bluuebunny/crossref_metadata_2025 huggingface dataset:
Carbene iridium complexes for efficient water oxidation: scope and mechanistic insights
Authors: Woods James A. , Lalrempuia Ralte , Petronilho Ana , McDaniel Neal D. , Müller-Bunz Helge , Albrecht Martin , Bernhard Stefan
Published: May 2014

Combined kinetic & in operando spectroscopic studies, factor analysis, and DFT calculations provide insight into the water oxidation reaction catalyzed by operationally homogeneous iridium mesoionic carbene complexes.
Controlling micro-phase separation in semi-crystalline/amorphous conjugated block copolymers
Authors: Chen Ying , Cui Haijun , Li Lianshan , Tian Zhiyuan , Tang Zhiyong
Published: May 2014

Bromine-functionalized polythiophene (P3BrHT) block copolymers with different block ratios were synthesized and their micro-phase separation features in the solid state were experimentally confirmed.
Facile cyclization in the synthesis of highly fused diaza cyclooctanoid compounds using retrievable nano magnetite-supported sulfonic acid catalyst
Authors: Pathak Sudipta , Debnath Kamalesh , Mollick Md. Masud Rahaman , Pramanik Animesh
Published: May 2014

Magnetically separable Fe3O4–SO3H nano particles have been prepared and established as an efficient catalyst for the synthesis of dihydrofuran fused cyclooctanoids via the dehydration reaction of dihydroxy cyclooctanoid heterocylces.
RIR-MAPLE deposition of multifunctional films combining biocidal and fouling release properties
Authors: Yu Qian , Ge Wangyao , Atewologun Ayomide , López Gabriel P. , Stiff-Roberts Adrienne D.
Published: May 2014

Multifunctional films combining switchable biocidal and fouling release properties were deposited on substrates using RIR-MAPLE.
Azobenzene moiety variation directing self-assembly and photoresponsive behavior of azo-surfactants
Authors: Peng Shuhua , Guo Qipeng , Hartley Patrick G. , Hughes Timothy C.
Published: May 2014

We report two photoresponsive amphiphiles with comparable structures consisting of hydrophilic oligooxyethylene units, a hydrophobic alkyl chain and a light-sensitive azobenzene moiety, demonstrating that self-assembly and photoresponsive behaviour is extremely sensitive to the position of the photoactive moiety within the surfactant molecular architecture.
The Effects of Energy Prices on Agricultural Groundwater Extraction from the High Plains Aquifer
Authors: Pfeiffer Lisa , Lin C.‐Y. Cynthia
Published: May 2014

We examine the effects of energy prices on groundwater extraction using an econometric model of a farmer's irrigation water pumping decision that accounts for both the intensive and extensive margins. Our results show that energy prices have an effect on both types of margins. Increasing energy prices would affect crop selection decisions, crop acreage allocation decisions, and farmers' demand for water. Our estimated total marginal effect, which sums the effects on the intensive and extensive margins, suggests that a $1 per million btu increase in the energy price would decrease water extraction by an individual farmer by 5.89 acre‐feet per year, a decrease of 3.6 percent of the average annual extraction rate. Our estimated elasticity of water extraction with respect to energy price is −0.26.
Non-coding RNA: a new frontier in regulatory biology
Authors: Fu Xiang-Dong
Published: May 2014

A striking finding in the past decade is the production of numerous non-coding RNAs (ncRNAs) from mammalian genomes. While it is entirely possible that many of those ncRNAs are transcription noises or by-products of RNA processing, increasing evidence suggests that a large fraction of them are functional and provide various regulatory activities in the cell. Thus, functional genomics and proteomics are incomplete without understanding functional ribonomics. As has been long suggested by the ‘RNA world’ hypothesis, many ncRNAs have the capacity to act like proteins in diverse biochemical processes. The enormous amount of information residing in the primary sequences and secondary structures of ncRNAs makes them particularly suited to function as scaffolds for molecular interactions. In addition, their functions appear to be stringently controlled by default via abundant nucleases when not engaged in specific interactions. This review focuses on the functional properties of regulatory ncRNAs in comparison with proteins and emphasizes both the opportunities and challenges in future ncRNA research.
Hypervirulent Klebsiella pneumoniae
Authors: Patel Payal K. , Russo Thomas A. , Karchmer Adolf W.
Published: May 2014

Hypervirulent strains of Klebsiella pneumoniae are associated with abscess formation, commonly hepatic, and metastatic spread, even in healthy patients. We describe a case of this clinical syndrome, genotypic and phenotypic features of the isolate, and briefly review epidemiology, clinical manifestations, and pathogenesis of this underappreciated syndrome.
Thermotolerant Bacillus kokeshiiformis sp. nov. isolated from marine animal resources compost
Authors: Poudel Pramod , Miyamoto Hirokuni , Miyamoto Hisashi , Okugawa Yuki , Tashiro Yukihiro , Sakai Kenji
Published: May 2014

A novel Gram-staining-positive, endospore-forming, rod-shaped, facultatively anaerobic, thermotolerant bacterium, designated strain MO-04T, was isolated from a marine animal resources (MAR) compost. The 16S rRNA gene sequence of strain MO-04T showed 99.4 % similarity with

Bacillus thermolactis

R-6488T, 94.1 % similarity with

Bacillus thermoamylovorans

CNCM I-1378T, 93.3 % similarity with

Bacillus humi

LMG 22167T, 93.2 % similarity with

Bacillus niacini

IFO 15566T and the similarities with other species were less than 93 %. DNA–DNA relatedness between strain MO-04T and

B. thermolactis

DSM 23332T was 45 %. The DNA G+C content of strain MO-04T was 33.4 mol%, comparatively lower than that of

B. thermolactis

R-6488T (35.0 mol%). Strain MO-04T grew at 35–61 °C (optimum 50 °C), pH 4.5–9.0 (optimum pH 7.2) and tolerated up to 8.0 % (w/v) NaCl (optimum 2 %). The MO-04T cell wall peptidoglycan type was meso-2,6-diaminopimelic acid, and the major fatty acids were C16 : 1, C14 : 1, C17 : 0 and C17 : 1. The major polar lipids were represented by diphosphatidylglycerol and phosphatidylglycerol and two unidentified phospholipids. The analysed polyphasic data presented here clearly indicate that the isolate MO-04T is considered to represent a novel species within the genus

Bacillus

for which the name Bacillus kokeshiiformis sp. nov. is proposed. The type strain of B. kokeshiiformis is MO-04T ( = JCM 19325T = KCTC 33163T).
Gramella
oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment
Authors: Hameed Asif , Shahina Mariyam , Lin Shih-Yao , Liu You-Cheng , Lai Wei-An , Young Chiu-Chung
Published: May 2014

A Gram-staining-negative, yellow-pigmented, strictly aerobic, zeaxanthin-producing, rod-shaped, non-endospore-forming, appendaged bacterial strain that exhibits gliding motility, designated CC-AMSZ-TT, was isolated from marine sediment off coastal Kending, Taiwan. Strain CC-AMSZ-TT shared 94.9 % and 96.7–94.1 % 16S rRNA gene sequence similarities with

Gramella echinicola

KMM 6050T and other species of the genus

Gramella

, respectively, and formed a distinct phyletic lineage in phylogenetic trees. The major (≥5 % of the total) fatty acids were C16 : 0, iso-C15 : 0, anteiso-C15 : 0, C16 : 1ω6c and/or C16 : 1ω7c and iso-C17 : 1ω9c and/or C16 : 0 10-methyl. Phosphatidylethanolamine, six unidentified lipids and three unidentified aminolipids were the polar lipid components. The DNA G+C content was 38.6 mol%. The predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMSZ-TT represents a novel species of the genus

Gramella

, for which the name Gramella oceani sp. nov. is proposed. The type strain is CC-AMSZ-TT ( = JCM 18809T = BCRC 80547T).
Identification of Mycobacterium avium genes associated with resistance to host antimicrobial peptides
Authors: Motamedi Nima , Danelishvili Lia , Bermudez Luiz E.
Published: May 2014

Antimicrobial peptides are an important component of the innate immune defence. Mycobacterium avium subsp. hominissuis (M. avium) is an organism that establishes contact with the respiratory and gastrointestinal mucosa as a necessary step for infection. M. avium is resistant to high concentrations of polymyxin B, a surrogate for antimicrobial peptides. To determine gene-encoding proteins that are associated with this resistance, we screened a transposon library of M. avium strain 104 for susceptibility to polymyxin B. Ten susceptible mutants were identified and the inactivated genes sequenced. The great majority of the genes were related to cell wall synthesis and permeability. The mutants were then examined for their ability to enter macrophages and to survive macrophage killing. Three clones among the mutants had impaired uptake by macrophages compared with the WT strain, and all ten clones were attenuated in macrophages. The mutants were also shown to be susceptible to cathelicidin (LL-37), in contrast to the WT bacterium. All but one of the mutants were significantly attenuated in mice. In conclusion, this study indicated that the M. avium envelope is the primary defence against host antimicrobial peptides.
Correlation between virulence and genetic structure of Escovopsis strains from leaf-cutting ant colonies in Costa Rica
Authors: Wallace Diego E. Elizondo , Asensio Juan G. Vargas , Tomás Adrián A. Pinto
Published: May 2014

Leaf-cutting ants (genera Atta and Acromyrmex) cultivate a specialized fungus for food in underground chambers employing cut plant material as substrate. Parasitism occurs in this agricultural system and plays an important role in colony fitness. The microfungi Escovopsis, a specialized mycoparasite of the fungal cultivar, is highly prevalent among colonies. In this study, we tested the antagonistic activity of several Escovopsis strains from different geographical areas in Costa Rica. We employed a combination of laboratory tests to evaluate virulence, including pure culture challenges, toxicity to fungus garden pieces and subcolony bioassays. We also performed a phylogenetic analysis of these strains in order to correlate their virulence with the genetic structure of this population. The bioassays yielded results consistent between each other and showed significant differences in antagonistic activity among the parasites evaluated. However, no significant differences were found when comparing the results of the bioassays according to the source of the ants’ fungal cultivar. The phylogenetic analyses were consistent with these results: whilst the fungal cultivar phylogeny showed a single clade with limited molecular variation, the Escovopsis phylogeny yielded several clades with the most virulent isolates grouping in the same well-supported clade. These results indicate that there are Escovopsis strains better suited to establish their antagonistic effect, whilst the genetic homogeneity of the fungal cultivars limits their ability to modulate Escovopsis antagonism. These findings should be taken into consideration when evaluating the potential of Escovopsis isolates as biocontrol agents for this important agricultural pest in the Neotropics.
Functionalized para-substituted benzenes as 1,8-cineole production modulators in an endophytic Nodulisporium species
Authors: Nigg Jared , Strobel Gary , Knighton W. Berk , Hilmer Jonathan , Geary Brad , Riyaz-Ul-Hassan Syed , Harper James K. , Valenti Domenic , Wang Yuemin
Published: May 2014

A Nodulisporium species (designated Ti-13) was isolated as an endophyte from Cassia fistula. The fungus produces a spectrum of volatile organic compounds (VOCs) that includes ethanol, acetaldehyde and 1,8-cineole as major components. Initial observations of the fungal isolate suggested that reversible attenuation of the organism via removal from the host and successive transfers in pure culture resulted in a 50 % decrease in cineole production unrelated to an overall alteration in fungal growth. A compound (CPM1) was obtained from Betula pendula (silver birch) that increases the production of 1,8-cineole by an attenuated Ti-13 strain to its original level, as measured by a novel bioassay method employing a 1,8-cineole-sensitive fungus (Sclerotinia sclerotiorum). The host plant produces similar compounds possessing this activity. Bioactivity assays with structurally similar compounds such as ferulic acid and gallic acid suggested that the CPM1 does not act as a simple precursor to the biosynthesis of 1,8-cineole. NMR spectroscopy and HPLC-ES-MS indicated that the CPM1 is a para-substituted benzene with alkyl and carboxyl substituents. The VOCs of Ti-13, especially 1,8-cineole, have potential applications in the industrial, fuel and medical fields.
A newly identified protein complex that mediates white spot syndrome virus infection via chitin-binding protein
Authors: Huang Po-Yu , Leu Jiann-Horng , Chen Li-Li
Published: May 2014

White spot syndrome virus (WSSV) is a large enveloped virus which has caused severe mortality and huge economic losses in the shrimp farming industry. The enveloped virus must be combined with the receptors of the host cell membrane by the virus envelope proteins. In the case of WSSV, binding of envelope proteins with receptors of the host cell membrane was discovered in a number of previous studies, such as VP53A and 10 other proteins with chitin-binding protein (CBP), VP28 with Penaeus monodon Rab7, VP187 with β-integrin, and so on. WSSV envelope proteins were also considered capable of forming a protein complex dubbed an ‘infectome’. In this study, the research was focused on the role of CBP in the WSSV infection process, and the relationship between CBP and the envelope proteins VP24, VP28, VP31, VP32 VP39B, VP53A and VP56. The results of the reverse transcription-PCR analyses showed that CBP existed in a variety of shrimp. The speed of WSSV infection could be slowed down by inhibiting CBP gene expression. Far-Western blot analysis and His pull-down assays were conducted, and a protein complex was found that appeared to be composed of a ‘linker’ protein consisting of VP31, VP32 and VP39B together with four envelope proteins, including VP24, VP28, VP53A and VP56. This protein complex was possibly another part of the infectome and the possible binding region with CBP. The findings of this study may have identified certain points for further WSSV research.
Development of an ante-mortem diagnostic test for enzootic nasal tumor virus and detection of neutralizing antibodies in host serum
Authors: Walsh Scott R. , Stinson Kevin J. , Menzies Paula I. , Wootton Sarah K.
Published: May 2014

Enzootic nasal adenocarcinoma (ENA) is a contagious neoplasm of the nasal mucosa of sheep and goats and is associated with enzootic nasal tumour virus (ENTV). As ENA is a common disease in North America and there are no vaccines against ENTV-1, diagnostic tests that can identify infected animals and assist with eradication and disease surveillance efforts are greatly needed. In this study, we endeavoured to develop a novel, non-invasive diagnostic tool that could be used not only to validate clinical signs of ENA but also to detect ENTV-1 infection prior to the onset of disease signs (i.e. pre-clinical diagnosis). Cytology, serology and reverse transcription (RT)-PCR-based diagnostic methods were investigated. Although the cytology-based assay was able to detect ENTV-1 infection in some animals, it had poor sensitivity and specificity and thus was not developed further as an ante-mortem diagnostic method. Three different assays, including ELISA, Western blotting and virus neutralization, were developed to detect the presence of ENTV-1-specific antibodies in sheep serum. Whilst a surprisingly large number of sheep mounted an antibody-mediated immune response against ENTV-1, and in some cases neutralizing, correlation with disease status was poor. In contrast, RT-PCR on RNA extracted from nasal swabs reliably detected exogenous ENTV-1 sequences, did not amplify endogenous ovine betaretroviral sequences, demonstrated high concordance with immunohistochemical staining for ENTV-1 envelope protein, and had perfect sensitivity and specificity. This report describes a practical and highly specific RT-PCR technique for the detection of clinical and pre-clinical ENA that may prove beneficial in future control or eradication programmes.
Immediate-early protein of equid herpesvirus type 1 as a target for cytotoxic T-lymphocytes in the Thoroughbred horse
Authors: Kydd Julia H. , Case Ruth , Minke Julius , Audonnet Jean-Christophe , Wagner Bettina , Antczak Douglas F.
Published: May 2014

Cytotoxic T-lymphocytes (CTLs) are associated with protective immunity against disease caused by equid herpesvirus type 1 (EHV-1). However, the EHV-1 target proteins for CTLs are poorly defined. This limits the development of vaccine candidates designed to stimulate strong CTL immunity. Here, classical CTL assays using lymphocytes from horses of three defined MHC class I types that experienced natural infection with EHV-1 and a modified vaccinia virus construct containing an EHV-1 gene encoding the immediate-early (IE) protein are reported. Horses homozygous for the equine leukocyte antigen (ELA)-A2 haplotype, but not the ELA-A5 haplotype, produced MHC-restricted CTL responses against the IE protein. Previously, horses homozygous for the ELA-A3 haplotype also mounted CTL responses against the IE protein. Both haplotypes are common in major horse breeds, including the Thoroughbred. Thus, the IE protein is an attractive candidate molecule for future studies of T-cell immunity to EHV-1 in the horse.
Novel gammaherpesvirus functions encoded by bovine herpesvirus 6 (bovine lymphotropic virus)
Authors: Jia J. , Delhon G. , Tulman E. R. , Diel D. G. , Osorio F. A. , Wen X. , Kutish G. F. , Rock D. L.
Published: May 2014

The genus Macavirus of the subfamily Gammaherpesvirinae includes viruses that infect lymphoid cells of domestic and wild ruminants and swine, causing asymptomatic latent infections in reservoir hosts. Here, we describe the genome of bovine herpesvirus 6 (BoHV-6), a macavirus ubiquitous in healthy cattle populations. The BoHV-6 genome exhibited architecture conserved in macaviruses, including a repetitive H-DNA region and unique 141 kbp L-DNA region predicted to encode 77 genes. BoHV-6 encoded, in variable genomic regions, a novel complement of genes relative to other characterized macaviruses, probably contributing to distinctive aspects of BoHV-6 infection biology and host range. Most notably, BoHV-6 encoded the first herpesviral protein (Bov2.b2) similar to cellular ornithine decarboxylase, an enzyme that catalyses the first and rate-limiting step in the biosynthesis of polyamines. Bov2.b2 conceivably mediates a novel mechanism by which BoHV-6 promotes cell-cycle-dependent viral replication.
Strategic Social Learning and the Population Dynamics of Human Behavior: The Game of Go
Authors: Beheim Bret A. , Thigpen Calvin , McElreath Richard
Published: May 2014

Human culture is widely believed to undergo evolution, via mechanisms rooted in the nature of human cognition. A number of theories predict the kinds of human learning strategies, as well as the population dynamics that result from their action. There is little work, however, that quantitatively examines the evidence for these strategies and resulting cultural evolution within human populations. One of the obstacles is the lack of individual-level data with which to link transmission events to larger cultural dynamics. Here, we address this problem with a rich quantitative database from the East Asian board game known as Go. We draw from a large archive of Go games spanning the last six decades of professional play, and find evidence that the evolutionary dynamics of particular cultural variants are driven by a mix of individual and social learning processes. Particular players vary dramatically in their sensitivity to population knowledge, which also varies by age and nationality. The dynamic patterns of opening Go moves are consistent with an ancient, ongoing arms race within the game itself.
SraTailor: GUI software for visualizing high-throughput sequence read archives
Authors: Oki Shinya , Maehara Kazumitsu , Ohkawa Yasuyuki , Meno Chikara
Published: May 2014

Raw high-throughput sequence data are deposited in public databases as SRAs (Sequence Read Archives) and are publically available to every researcher. However, in order to graphically visualize the sequence data of interest, the corresponding SRAs must be downloaded and converted into BigWig format through complicated command-line processing. This task requires users to possess skill with script languages and sequence data processing, a requirement that prevents a wide range of biologists from exploiting SRAs. To address these challenges, we developed SraTailor, a GUI (Graphical User Interface) software package that automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of SraTailor: entering an accession number of an SRA and clicking the mouse are the only steps required in order to obtain BigWig-formatted files and to graphically visualize the extents of reads at given loci. SraTailor is also able to make peak calls and files of other formats, and the software also accepts various command-line-like options. Therefore, this software makes SRAs fully exploitable by a wide range of biologists. SraTailor is freely available athttp://www.dev.med.kyushu-u.ac.jp/sra_tailor/.
A putative antiviral role of plant cytidine deaminases
Authors: Martín Susana , Cuevas José M. , Grande-Pérez Ana , Elena Santiago F.
Published: May 2014

A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade. Host cytidine deaminases (e.g., APOBEC3 proteins) edit viral genomes giving raise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis. By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity. To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation. The model plantArabidopsis thalianaencodes for nine cytidine deaminases (AtCDAs), raising the question of whether deamination is an antiviral mechanism in plants as well. Here we tested the effects of AtCDAs expression on the pararetrovirusCauliflower mosaic virus(CaMV). We show thatA. thaliana AtCDA1gene product exerts a mutagenic activity, which indeed generates a negative correlation between the level ofAtCDA1expression and CaMV accumulation in the plant, suggesting that deamination may also work as an antiviral mechanism in plants.
Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3/H4 heterodimer by the Hat1p/Hat2p complex
Authors: Li Yang , Zhang Li , Liu Tingting , Chai Chengliang , Fang Qianglin , Wu Han , Agudelo Garcia Paula A. , Han Zhifu , Zong Shuai , Yu You , Zhang Xinyue , Parthun Mark R. , Chai Jijie , Xu Rui-Ming , Yang Maojun
Published: May 2014

Post-translational modifications of histones are significant regulators of replication, transcription, and DNA repair. Particularly, newly synthesized histone H4 in H3/H4 heterodimers becomes acetylated on N-terminal lysine residues prior to its incorporation into chromatin. Previous studies have established that the histone acetyltransferase (HAT) complex Hat1p/Hat2p medicates this modification. However, the mechanism of how Hat1p/Hat2p recognizes and facilitates the enzymatic activities on the newly assembled H3/H4 heterodimer remains unknown. Furthermore, Hat2p is a WD40 repeat protein, which is found in many histone modifier complexes. However, how the WD40 repeat proteins facilitate enzymatic activities of histone modification enzymes is unclear. In this study, we first solved the high-resolution crystal structure of a Hat1p/Hat2p/CoA/H4 peptide complex and found that the H4 tail interacts with both Hat1p and Hat2p, by which substrate recruitment is facilitated. We further discovered that H3 N-terminal peptides can bind to the Hat2p WD40 domain and solved the structure of the Hat1p/Hat2p/CoA/H4/H3 peptide complex. Moreover, the interaction with Hat2p requires unmodified Arg2/Lys4 and Lys9 on the H3 tail, suggesting a novel model to specify the activity of Hat1p/Hat2p toward newly synthesized H3/H4 heterodimers. Together, our study demonstrated the substrate recognition mechanism by the Hat1p/Hat2p complex, which is critical for DNA replication and other chromatin remodeling processes.
The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation
Authors: Zhao Lei , Sun Ming-an , Li Zejuan , Bai Xue , Yu Miao , Wang Min , Liang Liji , Shao Xiaojian , Arnovitz Stephen , Wang Qianfei , He Chuan , Lu Xuemei , Chen Jianjun , Xie Hehuang
Published: May 2014

The faithful transmission of DNA methylation patterns through cell divisions is essential for the daughter cells to retain a proper cell identity. To achieve a comprehensive assessment of methylation fidelity, we implemented a genome-scale hairpin bisulfite sequencing approach to generate methylation data for DNA double strands simultaneously. We show here that methylation fidelity increases globally during differentiation of mouse embryonic stem cells (mESCs), and is particularly high in the promoter regions of actively expressed genes and positively correlated with active histone modification marks and binding of transcription factors. The majority of intermediately (40%–60%) methylated CpG dinucleotides are hemi-methylated and have low methylation fidelity, particularly in the differentiating mESCs. While 5-hmC and 5-mC tend to coexist, there is no significant correlation between 5-hmC levels and methylation fidelity. Our findings may shed new light on our understanding of the origins of methylation variations and the mechanisms underlying DNA methylation transmission.
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
Authors: Vanneste Kevin , Baele Guy , Maere Steven , Van de Peer Yves
Published: May 2014

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous–Paleogene (K–Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K–Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.
Monkeys rely on recency of stimulus repetition when solving short-term memory tasks
Authors: Wittig John H. , Richmond Barry J.
Published: May 2014

Seven monkeys performed variants of two short-term memory tasks that others have used to differentiate between selective and nonselective memory mechanisms. The first task was to view a list of sequentially presented images and identify whether a test matched any image from the list, but not a distractor from a preceding list. Performance was best when the test matched the most recently presented image. Response rates depended linearly on recency of repetition whether the test matched a sample from the current list or a distractor from a preceding list, suggesting nonselective memorization of all images viewed instead of just the sample images. The second task was to remember just the first image in a list selectively and ignore subsequent distractors. False alarms occurred frequently when the test matched a distractor presented near the beginning of the sequence. In a pilot experiment, response rates depended linearly on recency of repetition irrespective of whether the test matched the first image or a distractor, again suggesting nonselective memorization of all images instead of just the first image. Modification of the second task improved recognition of the first image, but did not abolish use of recency. Monkeys appear to perform nonspatial visual short-term memory tasks often (or exclusively) using a single, nonselective, memory mechanism that conveys the recency of stimulus repetition.
The Cysteine2/Histidine2-Type Transcription Factor ZINC FINGER OF ARABIDOPSIS THALIANA6 Modulates Biotic and Abiotic Stress Responses by Activating Salicylic Acid-Related Genes and C-REPEAT-BINDING FACTOR Genes in Arabidopsis
Authors: Shi Haitao , Wang Xin , Ye Tiantian , Chen Fangfang , Deng Jiao , Yang Pingfang , Zhang Yansheng , Chan Zhulong
Published: May 2014

The cysteine2/histidine2-type zinc finger proteins are a large family of transcription regulators, and some of them play essential roles in plant responses to biotic and abiotic stress. In this study, we found that expression of C2H2-type ZINC FINGER OF ARABIDOPSIS THALIANA6 (AtZAT6) was transcriptionally induced by salt, dehydration, cold stress treatments, and pathogen infection, and AtZAT6 was predominantly located in the nucleus. AtZAT6-overexpressing plants exhibited improved resistance to pathogen infection, salt, drought, and freezing stresses, while AtZAT6 knockdown plants showed decreased stress resistance. AtZAT6 positively modulates expression levels of stress-related genes by directly binding to the TACAAT motifs in the promoter region of pathogen-related genes (ENHANCED DISEASE SUSCEPTIBILITY1, PHYTOALEXIN DEFICIENT4, PATHOGENESIS-RELATED GENE1 [PR1], PR2, and PR5) and abiotic stress-responsive genes (C-REPEAT-BINDING FACTOR1 [CBF1], CBF2, and CBF3). Moreover, overexpression of AtZAT6 exhibited pleiotrophic phenotypes with curly leaves and small-sized plant at vegetative stage and reduced size of floral organs and siliques at the reproductive stage. Modulation of AtZAT6 also positively regulates the accumulation of salicylic acid and reactive oxygen species (hydrogen peroxide and superoxide radical). Taken together, our findings indicated that AtZAT6 plays important roles in plant development and positively modulates biotic and abiotic stress resistance by activating the expression levels of salicylic acid-related genes and CBF genes.
The RING-Finger E3 Ubiquitin Ligase COP1 SUPPRESSOR1 Negatively Regulates COP1 Abundance in Maintaining COP1 Homeostasis in Dark-Grown Arabidopsis Seedlings
Authors: Xu Dongqing , Lin Fang , Jiang Yan , Huang Xi , Li Jigang , Ling Junjie , Hettiarachchi Chamari , Tellgren-Roth Christian , Holm Magnus , Deng Xing Wang
Published: May 2014

CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) functions as an E3 ubiquitin ligase in both plants and animals. In dark-grown Arabidopsis thaliana seedlings, COP1 targets photomorphogenesis-promoting factors for degradation to repress photomorphogenesis. Little is known, however, about how COP1 itself is regulated. Here, we identify COP1 SUPPRESSOR1 (CSU1), a RING-finger E3 ubiquitin ligase, as a regulator of COP1. Genetic evidence demonstrates that csu1 mutations suppress cop1-6 phenotypes completely in the dark. Furthermore, CSU1 colocalizes with COP1 in nuclear speckles and negatively regulates COP1 protein accumulation in darkness. CSU1 can ubiquitinate COP1 in vitro and is essential for COP1 ubiquitination in vivo. Therefore, we conclude that CSU1 plays a major role in maintaining COP1 homeostasis by targeting COP1 for ubiquitination and degradation in dark-grown seedlings.
Non‐alcoholic fatty liver disease (NAFLD) fibrosis score predicts 6.6‐year overall mortality of Chinese patients with NAFLD
Authors: Xun Yun‐hao , Guo Jian‐chun , Lou Guo‐qiang , Jiang Yan‐ming , Zhuang Zhen‐jie , Zhu Meng‐fei , Luo Yan , Ma Xiao‐jie , Liu Jing , Bian Dong‐xue , Shi Jun‐ping
Published: May 2014

The non‐alcoholic fatty liver disease (NAFLD) fibrosis score (NFS) has emerged as a useful predictor of long‐term outcome in NAFLD patients. We evaluated the predictive performance of the NFS for overall mortality in a Chinese population with NAFLD. All NAFLD patients diagnosed ultrasonographically at Xixi Hospital of Hangzhou between 1996 and 2011 were retrospectively recruited to the study. Outcome was determined by interview and causes of death were confirmed by medical records. The area under the receiver operating characteristic curve (AUCROC) was used to determine the predictive accuracy of the NFS, BARD (body mass index, aspartate aminotransferase (AST)/alanine aminotransferase (ALT) ratio, diabetes) score, FIB‐4 index and the AST/platelet ratio index (APRI) for mortality. Data from a total of 180 eligible patients (median age 39 years; 96 men) were analysed, with 12 deaths over a median follow‐up period of 6.6 years (range 0.5–14.8 years). Using Cox model analysis, the NFS as a continuous variable was identified as the only predictor for all‐cause mortality (hazard ratio 2.743, 95% confidence interval (CI) 1.670–4.504). The NFS yielded the highest AUCROC of 0.828 (95% CI 0.728–0.928, P < 0.05), followed by the FIB‐4 index, APRI and BARD score (AUCROC 0.806 (P < 0.05), 0.732 (P < 0.05) and 0.632, respectively). The data indicated that the NFS is a useful predictor of 6.6‐year all‐cause mortality for Chinese patients with NAFLD.
Effects of long‐term application of metoprolol and propranolol in a rat model of smoking
Authors: Zhou Yujiao , Xu Ming , Zhang Yuan , Guo Yang , Zhang Youyi , He Bei
Published: May 2014

Beta‐blockers, especially selective β1‐adrenoceptor antagonists, are often used to treat cardiovascular disease, even when complicated by chronic obstructive pulmonary disease. The association of beta‐blocker selectivity and treatment effects is disputed, and the curative effects and side‐effects of various antagonists may differ. Herein we investigated the effects of 1 months treatment with the selective β1‐adrenoceptor antagonist metoprolol and the non‐selective β‐adrenoceptor antagonist propranolol on pulmonary function and pathology in a 4‐month rat model of passive cigarette smoke exposure and explored potential mechanisms of action. Lung function and general pathological changes were evaluated after 4 months exposure to cigarette smoke, with metoprolol and propranolol treatment (50 and 25 mg/kg per day, respectively; intragastrically) during the last month. Cytokine and mucin levels in bronchoalveolar lavage fluid (BALF) were determined by ELISA, whereas β1‐ and β2‐adrenoceptor expression in the lungs was evaluated by immunohistochemistry and western blot analysis. Chronic treatment with metoprolol and propranolol did not exacerbate peak expiratory flow or intra‐airway pressure in rats exposed to cigarette smoke. Propranolol significantly attenuated inflammatory cell infiltration, cytokine levels (tumour necrosis factor‐α and interleukin‐8) in BALF or mucus secretion, whereas metoprolol reduced only smooth muscle proliferation. Moreover, propranolol treatment was associated (albeit not significantly) with restoring β2‐adrenoceptor expression in airway epithelia. Propranolol had a more beneficial effect on cigarette smoking‐induced lung damage than metoprolol in a smoking rat model that may be associated with restoration of endogenous β2‐adrenoceptor density in the airway epithelial cells.
Emodin enhances cholesterol efflux by activating peroxisome proliferator‐activated receptor‐γ in oxidized low density lipoprotein‐loaded THP1 macrophages
Authors: Fu Xin , Xu Ai‐guo , Yao Meng‐ying , Guo Li , Zhao Luo‐sha
Published: May 2014

Peroxisome proliferator‐activated receptor (PPAR) γ is a nuclear receptor involved in the regulation of lipid metabolism. In the present study, we sought to investigate the effects of emodin, an anthraquinone derivative isolated from the roots of Rheum palmatum, on PPARγ signalling and cholesterol efflux in macrophage foam cells. Oxidized low‐density lipoprotein (oxLDL)‐stimulated THP1 macrophages were incubated with different concentrations of emodin (0–10 μmol/L) for 18 h. Western blot analysis and semiquantitative reverse transcription–polymerase chain reaction were used to assess the expression of key genes involved in cholesterol efflux, namely PPARγ, liver X receptor (LXR) α, ATP‐binding cassette transporter (ABC) A1 and ABCG1. In addition, apolipoprotein (apo) A‐I‐mediated cholesterol efflux in emodin‐treated cells was measured. Expresssion of PPARγ mRNA and protein was increased in emodin‐treated cells in a time‐ and dose‐dependent manner. Emodin treatment also concentration‐dependently induced LXRα, ABCA1 and ABCG1 expression. Moreover, emodin promoted apoA‐I‐mediated cholesterol efflux from oxLDL‐loaded THP1 macrophages, which was significantly abolished by pretreatment with the PPARγ‐selective antagonist GW9662 or the specific small interfering RNA for PPARγ. Together, the results demonstrate that emodin promotes cholesterol efflux from THP1 macrophages via activation of the PPARγ signalling pathway and may represent a potential anti‐atherosclerotic drug.
Oxidative stability and antioxidant activity of bovine, caprine, ovine and asinine milk
Authors: Bučević‐Popović Viljemka , Delaš Ivančica , Međugorac Sanja , Pavela‐Vrančić Maja , Kulišić‐Bilušić Tea
Published: May 2014

This study compares the oxidative stability of fat isolated from bovine, caprine, ovine and asinine milk as well as the antioxidant activity of casein and whey from these milks. Fat from bovine and asinine milk showed the highest oxidative stability. The antioxidant activity of casein and whey was examined before and after an in vitro digestion process. Whey from asinine milk showed the highest antioxidant activity. The antioxidant activity of whey and casein increased after simulated intestinal digestion. In addition, the results of this study showed that asinine whey exhibited radical scavenging activity comparable with the strong synthetic antioxidants butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT).
CFO's accounting talent, compensation and turnover
Authors: Loyeung Anna , Matolcsy Zoltan
Published: May 2014

This paper builds on and contributes to the literature on Chief Financial Officer's (CFO) compensation and turnover. We contend that the accounting talent of CFOs can be measured by accounting errors that occur when CFOs implement accounting standards. We find (i) a positive association between the CFO's accounting talent and the CFO's compensation ex ante in the transition year; (ii) a positive association between the CFO's accounting talent and the CFO's bonus in the subsequent year (adoption year); and (iii) an inverse association between the CFO's accounting talent and CFO turnover in the subsequent year (adoption year).
Expression of Concern: The labour scale – Assessment of the validity of a novel labour chart: A pilot study
Authors: Shazly Sherif A.M. , Embaby Lamiaa H.O. , Ali Shymaa S.
Published: May 2014

Background

Labour dystocia is the most common indication for caesarean section (CS). This study assessed the validity of the labour scale (WHO partograph modification) as an intrapartum management tool to minimise over‐diagnosis of labour dystocia.

Materials and Methods

The study included 77 women in the early active phase of labour using the scale. This scale covers the same titles as the partograph with the cervico‐graph modified using National Institute of Clinical Excellence (NICE) recommendations that adjust interference according to clinical circumstances. Labour progress was plotted on the labour scale then on the partograph to compare outcomes. Maternal and fetal outcomes were compared with international and local reports.

Results

Only 21 (27.3%) women crossed the ‘membrane line’, which promotes amniotomy, and 35 women (45.5%) crossed the ‘augmentation line’ and received oxytocin. Four women were delivered by CS for failure to progress. When the same data were re‐plotted on the partograph, twenty‐eight women were diagnosed with failure to progress. The outcome difference between the ‘labour scale’ and the partograph was significant (P < 0.0001). Maternal and neonatal outcomes were excellent.

Conclusions

We suggest that the ‘labour scale’ is a promising tool for labour management that minimises labour dystocia without additional maternal or fetal risk.
LAPCs contribute to the pathogenesis of allergen‐induced allergic airway inflammation in mice
Authors: Hawkshaw C. , Scott J. A. , Chow C.‐W. , Fish E. N.
Published: May 2014

Background

The inflammatory immune response associated with allergic airway inflammation in asthma involves T helper type 2 (Th2) immunity. Given the data that a newly described late activator antigen‐presenting cell (LAPC) population promotes Th2 immunity in viral infections, we undertook studies to investigate whether LAPCs have a pathogenic role in allergic airway inflammation.

Methods

We employed acute ovalbumin (OVA) and house dust mite (HDM) sensitization and challenge models to establish allergic airway inflammation in mice, followed by the analysis of lungs and draining lymph node (DLN) cell infiltrates, immunoglobulin E (IgE) production, and airway hyper‐responsiveness (AHR). We tested whether adoptive transfer of LAPCs isolated from mice with established allergic airway inflammation augments the development of sensitization in naïve mice.

Results

We provide evidence that in both OVA and HDM mouse models of allergic inflammation, LAPCs accumulate in the lungs and draining lymph nodes (DLNs), concomitant with the onset of lung pathology, allergen‐specific IgE production, eosinophilia, and Th2 cytokine production. Adoptive transfer experiments using OVA‐activated LAPCs reveal exacerbation of disease pathology with an increase in lung inflammatory cells, eosinophilia, circulating IgE, Th2 cytokine production, and a worsening of AHR. OVA‐activated LAPCs preferentially increased GATA‐3 induction in naïve CD4+ T cells.

Conclusions

Together, these data suggest an important role for LAPCs in polarizing the Th2 response in mouse models of allergic airway inflammation.
Deprived neighborhoods and adverse perinatal outcome: a systematic review and meta‐analysis
Authors: Vos Amber A. , Posthumus Anke G. , Bonsel Gouke J. , Steegers Eric A.P. , Denktaş Semiha
Published: May 2014

Objectives

This study aims to summarize evidence on the relation between neighborhood deprivation and the risks for preterm birth, small‐for‐gestational age, and stillbirth.

Design

The design was a systematic review and meta‐analysis.

Main outcome measures

The main outcome measures included studies that directly compared the risk of living in the most deprived neighborhood quintile with least deprived quintile for at least one perinatal outcome of interest (preterm delivery, small‐for‐gestational age and stillbirth).

Methods

Study selection was based on a search of Medline, Embase and Web of Science for articles published up to April 2012, reference list screening, and email contact with authors. Data on study characteristics, outcome measures, and quality were extracted by two independent investigators. Random‐effects meta‐analysis was performed to estimate unadjusted and adjusted summary odds ratios with the associated 95% confidence intervals.

Results

We identified 2863 articles, of which 24 were included in a systematic review. A meta‐analysis (n = 7 studies, including 2 579 032 pregnancies) assessed the risk of adverse perinatal outcomes by comparing the most deprived neighborhood quintile with the least deprived quintile. Compared with the least deprived quintile, odds ratios for adverse perinatal outcomes in the most deprived neighborhood quintile were significantly increased for preterm delivery (odds ratio 1.23, 95% confidence interval 1.18–1.28), small‐for‐gestational age (odds ratio 1.31, 95% confidence interval 1.28–1.34), and stillbirth (odds ratio 1.33, 95% confidence interval 1.21–1.45).

Conclusions

Living in a deprived neighborhood is associated with preterm birth, small‐for‐gestational age and stillbirth.
Asymmetric inheritance of Cyclin D2 maintains proliferative neural stem/progenitor cells: A critical event in brain development and evolution
Authors: Tsunekawa Yuji , Kikkawa Takako , Osumi Noriko
Published: May 2014

Asymmetric cell division and cell cycle regulation are fundamental mechanisms of mammalian brain development and evolution. Cyclin D2, a positive regulator of G1 progression, shows a unique localization within radial glial (RG) cells (i.e., the neural progenitor in the developing neocortex). Cyclin D2 accumulates at the very basal tip of the RG cell (i.e., the basal endfoot) via a unique cis‐regulatory sequence found in the 3′ untranslated region (3′UTR) of its mRNA. During RG division, Cyclin D2 protein is asymmetrically distributed to two daughter cells following mitosis. The daughter cell that inherits Cyclin D2 mRNA maintains its self‐renewal capability, while its sibling undergoes differentiation. A similar localization pattern of Cyclin D2 protein has been observed in the human fetal cortical primordium, suggesting a common mechanism of maintenance of neural progenitors that may be evolutionarily conserved across higher mammals such as primates. Here, we discuss our findings and the Cyclin D2 function in mammalian brain development and evolution.
Safety of early endarterectomy in patients with symptomatic carotid artery stenosis: an international multicenter study
Authors: Tsivgoulis G. , Krogias C. , Georgiadis G. S. , Mikulik R. , Safouris A. , Meves S. H. , Voumvourakis K. , Haršány M. , Staffa R. , Papageorgiou S. G. , Katsanos A. H. , Lazaris A. , Mumme A. , Lazarides M. , Vasdekis S. N.
Published: May 2014

Background and purpose

Although the latest recommendations suggest that carotid endarterectomy (CEA) should be performed in symptomatic carotid artery stenosis (sCAS) patients within 2 weeks of the index event, only a minority of patients undergo surgery within the recommended time‐frame. The aim of this international multicenter study was to prospectively evaluate the safety of early CEA in patients with sCAS in everyday clinical practice settings.

Methods

Consecutive patients with non‐disabling acute ischaemic stroke (AIS) or transient ischaemic attack (TIA) due to sCAS (≥70%) underwent early (≤14 days) CEA at five tertiary‐care stroke centers during a 2‐year period. Primary outcome events included stroke, myocardial infarction (MI) or death occurring during the 30‐day follow‐up period and were defined according to the International Carotid Stenting Study criteria.

Results

A total of 165 patients with sCAS [mean age 69 ± 10 years; 69% men; 70% AIS; 6% crescendo TIA; 8% with contralateral internal carotid artery (ICA) occlusion] underwent early CEA (median elapsed time from symptom onset 8 days). Urgent CEA (≤2 days) was performed in 20 cases (12%). The primary outcomes of stroke and MI were 4.8% [95% confidence interval (CI) 1.5%–8.1%] and 0.6% (95% CI 0%–1.8%). The combined outcome event of non‐fatal stroke, non‐fatal MI or death was 5.5% (95% CI 2.0%–9.0%). Crescendo TIA, contralateral ICA occlusion and urgent CEA were not associated (P > 0.2) with a higher 30‐day stroke rate.

Conclusions

Our findings indicate that the risk of early CEA in consecutive unselected patients with non‐disabling AIS or TIA due to sCAS is acceptable when the procedure is performed within 2 weeks (or even within 2 days) from symptom onset.