomerase II (TOP2) plays a pivotal role in faithful chromosome separation through its strand-passaging activity that resolves tangled genomic DNA during mitosis. Additionally, TOP2 controls progression of mitosis by activating cell cycle checkpoints. Recent work showed that the enzymatically inert C-terminal domain (CTD) of TOP2 and its posttranslational modification are critical to this checkpoint regulation. However, the molecular mechanism has not yet been determined. By using Xenopus laevis egg extract, we found that SUMOylation of DNA topoisomerase IIα (TOP2A) CTD regulates the localization of the histone H3 kinase Haspin and phosphorylation of histone H3 at threonine 3 at the centromere, two steps known to be involved in the recruitment of the chromosomal passenger complex (CPC) to kinetochores in mitosis. Robust centromeric Haspin localization requires SUMOylated TOP2A CTD binding activity through SUMO-interaction motifs and the phosphorylation of Haspin. We propose a novel mechanism through which the TOP2 CTD regulates the CPC via direct interaction with Haspin at mitotic centromeres.
Plasma membrane repairs by small GTPase Rab3a
Authors: Raiborg Camilla , Stenmark Harald
Published: June 2016

Lysosomes fuse with the plasma membrane to help repair membrane lesions, but how they are positioned close to these lesions is not fully understood. Now, Encarnação et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201511093) demonstrate that the lysosomal GTPase Rab3a and its effectors orchestrate lysosome positioning and plasma membrane repair.
Microtubule organization: A complex solution
Authors: Conduit Paul T.
Published: June 2016

Microtubule nucleation within cells is catalyzed by γ-tubulin ring complexes localized at specific microtubule-organizing centers. In this issue, Muroyama et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201601099) reveal heterogeneity in the composition and function of these complexes, with wide implications for how cells organize their microtubule arrays.
Compact non-orientable surfaces of genus 6 with extremal metric discs
Authors: Nakamura Gou
Published: June 2016

A compact hyperbolic surface of genus

g
g

is said to be extremal if it admits an extremal disc, a disc of the largest radius determined only by

g
g

. We discuss how many extremal discs are embedded in non-orientable extremal surfaces of genus 6. This is the final genus in our interest because it is already known for

g
=
3
,
4
,
5

g=3, 4, 5

, or

g
>
6

g>6

. We show that non-orientable extremal surfaces of genus 6 admit at most two extremal discs. The locus of extremal discs is also obtained for each surface. Consequently non-orientable extremal surfaces of arbitrary genus

g
≧
3

g\geqq 3

admit at most two extremal discs. Furthermore we determine the groups of automorphisms of non-orientable extremal surfaces of genus 6 with two extremal discs.
Local topological algebraicity of analytic function germs
Authors: Bilski Marcin , Parusiński Adam , Rond Guillaume
Published: June 2016

Mostowski showed that every (real or complex) germ of an analytic set is homeomorphic to the germ of an algebraic set. In this paper we show that every (real or complex) analytic function germ, defined on a possibly singular analytic space, is topologically equivalent to a polynomial function germ defined on an affine algebraic variety.