bluuebunny/crossref_metadata_2025 huggingface dataset:
Cby1 promotes Ahi1 recruitment to a ring-shaped domain at the centriole–cilium interface and facilitates proper cilium formation and function
Authors: Lee Yin Loon , Santé Joshua , Comerci Colin J. , Cyge Benjamin , Menezes Luis F. , Li Feng-Qian , Germino Gregory G. , Moerner W. E. , Takemaru Ken-Ichi , Stearns Tim
Published: August 2014

Defects in centrosome and cilium function are associated with phenotypically related syndromes called ciliopathies. Cby1, the mammalian orthologue of the Drosophila Chibby protein, localizes to mature centrioles, is important for ciliogenesis in multiciliated airway epithelia in mice, and antagonizes canonical Wnt signaling via direct regulation of β-catenin. We report that deletion of the mouse Cby1 gene results in cystic kidneys, a phenotype common to ciliopathies, and that Cby1 facilitates the formation of primary cilia and ciliary recruitment of the Joubert syndrome protein Arl13b. Localization of Cby1 to the distal end of mature centrioles depends on the centriole protein Ofd1. Superresolution microscopy using both three-dimensional SIM and STED reveals that Cby1 localizes to an ∼250-nm ring at the distal end of the mature centriole, in close proximity to Ofd1 and Ahi1, a component of the transition zone between centriole and cilium. The amount of centriole-localized Ahi1, but not Ofd1, is reduced in Cby1−/−cells. This suggests that Cby1 is required for efficient recruitment of Ahi1, providing a possible molecular mechanism for the ciliogenesis defect in Cby1−/−cells.
The circadian factor Period 2 modulates p53 stability and transcriptional activity in unstressed cells
Authors: Gotoh Tetsuya , Vila-Caballer Marian , Santos Carlo S. , Liu Jingjing , Yang Jianhua , Finkielstein Carla V.
Published: August 2014

Human Period 2 (hPer2) is a transcriptional regulator at the core of the circadian clock mechanism that is responsible for generating the negative feedback loop that sustains the clock. Its relevance to human disease is underlined by alterations in its function that affect numerous biochemical and physiological processes. When absent, it results in the development of various cancers and an increase in the cell's susceptibility to genotoxic stress. Thus we sought to define a yet-uncharacterized checkpoint node in which circadian components integrate environmental stress signals to the DNA-damage response. We found that hPer2 binds the C-terminal half of human p53 (hp53) and forms a stable trimeric complex with hp53’s negative regulator, Mdm2. We determined that hPer2 binding to hp53 prevents Mdm2 from being ubiquitinated and targeting hp53 by the proteasome. Down-regulation of hPer2 expression directly affects hp53 levels, whereas its overexpression influences both hp53 protein stability and transcription of targeted genes. Overall our findings place hPer2 directly at the heart of the hp53-mediated response by ensuring that basal levels of hp53 are available to precondition the cell when a rapid, hp53-mediated, transcriptional response is needed.
AliView: a fast and lightweight alignment viewer and editor for large datasets
Authors: Larsson Anders
Published: August 2014

Summary: AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets.

Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub ( www.github.com/AliView ). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview

Contact:  anders.larsson@ebc.uu.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Arginine methylation of hnRNPK negatively modulates apoptosis upon DNA damage through local regulation of phosphorylation
Authors: Yang Jen-Hao , Chiou Yi-Ying , Fu Shu-Ling , Shih I-Yun , Weng Tsai-Hsuan , Lin Wey-Jinq , Lin Chao-Hsiung
Published: August 2014

Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an RNA/DNA-binding protein involved in chromatin remodeling, RNA processing and the DNA damage response. In addition, increased hnRNPK expression has been associated with tumor development and progression. A variety of post-translational modifications of hnRNPK have been identified and shown to regulate hnRNPK function, including phosphorylation, ubiquitination, sumoylation and methylation. However, the functional significance of hnRNPK arginine methylation remains unclear. In the present study, we demonstrated that the methylation of two essential arginines, Arg296 and Arg299, on hnRNPK inhibited a nearby Ser302 phosphorylation that was mediated through the pro-apoptotic kinase PKCδ. Notably, the engineered U2OS cells carrying an Arg296/Arg299 methylation-defective hnRNPK mutant exhibited increased apoptosis upon DNA damage. While such elevated apoptosis can be diminished through addition with wild-type hnRNPK, we further demonstrated that this increased apoptosis occurred through both intrinsic and extrinsic pathways and was p53 independent, at least in part. Here, we provide the first evidence that the arginine methylation of hnRNPK negatively regulates cell apoptosis through PKCδ-mediated signaling during DNA damage, which is essential for the anti-apoptotic role of hnRNPK in apoptosis and the evasion of apoptosis in cancer cells.
AvrXa7-Xa7 Mediated Defense in Rice Can Be Suppressed by Transcriptional Activator-Like Effectors TAL6 and TAL11a from Xanthomonas oryzae pv. oryzicola
Authors: Ji Zhi-Yuan , Xiong Li , Zou Li-Fang , Li Yu-Rong , Ma Wen-Xiu , Liu Liang , Zakria Muhammad , Ji Guang-Hai , Chen Gong-You
Published: August 2014

Readers of Ji et al., 27:983-995 (2014) have advised the Editor-in-Chief of several identical images used to represent different experiments. The corresponding author of this paper agrees to be responsible for the misrepresentation of these data and to retract the paper.
Relationship between Lung Volume and Pulmonary Function in Patients With Adolescent Idiopathic Scoliosis
Authors: Wen Yu , Kai Song , Yong-gang Zhang , Guo-quan Zheng , Tian-xiang Dong
Published: August 2014

Study Design:

Retrospective.

Objectives:

We determined values for the volume of right lung (Vr), left lung (Vl), total lung volume (Vt), and left/right lung volume ratio (Vl/Vr), allowing comparison between those data measured and those of age-matched controls. To find whether lung volume correlates with preoperative pulmonary function.

Summary of Background Data:

To our knowledge, no study on relationship between computed tomographic (CT) scans determined lung volume and pulmonary function test (PFT) in scoliosis have been published.

Methods:

All examinations with PFT (31 cases) were identified. Three-dimensional volumetric reconstruction of lung parenchyma was performed on existing preoperative CT scans for 26 idiopathic scoliosis patients. Vl, Vr, Vt, Vl/Vr, and absolute value of right volume minus left volume (|Vr−Vl|) were calculated and correlated with PFTs. To determine if significant difference of preoperative lung volume exists between idiopathic scoliosis patients and controls. Linear regression models, using 3-dimensional lung volume parameters as predictors for vital capacity (VC), forced vital capacity (FVC), and total lung capacity (TLC), were created.

Results:

Vt was positively correlated with VC, FVC, forced expiratory volume in 1 second (FEV1), TLC, predicted value for FVC (FVC%), predicted value for FEV1 (FEV1%), predicted value for TLC (TLC%), and predicted value for maximal ventilator volume (MVV%) (P<0.05); |Vr−Vl| was not correlated with ventilation parameters (P>0.05); Diffusion parameters were not correlated with CT-reconstructed lung volume parameters (P>0.05); male and female adolescent idiopathic scoliosis patients had less Vt, Vr, and Vl compared with those of age-matched controls (P<0.05).

Conclusions:

Vt was positively correlated with VC, FVC, FEV1, TLC, FVC%, FEV1%, TLC%, and MVV%. Vt, Vr, and Vl of adolescent idiopathic scoliosis patients were less than those of age-matched controls.
John Frederick Clarke. 1 May 1927 — 11 June 2013
Authors: Bray K. N. C. , Riley N.
Published: August 2014

Flying, and an enthusiasm for aviation, motivated John Clarke’s early career choices: he flew Fairey Fireflys in the Fleet Air Arm, worked in the Gas Turbine Division of Armstrong Siddeley Motors, and studied aeronautical engineering at Queen Mary College, where he graduated with first-class honours. He stayed on there to do a PhD, and then worked at English Electric, before moving to Cranfield in 1958. John Clarke’s many important publications, mainly in the general area of chemically reacting flows, cover a wide range of topics including flames, ignition processes, shock waves and detonations, the dynamics and physics of burning gases and internal ballistics, to name but a few. In all of his contributions to his subject it is perhaps too easy to overlook the individual. He had a delightful sense of humour, wore his distinctions lightly and was a most generous and friendly man.
Bruce Alexander Bilby. 3 September 1922 — 20 November 2013
Authors: Greenwood G. W.
Published: August 2014

Emeritus Professor Bruce Bilby, who died in November 2013 at the age of 91 years, was among the few pioneers who made great contributions to the understanding of crystal defects, notably of dislocations, in providing precise geometrical descriptions of their form, arrangement, interaction and movement. This has led to a clear and experimentally verifiable interpretation of phenomena that include the occurrence of yield points, strain ageing, mechanisms of twinning and martensitic transformations, and the characteristics of atomic separation that lead to fracture. Bruce’s approach often made use of areas of pure mathematics, whose relevance had not previously been suspected, in elegant descriptions of defected crystal structures. Much of his work is related to the role of defects in metals and alloys in their influence on mechanical properties. It assists in considerations of safety assurance of large structures. It links macroscopic behaviour with phenomena on an atomic scale and has underpinned technological judgements.
Evaluation of the Luminex xTAG Gastrointestinal Pathogen Panel and the Savyon Diagnostics Gastrointestinal Infection Panel for the detection of enteric pathogens in clinical samples
Authors: Perry Michael D. , Corden Sally A. , Howe Robin A.
Published: August 2014

Infectious gastrointestinal disease is caused by a diverse array of pathogens, and is a challenging syndrome to correctly diagnose and manage. Conventional laboratory diagnostic methods are often time-consuming and frequently suffer from low detection rates. Two commercial multiplex nucleic acid amplification tests [Luminex xTAG Gastrointestinal Pathogen Panel (GPP) and Savyon Diagnostics Gastrointestinal Infection Panel (GIP)] were applied to 1000 stored diarrhoeal clinical stool samples. The Luminex xTAG GPP and Savyon GIP detected Campylobacter in 42/44 and 44/44 culture-positive samples, Salmonella in 4/4 and 3/4 culture-positive samples, Shigella in 1/1 culture-positive sample, Clostridium difficile toxin in 32/35 ELISA-positive samples, and Giardia in 6/6 wet-preparation-microscopy-positive samples, respectively. When the Luminex GPP assay was used concurrently with conventional methods for 472 clinical samples, it detected Campylobacter in 22/22 culture-positive samples, Salmonella in 1/1 culture-positive sample, Clostridium difficile toxin in 14/14 ELISA-positive samples and Giardia in 4/4 wet-preparation-microscopy-positive samples. The pathogen/toxin detection rate for conventional methods in both sample sets was <10 %. The Luminex xTAG GPP detection rate was 24.8 % in the stored samples and 32.6 % in the concurrently tested samples. The Savyon GIP detection rate was 22.5 %. From stored samples, 2.4 % of Luminex xTAG GPP detections and 3.1 % of Savyon GIP detections could not be confirmed using alternative nucleic acid amplification tests. Enhanced detection rates resulted from increased detection of pathogens routinely sought using conventional methods and were also due to ascertainment of micro-organisms that current testing strategies do not diagnose. Use of multiplex nucleic acid amplification tests will allow clinical laboratories to diagnose infectious gastroenteritis in more patients with diarrhoeal disease by increasing the sensitivity of pathogen detection and by reducing the selective bias of current strategies. The clinical and economic impact of these results warrants further investigation.
Novel inhibitors of human immunodeficiency virus type 2 infectivity
Authors: Beach Lauren B. , Rawson Jonathan M. , Kim Baek , Patterson Steven E. , Mansky Louis M.
Published: August 2014

Human immunodeficiency virus type 2 (HIV-2) infects about two million people worldwide. HIV-2 has fewer treatment options than HIV-1, yet may evolve drug resistance more quickly. We have analysed several novel drugs for anti-HIV-2 activity. It was observed that 5-azacytidine, clofarabine, gemcitabine and resveratrol have potent anti-HIV-2 activity. The EC50values for 5-azacytidine, clofarabine and resveratrol were found to be significantly lower with HIV-2 than with HIV-1. A time-of-addition assay was used to analyse the ability of these drugs to interfere with HIV-2 replication. Reverse transcription was the likely target for antiretroviral activity. Taken together, several novel drugs have been discovered to have activity against HIV-2. Based upon their known activities, these drugs may elicit enhanced HIV-2 mutagenesis and therefore be useful for inducing HIV-2 lethal mutagenesis. In addition, the data are consistent with HIV-2 reverse transcriptase being more sensitive than HIV-1 reverse transcriptase to dNTP pool alterations.
Storage characteristics of milled rice according to milling system types
Authors: Kim Oui-Woung , Kim Hoon , Han Jae-Woong , Lee Hyo-Jai
Published: August 2014

The storage characteristics of milled rice produced using the dry-type (DT), semi-dry-type (SDT), and wet-type (WT) systems were studied. Immediately after rice was milled with these systems, storage experiments on the milled rice were conducted for 12 weeks at three temperatures (10, 20, and 30°C). As the storage period increased, the color (b value) and the fat acidity slowly increased, and the whiteness, moisture content, turbidity, solid matter, and number of total bacteria decreased. The effects of the storage temperature on the moisture content, total number of bacteria, and fat acidity were greater than those of the milling system type. The high storage temperature showed greater potential for increasing the moisture content and the fat acidity and decreasing the total number of bacteria. The initial moisture content of the sample produced using the WT milling system was higher than that of the other samples. Also, the initial turbidity and solid matter of the WT system sample were lower than those of the other samples, but the degree of the decrease was similar to that of the others as the storage period passed. These results showed that the system type and the storage temperature are important factors in the safe storage of wash-free rice. Specifically, the wet type milling system affected the initial quality properties, which made its safe storage period shorter than in the other types.
Quality characteristics of Maejakgwa with added Nelumbo nucifera leaf powder
Authors: Park Bock-Hee , Park Mee-Young , Cho Hee-Sook
Published: August 2014

The principal objective of this study was to determine the quality characteristics of Maejakgwa prepared with the addition of lotus leaf powder. The moisture, crude ash, crude protein, crude lipid, and carbohydrate contents of the used lotus leaf powder were 2.97%, 8.09%, 22.83%, 0.93%, and 65.18%, respectively. The pH of the Maejakgwas dough decreased significantly as the level of lotus leaf powder increased; however, there were no significant differences in dough values among the test groups. Furthermore, the spread factor values and water contents of the groups increased significantly as the level of the lotus leaf powder concentration. In addition, the Hunter's color L, a, and b values decreased significantly with increasing amounts of lotus leaf powder. In the texture meter test, the hardness increased according to increasing concentrations of lotus leaf powder. Finally, the results of a sensory properties showed that Maejakgwas containing 2% lotus leaf powder had the highest scores. These results suggest that lotus leaf powder can be applied to Maejakgwas to achieve high quality and functionality.
Effects of drying methods on quality characteristics and antioxidative effects of Omija (Schizandra chinesis bailon)
Authors: Lee Seul , Moon Hey-Kyung , Lee Su-Won , Moon Jae-Nam , Kim Jong-Kuk
Published: August 2014

The antioxidative effect and quality characteristics of different drying methods (hot air drying, far-infrared radiation drying, vacuum freeze drying) from Schizandra Chinensis Baillon were investigated. The moisture contents and water activity(Aw) contents each 4.46% and 0.38 values of the vacuum freeze drying were lower than those of other samples. A significant not difference in pH values occurred in all samples (p<0.05). The highest content °brix vacuum freeze drying was 6.60 °Brix respectively. The turbidity values of the samples were hot air drying 8.24 T%, far infrared radiation drying 0.32 T%, vacuum freeze drying 71.85 T%. The Hunter’s L, a and b values of vacuum freeze drying were higher than those of other samples. The order of the free sugar content was glucose> fructose>sucrose, and that of the total free sugar contents were vacuum freeze drying (6.33 g/100 g) > far infrared drying (5.01 g/100 g) > hot air drying (3.73 g/100g). Antioxidant acitivy (DPPH radical scavenging, ABTS radical scavenging) and total phenol, total flavonoid, and total tannin content was highest in vaccum freeze drying than other different drying methods except nitrite scavenging ability.
Analysis of radiation induced hydrocarbons by electron-beam irradiation in dried squid (Todarodes pacificus) and octopus (Paroctopus dofleini)
Authors: Hong Young Shin , Ryu Keun Young , Kim Kyong Su
Published: August 2014

Food irradiation is one of the successful modern techniques used to preserve food. However, it needs very careful control. Detection of irradiated food is of prime importance to facilitate global trade and consumer assurance, choice, and protection. This study was performed to evaluate the radiation-induced hydrocarbon content of dried squid and octopus by e-beam irradiation. The samples were collected from supermarkets all over South Korea and irradiated with an e-beam at 0, 1, 3, 5, 7, and 10 kGy doses. Lipids were extracted with soxhelt, and the hydrocarbons induced with irradiation were separated via solid phase extraction (SPE) and identified via gas chromatography mass spectrometry (GC/MS). The major induced hydrocarbons in the irradiated dried squid and octopus were 1-tetradecene and pentadecane derived from palmitic acid and 1-hexadecene and heptadecane from stearic acid. The concentration of hydrocarbons differed from the composition of the fatty acid at the same radiation and increased according to the level of the radiation dose. The hydrocarbons induced by e-beam irradiation, including 1-tetradecene, 1-hexadecene, and heptadecane, were confirmed to have been the irradiation marker compounds. Therefore, they can be used to distinguish the e-beam-irradiated dried squid and octopus from the non-irradiated ones.
Antioxidant activity of extracts from soybean and small black bean
Authors: Hong Ju-Yeon , Shin Seung-Ryeul , Kong Hyun-Joo , Choi Eun-Mi , Woo Sang-Chul , Lee Myoung-Hee , Yang Kyung-Mi
Published: August 2014

This study was carries out to analyzed the antioxidant activities of extracts extrated from soybean and small black bean for the development of functional materials. Yields of hot-water and ethanol extracts were higher in the soybean than small black bea, and yields of hot-water extracts were higher than ethanol extracts. Total phenol contents were 26.22 mg/g in the ethanol extracts from small black bean, and were higher than those in the soybean extracts. Total flavonoid contents were 30.52 mg/g of hot-water extracts from small black bean. The EDA values were increased by the increase of extract concentrations and were high in the hot-water and ethanol extracts from bean and small black bean The EDA values was high in the extracts of small black bean from low concentrations. The SOD-like activity of hot-water and ethanol extracts from small black bean was higher than those of soybean extracts. The SOD-like activity was 73%, 62% of the hot-water and ethanol extracts from small black bean in 10 ml/mL extract concentration, respectably. The nitrite scavenging ability was high extracts from soybean was 47.60% in pH 1.2, Those of hot-water extracts were higher than in ethanol extracts in 10 ml/mL extract concentration. The xanthine oxidase inhibitory activities were increased by the increase of extract concentrations and were high in ethanol extracts from small black bean of low concentration. The xanthine oxidase inhibitory activities was hot-water extracts from soybean were higher than 5 ml/mL extract concentration than those of other extracts. The inhibitory activities of tyrosinase were increased by increase of extract concentrations and were high each other 42.05%, 45.67% of hot-water and ethanol extracts from small black bean in 10 ml/mL extract concentration. Reducing power was increased by increase of extract concentrations in extracts of small black bean, and were high more than double in hot-water and ethanol from small black bean than extracts of soybean.
Antimicrobial activities of Lindera obtusiloba Blume and Zanthoxylum piperitum DC extracts
Authors: Kim Se-Hun , Do Jung-Sun , Chung Hyun-Jung
Published: August 2014

Ethanol and hot water extracts were prepared from Lindera obtusiloba Blume (LO) and Zanthoxylum piperitum DC (ZP) and used to evaluate their antimicrobial activities and thermal stability against six foodborne pathogens (3 gram-positive and 3 gram-negative bacteria). The antimicrobial activities were assessed using the agar diffusion method, and the thermal stabilities of extracts were examined after heat treatment at 60, 70, 80, and 100°C for 10 min. The zones of inhibition by the LO extract or the ZP extract of the tested microorganisms were in the range of 21-30 mm and 19-25 mm, respectively, at 100 mg/mL concentrations. The 60% ethanol extract and the hot water extracts from LO showed the strongest antimicrobial effects against MRSA and Staphylococcus aurues, respectively. For the extract from ZP, the strongest antimicrobial effect was shown against S. aurues by 60% ethanol, and the weakest antimicrobial effect was shown against E. coli by the hot water extracts. The ZP extracts showed that the gram-positive bacteria were more sensitive than gram-negative bacteria. For the thermal stability of the extracts, the antimicrobial effects stabilized after heat treatment. Overall, the data suggest that the extracts have a potential for application in various food products for which a natural antimicrobial additive is desired.
Quality characteristics of Doenjang manufactured with soybean Koji
Authors: Kim Do-Yoon , Kwon Dong-Jin
Published: August 2014

This study investigated the quality characteristics and sensory evaluation of Doenjang samples made of soybean koji and prepared with Bacillus subtillus 3-B-1 and/or Aspergillus oryzae 6-M-1 isolated from traditional Meju, to replace the koji with wheat flour. Among the quality characteristics of doenjang during its fermentation at 30°C for 40 days, its moisture decreased by degrees, but its amino-type nitrogen and reducing sugar increased by degrees. The color of the doenjang made of koji and prepared with Aspergillus oryzae 6-M-1 changed more significantly than that of the doenjang with Bacillus subtilis 3-B-1. The viable cell and mold counts increased by degrees during the fermentation. The results of the sensory evaluation of the doenjang made with koji and prepared with Aspergillus oryzae 6-M-1 did not significantly differ from those of the doenjang with Bacillus subtilis 3-B-1 and of the commercial doenjang. These results showed the possibility of preparing doenjang with soybean koji instead of wheat flour koji.
Characterization of alkaline cellulase from Bacillus subtilis 4-1 isolated from Korean traditional soybean paste
Authors: Baek Seong Yeol , Lee You Jung , Yun Hye Ju , Park Hye Young , Yeo Soo-Hwan
Published: August 2014

In this study, we isolated a cellulase-producing bacterium isolated from traditional Korean fermented soybean paste and investigated the effect of culture conditions on the production of cellulase. This bacterium, which was identified as Bacillus subtilis 4-1 through 16S rRNA gene sequence analysis, showed the highest cellulase activity when the cells were grown at 45°C for 24 hours in the CMC medium supplemented with 1.0% of soluble starch and 0.1% yeast extract. The initial optimum pH of the medium was observed in the range of 5.0~9.0. The optimal pH and temperature for the production of cellulase from B. subtilis 4-1 were pH 9.0 and 60°C respectively. In addition, the enzyme showed significant activity in the temperature range of 20~90°C, which indicates that B. subtilis 4-1 cellulase is an alkaline-resistance and thermo-stable enzyme. This enzyme showed higher activity with CMC as the substrate for endo-type cellulase than avicel or pNPG as the exo-type substrates for exo-type cellulase and β-glucosidase. These results suggest that the cellulase produced from B. subtilis 4-1 is a complex enzyme rather than a mono-enzyme.
The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript
Authors: Malone Colin D. , Mestdagh Claire , Akhtar Junaid , Kreim Nastasja , Deinhard Pia , Sachidanandam Ravi , Treisman Jessica , Roignant Jean-Yves
Published: August 2014

The exon junction complex (EJC) is a highly conserved ribonucleoprotein complex that binds RNAs during splicing and remains associated with them following export to the cytoplasm. While the role of this complex in mRNA localization, translation, and degradation has been well characterized, its mechanism of action in splicing a subset of Drosophila and human transcripts remains to be elucidated. Here, we describe a novel function for the EJC and its splicing subunit, RnpS1, in preventing transposon accumulation in both Drosophila germline and surrounding somatic follicle cells. This function is mediated specifically through the control of piwi transcript splicing, where, in the absence of RnpS1, the fourth intron of piwi is retained. This intron contains a weak polypyrimidine tract that is sufficient to confer dependence on RnpS1. Finally, we demonstrate that RnpS1-dependent removal of this intron requires splicing of the flanking introns, suggesting a model in which the EJC facilitates the splicing of weak introns following its initial deposition at adjacent exon junctions. These data demonstrate a novel role for the EJC in regulating piwi intron excision and provide a mechanism for its function during splicing.
Herbicides as Weed Control Agents: State of the Art: II. Recent Achievements
Authors: Kraehmer Hansjoerg , van Almsick Andreas , Beffa Roland , Dietrich Hansjoerg , Eckes Peter , Hacker Erwin , Hain Ruediger , Strek Harry John , Stuebler Hermann , Willms Lothar
Published: August 2014

In response to changing market dynamics, the discovery of new herbicides has declined significantly over the past few decades and has only seen a modest upsurge in recent years. Nevertheless, the few introductions have proven to be interesting and have brought useful innovation to the market. In addition, herbicide-tolerant or herbicide-resistant crop technologies have allowed the use of existing nonselective herbicides to be extended into crops. An increasing and now major challenge is being posed by the inexorable increase in biotypes of weeds that are resistant to herbicides. This problem is now at a level that threatens future agricultural productivity and needs to be better understood. If herbicides are to remain sustainable, then it is a must that we adopt diversity in crop rotation and herbicide use as well as increase the use of nonchemical measures to control weeds. Nevertheless, despite the difficulties posed by resistant weeds and increased regulatory hurdles, new screening tools promise to provide an upsurge of potential herbicide leads. Our industry urgently needs to supply agriculture with new, effective resistance-breaking herbicides along with strategies to sustain their utility.
Crystal structure of 1-ferrocenyl-2-(4-methylbenzoyl)spiro[11H-pyrrolidizine-3,11′-indeno[1,2-b]quinoxaline]
Authors: Chandralekha Kuppan , Gavaskar Deivasigamani , Sureshbabu Adukamparai Rajukrishnan , Lakshmi Srinivasakannan
Published: August 2014

In the title compound, [Fe(C5H5)(C34H28N3O)], the four-fused-rings system of the 11H-indeno[1,2-b]quinoxaline unit is approximately planar [maximum deviation = 0.167 (4) Å] and forms a dihedral angle of 37.25 (6)° with the plane of the benzene ring of the methylbenzoyl group. Both pyrrolidine rings adopt a twist conformation. An intramolecular C—H...O hydrogen bond is observed. In the crystal, molecules are linked by C—H...O hydrogen bonds and weak C—H...π interactions, forming double chains extending parallel to thecaxis.
Crystal structure ofN,N′-bis[(pyridin-4-yl)methyl]naphthalene diimide
Authors: Nicolas-Gomez Mariana , Martínez-Otero Diego , Dorazco-González Alejandro
Published: August 2014

In the centrosymmetric title compound, C26H16N4O4{systematic name: 6,13-bis[(pyridin-4-yl)methyl]-6,13-diazatetracyclo[6.6.2.04,16011,15]hexadeca-1,3,8,10,15-pantaene-5,7,12,14-tetrone}, the central ring system is essentially planar [maximum deviation = 0.0234 (8) Å] and approximately perpendicular to the terminal pyridine ring [dihedral angle = 84.38 (3)°]. The molecules displays atransconformation with the (pyridin-4-yl)methyl groups on both sides of the central naphthalene diimide plane. In the crystal, molecules are linked by π–π stacking between parallel pyridine rings [centroid–centroid distances = 3.7014 (8) and 3.8553 (8) Å] and weak C—H...O hydrogen bonds, forming a three-dimensional supramolecular architecture.
Crystal structure of 4-(prop-2-ynyloxy)-2,2,6,6-tetramethylpiperidin-1-oxyl
Authors: Goswami Shailesh K. , Hanton Lyall R. , McAdam C. John , Moratti Stephen C. , Simpson Jim
Published: August 2014

The title compound, C12H20NO2, was synthesized from 4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl (hydroxy-TEMPO) and propargyl bromide. The six-membered ring adopts a flattened chair conformation and carries a propynyloxy substituent in an equatorial orientation at the 4-position. The N—O bond length of the piperidin-1-oxyl unit is 1.289 (3) Å. In the crystal, C—H...O hydrogen bonds combine with unusual C—H...π interactions involving the alkyne unit as acceptor to generate a three-dimensional network.
The choice of growth method: strategies and resources
Authors: Ortiz-de-Urbina-Criado Marta , Ángel Guerras-Martín Luis , Montoro-Sánchez Ángeles
Published: August 2014

Purpose

The purpose of this paper is to investigate the effect of a firm's growth strategy (specialization and diversification) and its specific resources, such as intangible assets and previous experience in the choice of growth method (organic or external).

Design-methodology-approach

The paper analyses 859 external growth arrangements and 1,057 cases of organic growth. A binomial logistic regression is used to test the hypotheses.

Findings

Results show that firms prefer to grow internally when their growth strategy is specialization, but prefer external growth methods – such as mergers, acquisitions and alliances – when their growth strategy is diversification and they have previous experience in these methods.

Research limitations-implications

This study applies only to the European case and could be extended to Latin American companies for a comparative analysis.

Practical implications

This paper may help managers to identify important factors and issues to be considered when deciding upon a growth method. The European experience can be useful for Latin American companies following a similar growth strategy.

Originality-value

The results confirm a large part of the prior literature, but also go a stage further by including in the same study all the growth options available to a firm and providing empirical evidence of each one's preference according to the different situations analysed.
Impediments to the Emergence of Political Parties in Ukraine
Authors: Kuzio Taras
Published: August 2014

This article analyses why, after a quarter of century of post-Soviet transition, political parties in Ukraine remain weak. Ukraine's newly elected President Petro Poroshenko and his ally Kyiv City Mayor Vitaliy Klitschko both lead virtual political parties. The weakness of Ukrainian political parties is analysed through five impediments to their development: Soviet political culture; corruption and cynicism; provincial elites; regional and linguistic diversity; and weak party structure. The Soviet legacy has left an ideological wasteland in Eurasia upon which it has proven difficult to build political parties. The absence of pre-Soviet party roots from which to draw makes Eurasia different from the three Baltic States and Eastern Europe, while the late Soviet ‘era of stagnation’ and rapid, often violent and corrupt drive to a market economy in the 1990s deepened cynicism and corruption. The Soviet legacy of provincialism in non-Russian republics such as Ukraine remains predominant among business and political elites. Regional and linguistic diversity has negatively impacted on the ability of political parties to garner support throughout the country, undermining national integration, as seen during the Eastern Ukrainian violent counter-revolution in Donetsk, home base of the Party of Regions. Ukraine's parties remain structurally weak in their top-down approach and there is an absence of internal democracy, disrespect for voters and reliance on opaque sources of funding.
The uncertainty challenge of contingent collaboration
Authors: Auer Jennifer Claire , Kao Chen‐Yu , Hemphill Libby , Johnston Erik W. , Teasley Stephanie D.
Published: August 2014

Contingent knowledge workers will play an increasingly important role in organisational success as workers transition in and out of project‐based innovation teams with more frequency. Our research finds that collaborators in the contingent, high‐skill workforce face uncertainty challenges to their work that are unique from the independent, contingent professionals more often studied. The article proposes a theoretical framework of uncertainty to guide us in understanding collaborative contingent knowledge workers’ work experience. Interviews with postdoctoral researchers reveal four findings about the influence of these highly uncertain work environments on collaborative contingent knowledge workers – collaboration isolation, frustrated independence, performance anxiety and internalised blame. Perhaps most concerning is that the workers internalise the negative impacts as personal failings instead of recognising them as consequences of a poorly designed work environment. This study argues for the need to manage and mitigate different sources of uncertainty to avoid creating an unnecessary burden on contingent knowledge workers, and to enable a sustainable, contingent knowledge workforce.
phylin: an r package for phylogeographic interpolation
Authors: Tarroso Pedro , Velo‐Antón Guillermo , Carvalho Sílvia B.
Published: August 2014

phylin is a package for the r programming environment which offers different methods to spatially interpolate genetic information from phylogeographic data. These interpolations can be used to predict the spatial occurrence of different lineages within a phylogeny using a modified method of kriging, which allows the usage of a genetic distance matrix to derive a model of spatial dependence. phylin improves the available methods to generate interpolated surfaces from a phylogenetic trees by assessing the autocorrelation structure of the genetic information, interpolating the genetic data based on a statistical model, estimating the uncertainty of the predictions and identifying lineage occurrence and contact zones probability without projection of pairwise genetic distances into mid‐points between sample locations. The package also includes methods to plot interpolation surfaces and provide summary tables from the generated data and models. We provide an example of the usefulness of this tool by inferring the spatial occurrence of distinct historical evolutionary lineages of the Lataste's viper (Vipera latastei Boscá, 1878) in the Iberian Peninsula and identifying potential contact areas. The maps of phylogenetic patterns obtained with these methods provide a spatial context to test hypotheses related to processes underlying the geographic distribution of genetic diversity and to inform conservation planning.
MEMGENE: Spatial pattern detection in genetic distance data
Authors: Galpern Paul , Peres‐Neto Pedro R. , Polfus Jean , Manseau Micheline
Published: August 2014

Landscape genetics studies using neutral markers have focused on the relationship between gene flow and landscape features. Spatial patterns in the genetic distances among individuals may reflect spatially uneven patterns of gene flow caused by landscape features that influence movement and dispersal.

We present a method and software for identifying spatial neighbourhoods in genetic distance data that adopts a regression framework where the predictors are generated using Moran's eigenvectors maps (MEM), a multivariate technique developed for spatial ecological analyses and recommended for genetic applications.

Using simulated genetic data, we show that our MEMGENE method can recover patterns reflecting the landscape features that influenced gene flow. We also apply MEMGENE to genetic data from a highly vagile ungulate population and demonstrate spatial genetic neighbourhoods aligned with a river likely to reduce, but not eliminate, gene flow.

We developed the MEMGENE package for R in order to detect and visualize relatively weak or cryptic spatial genetic patterns and aid researchers in generating hypotheses about the ecological processes that may underlie these patterns. MEMGENE provides a flexible set of R functions that can be used to modify the analysis. Detailed supplementary documentation and tutorials are provided.
The Neonatal Pain, Agitation and Sedation Scale reliably detected oversedation but failed to differentiate between other sedation levels
Authors: Giordano V. , Deindl P. , Kuttner S. , Waldhör T. , Berger A. , Olischar M.
Published: August 2014

Aim

The aim of this study was to analyse the sedation subscale of the Neonatal Pain, Agitation and Sedation Scale (N‐PASS), because the N‐PASS has only been validated for the assessment of acute and prolonged pain.

Methods

The nurses’ expert opinion regarding the level of sedation of the study patients was used as reference scale. Paired assessments of both the N‐PASS sedation subscale and the nurses’ expert opinion were performed in 50 sedated neonates from 23 to 44 weeks of postmenstrual age.

Results

A total set of 503 paired observations was included into analysis. The median N‐PASS sedation subscale scores were significantly different for the three nurses’ expert opinion categories, with minus eight for oversedation, minus two for adequate sedation and zero for undersedation (p < 0.0001). Interobserver agreement for the N‐PASS sedation subscale was excellent – linearly weighted Cohen's Kappa was 0.93 – as was the internal consistency of 0.88, estimated by a Cronbach's alpha. The internal consistency increased to 0.90 if the vital sign item of the subscale was deleted.

Conclusion

The N‐PASS sedation subscale reliably detected oversedation, but failed to differentiate between adequate and undersedation. We therefore recommend using additional methods to ensure adequate assessment of sedation in neonates.
Increased prevalence of autoimmune diseases in functional gastrointestinal disorders: case–control study of 23 471 primary care patients
Authors: Ford A. C. , Talley N. J. , Walker M. M. , Jones M. P.
Published: August 2014

Background

There is increasing evidence that impaired mucosal defence mechanisms are implicated in the pathogenesis of the functional gastrointestinal disorders (FGIDs), allowing inappropriate immune activation.

Aim

To test the hypothesis that an excess of autoimmune disorders among sufferers, using a large primary care database to examine this.

Methods

Cases were diagnosed with FGIDs – irritable bowel syndrome (IBS), functional dyspepsia (FD), chronic idiopathic constipation (CIC), and multiple FGIDs. Controls were those without FGIDs. Prevalence of autoimmune disorders was compared between cases and controls using odds ratios (ORs) and 95% confidence intervals (CIs).

Results

We included 23 471 patients (mean age 51.4 years, 66.1% female). Prevalence of autoimmune disorders was greater among all FGIDs, compared with controls without. In those with FD (OR 1.35; 95% CI 1.12–1.63), CIC (OR 1.75; 95% CI 1.11–2.75), or multiple FGIDs (OR 1.49; 95% CI 1.25–1.77) this was statistically significant after controlling for age and gender. Rheumatological autoimmune disorders were significantly more frequent in those with FD (OR 1.44; 95% CI 1.15–1.80), CIC (OR 1.84; 95% CI 1.08–3.13), or multiple FGIDs (OR 1.53; 95% CI 1.24–1.88), after controlling for age and gender. However, endocrine autoimmune disorders were no more frequent in those with FGIDs, after controlling for age and gender.

Conclusions

In a large sample of primary care patients, there was a significantly higher prevalence of autoimmune disorders among those with FD, CIC, or multiple FGIDs not explained by differences in age or gender. We were unable to control for concomitant drug use, which may partly explain this association.
Regional Multiple Pathology Scores Are Associated with Cognitive Decline in Lewy Body Dementias
Authors: Howlett David R. , Whitfield David , Johnson Mary , Attems Johannes , O'Brien John T. , Aarsland Dag , Lai Mitchell K.P. , Lee Jasinda H. , Chen Christopher , Ballard Clive , Hortobágyi Tibor , Francis Paul T.
Published: August 2014

Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by the presence of α‐synuclein‐containing Lewy bodies and Lewy neurites. However, both dementias also show variable degrees of Alzheimer's disease (AD) pathology (senile plaques and neurofibrillary tangles), particularly in areas of the cortex associated with higher cognitive functions. This study investigates the contribution of the individual and combined pathologies in determining the rate of cognitive decline. Cortical α‐synuclein, phosphorylated tau (phosphotau) and Aβ plaque pathology in 34 PDD and 55 DLB patients was assessed semi‐quantitatively in four regions of the neocortex. The decline in cognition, assessed by Mini Mental State Examination, correlated positively with the cortical α‐synuclein load. Patients also had varying degrees of senile Aβ plaque and phosphotau pathology. Regression analyses pointed to a combined pathology (Aβ plaque plus phosphotau plus α‐synuclein‐positive features), particularly in the prefrontal cortex (BA9) and temporal lobe neocortex with the superior and middle temporal gyrus (BA21, 22), being a major determining factor in the development of dementia. Thus, cognitive decline in Lewy body dementias is not a consequence of α‐synuclein‐induced neurodegeneration alone but senile plaque and phosphorylated tau pathology also contribute to the overall deficits.
The impact of telemonitoring on adherence to nasal corticosteroid treatment in children with seasonal allergic rhinoconjunctivitis
Authors: Pizzulli A. , Perna S. , Florack J. , Pizzulli A. , Giordani P. , Tripodi S. , Pelosi S. , Matricardi P. M.
Published: August 2014

Background

Adherence to controller therapy in allergic diseases is low. Telemonitoring has been proposed to improve adherence to treatment in chronic diseases. However, this strategy has never been tested in allergic rhinoconjunctivitis.

Objective

To test whether Internet‐based telemonitoring during the grass‐pollen season of children with allergic rhinoconjunctivitis may enhance adherence to treatment.

Methods

Children and adolescents, 5–18 years old, with moderate‐to‐severe seasonal allergic rhinoconjunctivitis to grass pollen requiring daily administration of nasal corticosteroid (NCS) (mometasone) were recruited (April 2013) in a paediatric allergy practice. Participants were randomized to Internet‐based monitoring (AllergyMonitor™, AM) or to usual care (no diary at all, controls) and followed from 13 May (T0) to 15 June 2013 (T2). An intermediate visit (T1) was performed between 31 May and 2 June. Optimal adherence to therapy was expressed as the use of at least 0.190 g/day of mometasone, corresponding to 1 puff/nostril/day, and it was measured by canister weights during (T1) and at the end (T2) of the study period. Main secondary outcomes included the reported disease severity (validated self‐questionnaire) and quality of life (AdoIRQLQ questionnaire), disease knowledge (multiple‐choice questionnaire), nasal flow and resistance at baseline and at T2.

Results

The use of mometasone, expressed as both optimal adherence rate (48.4% vs. 12.5%; P = 0.002) and average daily use (0.20 ± 0.12 g/day vs. 0.15 ± 0.07 g/day; P = 0.037), was higher in the AM group (n = 31) than among controls (n = 32). Disease knowledge improved among the patients using AM (83.3% vs. 68.3%; P < 0.001) but not among controls (68.2% vs. 67.7% right answers; P > 0.05). No differences were observed in the reported severity of disease, nasal flow and resistance and quality of life both at baseline and at follow‐up visits.

Conclusions

Internet‐based telemonitoring improves adherence to NCS treatment and disease knowledge among children and adolescents with seasonal allergic rhinoconjunctivitis.