bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian Models of Attention
Authors: Yu Angela J.
Published: April 2014

Traditionally, attentional selection has been thought of as arising naturally from resource limitations, with a focus on what might be the most apt metaphor, e.g. whether it is a ‘bottleneck’ or ‘spotlight’. However, these simple metaphors cannot account for the specificity, flexibility, and heterogeneity of the way attentional selection manifests itself in different behavioural contexts. A recent body of theoretical work has taken a different approach, focusing on the computational needs of selective processing, relative to environmental constraints and behavioural goals. They typically adopt a normative computational framework, incorporating Bayes-optimal algorithms for information processing and action selection. This chapter reviews some of this recent modelling work, specifically in the context of attention for learning, covert spatial attention, and overt spatial attention.
Computational Models
Authors: Itti Laurent , Borji Ali
Published: April 2014

This chapter reviews recent progress in computational modelling of visual attention. The authors start with early concepts and models, which have emphasized stimulus-driven guidance of attention towards salient objects in the visual world. They then present a taxonomy of the many different approaches which have emerged in recent research efforts. They then turn to the more complex problem of modelling top-down, task- and goal-driven influences on attention. While early top-down models have been more qualitative in nature, the authors describe several recent fully computational approaches that address top-down biasing in space, over features, and towards objects. This chapter finally provides an outlook and describes promising future research directions.
Neurological Disorders of Attention
Authors: Manohar Sanjay , Bonnelle Valerie , Husain Masud
Published: April 2014

Attention deficits are a frequent and particularly disabling consequence of many neurological disorders, from patients with focal brain lesions through to individuals with traumatic brain injury or neurodegenerative conditions, such as Parkinson’s disease. They are often associated with apparent confusion, fatigue, irritability, and increased time and effort to perform even simple everyday tasks, and constitute a real challenge for rehabilitation. In many cases, attention deficits may be crucial factors underlying failures of memory and higher cognitive functions, contributing to difficulties in resuming previous activities and independent daily living. Here the authors first consider four aspects of attention—selective, sustained, executive, and divided—together with brain regions and networks considered to underpin normal attention and disorders of attention. The authors focus on focal brain lesions, traumatic brain injury and Parkinson’s disease as important examples illustrating the effects of different brain pathologies on attention function.
Balint’s Syndrome and the Study of Attention
Authors: Robertson Lynn C.
Published: April 2014

Balint’s syndrome is the most severe neuropsychological disorder affecting spatial attention that has been observed. In humans, it can be observed after bilateral occipital-parietal damage. The signs and symptoms of this syndrome are first described and then discussed in terms of how research with patients with Balint’s syndrome has helped and/or limited our understanding of object-based attention, visual search, and feature binding in visual perception. The findings have also supported the existence of implicit spatial maps that are available in the face of severely limited conscious spatial awareness. The results of such studies have led to advancements in attentional theory, especially as related to spatial attention and its interaction with object perception.
Developmental Disorders
Authors: Scerif Gaia , Wu Rachel
Published: April 2014

Tracing the development of attentional deficits and their cascading effects in genetically and functionally defined disorders allows an understanding of intertwined developing systems on three levels. At the cognitive level, attention influences perception, learning, and memory. Attention and other cognitive processes interact to produce cascading effects across developmental time. At a systems neuroscience level, developmental disorders can reveal the systems and mechanisms necessary to attain adults’ efficient attentional processes. At the level of cellular neuroscience and functional genomics, disorders of known genetic aetiology provide inroads into cellular pathways and protein networks leading to attentional deficits across development. This chapter draws from both genetically defined and functionally defined disorders to delineate the complexities and necessity of studying attentional deficits and their neural correlates. Studying developmental disorders highlights the need to study attentional processes and other cognitive processes (e.g. memory and learning) in tandem, given their inseparable nature.
Large-scale Networks for Attentional Biases
Authors: Nobre Anna C. (Kia) , Mesulam M-Marsel
Published: April 2014

Selective attention is essential for all aspects of cognition. Using the paradigmatic case of visual spatial attention, we present a theoretical account proposing the flexible control of attention through coordinated activity across a large-scale network of brain areas. It reviews evidence supporting top-down control of visual spatial attention by a distributed network, and describes principles emerging from a network approach. Stepping beyond the paradigm of visual spatial attention, we consider attentional control mechanisms more broadly. The chapter suggests that top-down biasing mechanisms originate from multiple sources and can be of several types, carrying information about receptive-field properties such as spatial locations or features of items; but also carrying information about properties that are not easily mapped onto receptive fields, such as the meanings or timings of items. The chapter considers how selective biases can operate on multiple slates of information processing, not restricted to the immediate sensory-motor stream, but also operating within internalized, short-term and long-term memory representations. Selective attention appears to be a general property of information processing systems rather than an independent domain within our cognitive make-up.
Working Memory Biases in Human Vision
Authors: Soto David , Humphreys Glyn W.
Published: April 2014

The current conceptualization of working memory highlights its pivotal role in the cognitive control of goal-directed behaviour, for example, by keeping task-priorities and relevant information ‘online’. Evidence has accumulated, however, that working memory contents can automatically misdirect attention and observers can only exert little intentional control to overcome irrelevant contents held in memory that are known to be misleading for behaviour. The authors discuss extant evidence on this topic and argue that obligatory functional coupling between working memory and attentional selection reflects a default property of the brain which is hardwired in overlapping substrates for memory and perception. They further argue that the neuroanatomical substrates for working memory biases in vision are distinct from the classical fronto-parietal networks involved in attentional control and distinct from the mechanisms that mediate attention biases from long-term memory. Finally the authors present emerging evidence that working memory ‘guiding’ processes may operate outside conscious awareness.
Correlation of Quality Parameters with the Baking Performance of Wheat Flours
Authors: Thanhaeuser Silvia Maria , Wieser Herbert , Koehler Peter
Published: April 2014

The baking performance of a set of flours from 13 wheat cultivars was determined by means of two different microscale baking tests (10 g of flour each). In the micro‐rapid‐mix test the dough was mixed for a fixed time at a high speed, whereas the microbaking test used mixing to optimum dough consistency in a microfarinograph. Quality parameters such as sedimentation value, crude protein content, dough and gluten extension data, and microfarinograph data were also determined. Finally, quality‐related protein fractions (gliadins, glutenins, SDS‐soluble proteins, and glutenin macropolymer) were quantitated by extraction/HPLC methods with reversed‐phase and gel‐permeation columns. All quality parameters were correlated with the bread volumes of both baking tests. The results demonstrated that the microbaking test (adapted mixing time) was much more closely related to the quality parameters than the micro‐rapid‐mix test (fixed mixing time), which hardly showed any correlation. Among the standard quality parameters, only the crude protein content showed a medium correlation with the bread volume of the microbaking test (r = 0.71), whereas the contents of gliadins (r = 0.80), glutenins (r = 0.76), and glutenin macropolymer (r = 0.80) appeared to be suitable parameters to predict the baking performance of wheat flour. All other quality parameters were not or were only weakly correlated and unsuitable for predicting baking performance.
Improved Temperature Homogeneity of Cake Batter and Cake Quality with Reduction in Heat Conductivity of the Baking Pan at the Ends
Authors: Lee Seung Ju , Boonsupthip Waraporn
Published: April 2014

With high competition in bakery markets, baking process improvements in efficiency are necessary. Sliced butter cake is a well‐known bakery product. It is baked in a long, rectangular aluminum pan in which it is difficult to manage homogeneous heat distribution throughout the whole cake. Alteration of pan thermal properties through the Biot number concept (reducing thermal conductivity at the ends of the pan to increase Bi to 1.30) improved homogeneity of the heat distribution as well as the cake qualities throughout the whole cake piece by modifying the cake properties at the problematic location adjacent to the ends of the pan (hot zones, where crust thickness was reduced from 0.32 to 0.23 cm, cake height increased from 6.8 to 7.4 cm, and cake and crust colors improved). Waste from size defects (cake height too short and crust too thick) of butter cake in the hot zones was also reduced. The sensory results revealed improvement in the softness, moistness, and overall liking of the cake. Higher homogeneity in the cake temperature improved cake production by reducing baking time through application of higher thermal convection of hot air in the baking oven. Such findings confirm a simple approach for baking improvement through selection of proper baking tray materials. Biot number is a useful concept for baking optimization process design.
Headspace Solid-Phase Microextraction and Gas Chromatography-Mass Spectrometry for Analysis of VOCs Produced by Phytophthora cinnamomi
Authors: Qiu Rui , Qu Dong , Trengove Robert , Agarwal Manjree , Hardy Giles E. St. J. , Ren Yonglin
Published: April 2014

Volatile organic compounds (VOCs) from Phytophthora cinnamomi–infected lupin seedlings were collected by headspace solid-phase microextraction (HS-SPME). The sampling was done 28 to 44, 52 to 68, and 76 to 92 h after inoculation (HAI). The HS-SPME samples were analyzed by gas chromatography-flame ionization detector (GC-FID) to assess the differences in volatile compounds between the P. cinnamomi–infected lupin seedlings and the control. Three specific peaks were identified after 52 to 68 h with the infected lupin seedlings, at which time there were no visible aboveground symptoms of infection. Subsequently, the VOCs of five different substrates (V8A, PDA, lupin seedlings, soil, and soil + lupin seedlings) infected with P. cinnamomi and the corresponding controls were analyzed by gas chromatography-mass spectrometry (GC/MS). A total of 87 VOCs were identified. Of these, the five most abundant that were unique to all five inoculated substrates included: 4-ethyl-2-methoxyphenol, 4-ethylphenol, butyrolactone, phenylethyl alcohol, and 3-hydroxy-2-butanone. Therefore, these metabolites can be used as markers for the identification of P. cinnamomi in different growing environments. Some VOCs were specific to a particular substrate; for example, 2,4,6-rrimethyl-heptanes, dl-6-methyl-5-hepten-2-ol, dimethyl trisulfide, 6,10-dimethyl- 5,9-undecadien-2-ol, and 2-methoxy-4-vinylphenol were specific to P. cinnamomi + V8A; heptanes and 5-methyl-3-heptaneone were specific to P. cinnamomi + PDA; 3-methyl-1-butanol, ethyl acetate, 2-methyl-propanoic acid, ethyl ester, and ethyl ester 2-methyl-butanoic acid were specific to P. cinnamomi–inoculated lupin seedlings; and benzyl alcohol and 4-ethyl-1, 2-dimethoxybenzene were only detected in the headspace of inoculated soil + lupin seedlings. Results from this investigation have multiple impacts as the volatile organic profiles produced by the pathogen can be utilized as an early warning system to detect the pathogen from contaminated field soil samples. Data from this investigation have also illuminated potential metabolic pathways utilized by the oomycete during infection which may serve as potential targets for the development of specific control strategies.
The First Report of Stolbur Phytoplasma Associated with Phyllody of Calendula officinalis in Serbia
Authors: Pavlovic S. , Starovic M. , Stojanovic S. , Aleksic G. , Kojic S. , Zdravkovic M. , Josic D.
Published: April 2014

Pot marigold (Calendula officinalis L.) is native to southern Europe. Compounds of marigold flowers exhibit anti-inflammatory, anti-tumor-promoting, and cytotoxic activities (4). In Serbia, pot marigold is cultivated as an important medicinal and ornamental plant. Typical phyllody, virescence, proliferation of axillary buds, and witches' broom symptoms were sporadically observed in 2011 in Pancevo plantation, Serbia (44°51′49″ N, 20°39′33″ E, 80 m above sea level). Until 2013, the number of uniformly distributed affected pot marigold plants reached 20% in the field. Due to the lack of seed production, profitability of the cultivation was seriously affected. Leaf samples from 10 symptomatic and 4 symptomless marigold plants were collected and total nucleic acid was extracted from midrib tissue (3). Direct PCR and nested PCR were carried out with primer pairs P1/16S-SR and R16F2n/R16R2n, respectively (3). Amplicons 1.5 and 1.2 kb in length, specific for the 16S rRNA gene, were amplified in all symptomatic plants. No PCR products were obtained when DNA isolated from symptomless plants was used. Restriction fragment length polymorphism (RFLP) patterns of the 1.2-kb fragments of 16S rDNA were determined by digestion with four endonucleases separately (TruI1, AluI, HpaII, and HhaI) and compared with those of Stolbur (Stol), Aster Yellows (AY), Flavescence dorée-C (FD-C), Poinsettia Branch-Inducing (PoiBI), and Clover Yellow Edge (CYE) phytoplasmas (2). RFLP patterns from all symptomatic pot marigold plants were identical to the Stol pattern, indicating Stolbur phytoplasma presence in affected plants. The 1.2-kb amplicon of representative Nv8 strain was sequenced and the data were submitted to GenBank (accession no. KJ174507). BLASTn analysis of the sequence was compared with sequences available in GenBank, showing 100% identity with 16S rRNA gene of strains from Paeonia tenuifolia (KF614623) and corn (JQ730750) from Serbia, and peach (KF263684) from Iran. All of these are members of the 16SrXII ‘Candidatus Phytoplasma solani’ group, subgroup A (Stolbur). Phytoplasmas belonging to aster yellows (16SrI) (Italy and Canada) and peanut witches' broom related phytoplasma (16SrII) group (Iran) have been identified in diseased pot marigold plants (1). To our knowledge, this is the first report of natural infection of pot marigold by Stolbur phytoplasma in Serbia.

References: (1) S. A. Esmailzadeh-Hosseini et al. Bull. Insectol. 64:S109, 2011. (2) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) J. P. Prince. Phytopathology 83:1130, 1993. (4) M. Ukiya et al. J. Nat. Prod. 69:1692, 2006.
First Report of Dollar Spot of Sandbur Caused by Sclerotinia homoeocarpa in Oklahoma
Authors: Flores F. , Walker N. R.
Published: April 2014

Sandbur (Cenchrus incertus Curtis) is a warm-season, annual, noxious, grassy weed native to southern North America. It is common in sandy, disturbed soils and can also be found in home lawns and sport fields where low turf density facilitates its establishment. In July 2013, after a period of frequent rainfall and heavy dew, symptoms of dollar spot-like lesions (1) were observed on sandbur plants growing in a mixed stand of turf-type and native warm-season grasses in Logan County, Oklahoma. Lesions, frequently associated with leaf sheaths, were tan and surrounded by a dark margin. Symptomatic leaves were surface sterilized and plated on potato dextrose agar amended with 10 ppm rifampicin, 250 ppm ampicillin, and 5 ppm fenpropathrin. After incubation, a fungus morphologically identical to Sclerotinia homoeocarpa Bennett was consistently isolated. The nuclear ribosomal internal transcribed spacer (ITS) region of two different isolates, SCL2 and SCL3, were amplified using primers ITS4 and ITS5 (2). The DNA products were sequenced and BLAST analyses were used to compare sequences with those in GenBank. The sequence for isolate SLC2 was 869 bp, contained a type I intron in the 18S small subunit rDNA, and was identical to accession EU123803. The ITS sequence for isolate SLC3 was 535 bp and identical to accession EU123802. Twenty-five-day-old seedlings of C. incertus were inoculated by placing 5-mm-diameter agar plugs, colonized by mycelia of each S. homoeocarpa isolate, onto two of the plants' leaves. Plugs were held in place with Parafilm. Two plants were inoculated with each isolate and sterile agar plugs were placed on two leaves of another seedling as control. Plants were incubated in a dew chamber at 20°C and a 12-h photoperiod. After 3 days of incubation, water-soaked lesions surrounded by a dark margin appeared on inoculated plants only. Fungi that were later identified as S. homoeocarpa isolates SLC2 and SLC3 by sequencing of the ITS region were re-isolated from symptomatic leaves, fulfilling Koch's postulates. To our knowledge, this is the first report of dollar spot on sandbur.

References: (1) R. W. Smiley et al. Page 22 in: Compendium of Turfgrass Diseases. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2005. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990.
Identifying Rates of Meadowfoam (Limnanthes alba) Seed Meal Needed for Suppression of Meloidogyne hapla and Pythium irregulare in Soil
Authors: Erşahin Yurdagül Şimşek , Weiland Jerry E. , Zasada Inga A. , Reed Ralph L. , Stevens J. Fred
Published: April 2014

Meadowfoam (Limnanthes alba) is a commercial oilseed annual crop grown in Oregon. After extracting oil from seed, the remaining seed meal is rich in the secondary plant metabolite glucolimnanthin, which can be converted into pesticidal compounds such as 3-methoxybenzyl isothiocyanate (ITC) and 3-methoxyphenylacetonitrile (nitrile) in the presence of the enzyme myrosinase. In previous studies, we demonstrated that ITC and nitrile, produced by mixing freshly ground meadowfoam seed with meadowfoam seed meal, are toxic to the plant-parasitic nematode Meloidogyne hapla and the plant pathogen Pythium irregulare. In this study, we evaluated factors that might influence the implementation of meadowfoam seed meal into agricultural production systems for soilborne pathogen and nematode control. Rate-finding experiments demonstrated that a minimum 1.0% seed/seed meal formulation (wt/wt) was necessary to achieve nematode and pathogen suppression; seed meal alone was insufficient for complete control of M. hapla and stimulated the growth of P. irregulare. When this 1.0% seed/seed meal formulation was used, a greater soil amendment rate was required to cause 100% mortality of P. irregulare (1.0% wt/wt) than for M. hapla (0.5% wt/wt). In phytotoxicity experiments, soil amended with the 1.0% seed/seed meal formulation was consistently phytotoxic to wheat, cucumber, and tomato. However, phytotoxic effects were mitigated by a delayed planting into the amended soil. A final assay to monitor concentrations of ITC and nitrile in conjunction with assessing M. hapla and P. irregulare mortality was conducted over a 6-day period in soils amended at 0.5 and 1.0% (wt/wt) with the 1.0% seed/seed meal formulation. The response was rapid, with 100% mortality of both organisms within 2 h after exposure to amended soil. Concentrations of nitrile remained relatively constant over the 6-day period (approximately 0.017 and 0.032 mg/ml at 0.5 and 1.0% amendment rates, respectively), whereas ITC production increased rapidly and peaked 12 to 24 h after amendment (0.083 and 0.171 mg/ml at 0.5 and 1.0% amendment rates, respectively) before returning to near undetectable levels.
Species of Pythium Associated with Seedling Root and Hypocotyl Disease on Common Bean (Phaseolus vulgaris) in Western Australia
Authors: Li Yu Pin , You Ming Pei , Barbetti Martin J.
Published: April 2014

The occurrence and distribution of Pythium spp. were determined by collecting isolates of Pythium from common bean (Phaseolus vulgaris) plants showing root or hypocotyl disease symptoms from different areas of Western Australia in 2012. Eight different Pythium species (Pythium conidiophorum, P. diclinum, P. intermedium, P. irregulare, P. lutarium, P. mamillatum, P. pachycaule, and P. perplexum) were isolated and identified according to molecular sequences. P. irregulare was the most widespread Pythium sp. All species, except P. perplexum, were pathogenic to the hypocotyl and root of common bean. We believe this is the first report of P. intermedium as a pathogen on common bean worldwide. This is also the first report of P. conidiophorum, P. intermedium, P. lutarium, P. mamillatum, P. pachycaule, and P. diclinum as pathogens on common bean in Australia and the first report of P. irregulare as a pathogen on common bean in Western Australia. P. intermedium was the most pathogenic species, causing the most severe disease on ‘Gourmet Delight’ (percent root disease index [%RDI] 75 ± 2.9 and percent hypocotyl disease index [%HDI] 59.2 ± 3.2) and ‘Pioneer’ (%RDI 75 ± 2.9 and %HDI 65.8 ± 3.2). That the relative susceptibility or resistance (the ability of a plant to reduce the extent of invasion by the pathogen) of a given bean variety to one Pythium sp. was, in general, similar across the other Pythium spp. was an important finding, because this opens up opportunities to utilize a single virulent isolate of one Pythium sp. to identify general resistance to a wider spectrum of Pythium spp.
Phytophthora Community Structure Analyses in Oregon Nurseries Inform Systems Approaches to Disease Management
Authors: Parke Jennifer L. , Knaus Brian J. , Fieland Valerie J. , Lewis Carrie , Grünwald Niklaus J.
Published: April 2014

Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora spp. associated with different sources and stages in the nursery production cycle. Plants, potting media, used containers, water, greenhouse soil, and container yard substrates were systematically sampled from propagation to the field. From 674 Phytophthora isolates recovered, 28 different species or taxa were identified. The most commonly isolated species from plants were Phytophthora plurivora (33%), P. cinnamomi (26%), P. syringae (19%), and P. citrophthora (11%). From soil and gravel substrates, P. plurivora accounted for 25% of the isolates, with P. taxon Pgchlamydo, P. cryptogea, and P. cinnamomi accounting for 18, 17, and 15%, respectively. Five species (P. plurivora, P. syringae, P. taxon Pgchlamydo, P. gonapodyides, and P. cryptogea) were found in all nurseries. The greatest diversity of taxa occurred in irrigation water reservoirs (20 taxa), with the majority of isolates belonging to internal transcribed spacer clade 6, typically including aquatic opportunists. Nurseries differed in composition of Phytophthora communities across years, seasons, and source within the nursery. These findings suggest likely contamination hazards and target critical control points for management of Phytophthora disease using a systems approach.
Effect of a Cognitive Aid on Adherence to Perioperative Assessment and Management Guidelines for the Cardiac Evaluation of Noncardiac Surgical Patients
Authors: Hand William R. , Bridges Kathryn H. , Stiegler Marjorie P. , Schell Randall M. , DiLorenzo Amy N. , Ehrenfeld Jesse M. , Nietert Paul J. , McEvoy Matthew D.
Published: April 2014

Background:

The 2007 American College of Cardiologists/American Heart Association Guidelines on Perioperative Cardiac Evaluation and Care for Noncardiac Surgery is the standard for perioperative cardiac evaluation. Recent work has shown that residents and anesthesiologists do not apply these guidelines when tested. This research hypothesized that a decision support tool would improve adherence to this consensus guideline.

Methods:

Anesthesiology residents at four training programs participated in an unblinded, prospective, randomized, cross-over trial in which they completed two tests covering clinical scenarios. One quiz was completed from memory and one with the aid of an electronic decision support tool. Performance was evaluated by overall score (% correct), number of incorrect answers with possibly increased cost or risk of care, and the amount of time required to complete the quizzes both with and without the cognitive aid. The primary outcome was the proportion of correct responses attributable to the use of the decision support tool.

Results:

All anesthesiology residents at four institutions were recruited and 111 residents participated. Use of the decision support tool resulted in a 25% improvement in adherence to guidelines compared with memory alone (P < 0.0001), and participants made 77% fewer incorrect responses that would have resulted in increased costs. Use of the tool was associated with a 3.4-min increase in time to complete the test (P < 0.001).

Conclusions:

Use of an electronic decision support tool significantly improved adherence to the guidelines as compared with memory alone. The decision support tool also prevented inappropriate management steps possibly associated with increased healthcare costs.
Streptomyces catbensis sp. nov., isolated from soil
Authors: Sakiyama Yayoi , Giang Nguyen M. , Miyadoh Shinji , Luong Dao Thi , Van Hop Duong , Ando Katsuhiko
Published: April 2014

Strain VN07A0015T was isolated from soil collected on Cat Ba Island, Vietnam. The taxonomic position of strain VN07A0015T was near

Streptomyces aomiensis

M24DS4T (98.5 % 16S rRNA gene sequence similarity) and

Streptomyces scabrisporus

NBRC 100760T (95.6 %), and it clustered within them; however, this cluster was distant from the type strains of other species of the genus

Streptomyces

. The aerial mycelia of strain VN07A0015T were greyish and formed imperfect spiral spore chains (retinaculiaperti type) with smooth-surfaced spores. The morphological features of strain VN07A0015T were different from those of the type strains of

S. aomiensis

and

S. scabrisporus

. The chemotaxonomic characteristics of strain VN07A0015T were typical for all members of the genus

Streptomyces

, which possessed ll-type diaminopimelic acid, menaquinone MK-9(H6, H8) and the major fatty acids iso-C16 : 0 and iso-C15 : 0. DNA–DNA relatedness between strain VN07A0015T and

S. aomiensis

NBRC 106164T was less than 30 %. In addition, some physiological and biochemical traits differed from those of

S. aomiensis

. Therefore, we propose that strain VN07A0015T be classified in the genus

Streptomyces

as a representative of Streptomyces catbensis sp. nov. (type strain VN07A0015T = VTCC-A-1889T = NBRC 107860T).
Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment
Authors: Fan Xiaoyang , Qiao Yanlu , Gao Xin , Zhang Xiao-Hua
Published: April 2014

A Gram-stain-positive, strictly aerobic, rod-shaped, non-motile bacterium, designated strain XH274T, was isolated from a deep sub-seafloor sediment sample collected from the South Pacific Gyre (41° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH274T belonged to the genus

Nocardioides

and shared the highest 16S rRNA gene sequence similarity with

Nocardioides kribbensis

KSL-2T (96.81 %),

Nocardioides daedukensis

MDN22T (96.74 %) and

Nocardioides psychrotolerans

RHLT2-1T (96.61 %). The DNA G+C content of strain XH274T was 74.6 mol%. The cell wall of strain XH274T contained ll-2,6-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose, galactose and mannose as the major whole-cell sugars. The major fatty acids were iso-C16 : 0, C18 : 1ω9c and C17 : 1ω8c. The major respiratory quinone was menaquinone-8(H4). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. On the basis of data from the polyphasic analysis, strain XH274T is considered to represent a novel species in the genus

Nocardioides

, for which the name Nocardioides
pacificus sp. nov. is proposed. The type strain is XH274T ( = DSM 27278T = JCM 19260T).
Proposal to modify Rule 6, Rule 10a, and Rule 12c of the International Code of Nomenclature of Prokaryotes
Authors: Oren Aharon , Garrity George M. , Schink Bernhard
Published: April 2014

According to the current versions of Rule 10a and Rule 12c of the International Code of Nomenclature of Prokaryotes, names of a genus or subgenus and specific epithets may be taken from any source and may even be composed in an arbitrary manner. Based on these rules, names may be composed of any word or any combination of elements derived from any language with a Latin ending. We propose modifying these rules by adding the text, currently part of Recommendation 6, according to which words from languages other than Latin or Greek should be avoided as long as equivalents exist in Latin or Greek or can be constructed by combining word elements from these two languages. We also propose modification of Rule 6 by adopting some of the current paragraphs of Recommendation 6 to become part of the Rule.
Phylogenetic and comparative functional analysis of the cell-separation α-glucanase Agn1p in Schizosaccharomyces
Authors: Sipiczki Matthias , Balazs Anita , Monus Aniko , Papp Laszlo , Horvath Anna , Sveiczer Akos , Miklos Ida
Published: April 2014

The post-cytokinetic separation of cells in cell-walled organisms involves enzymic processes that degrade a specific layer of the division septum and the region of the mother cell wall that edges the septum. In the fission yeast Schizosaccharomyces pombe, the 1,3-α-glucanase Agn1p, originally identified as a mutanase-like glycoside hydrolase family 71 (GH71) enzyme, dissolves the mother cell wall around the septum edge. Our search in the genomes of completely sequenced fungi identified GH71 hydrolases in Basidiomycota, Taphrinomycotina and Pezizomycotina, but not in Saccharomycotina. The most likely Agn1p orthologues in Pezizomycotina species are not mutanases having mutanase-binding domains, but experimentally non-characterized hypothetical proteins that have no carbohydrate-binding domains. The analysis of the GH71 domains corroborated the phylogenetic relationships of the Schizosaccharomyces species determined by previous studies, but suggested a closer relationship to the Basidiomycota proteins than to the Ascomycota proteins. In the Schizosaccharomyces genus, the Agn1p proteins are structurally conserved: their GH71 domains are flanked by N-terminal secretion signals and C-terminal sequences containing the conserved block YNFNAY/HTG. The inactivation of the agn1Sj
gene in Schizosaccharomyces japonicus, the only true dimorphic member of the genus, caused a severe cell-separation defect in its yeast phase, but had no effect on the hyphal growth and yeast-to-mycelium transition. It did not affect the mycelium-to-yeast transition either, only delaying the separation of the yeast cells arising from the fragmenting hyphae. The heterologous expression of agn1Sj
partially rescued the separation defect of the agn1Δ cells of Schizosaccharomyces pombe. The results presented indicate that the fission yeast Agn1p 1,3-α-glucanases of Schizosaccharomyces japonicus and Schizosaccharomyces pombe share conserved functions in the yeast phase.
Interactions among Dendrolimus punctatus cypovirus proteins and identification of the genomic segment encoding its A-spike
Authors: Cheng Chuangang , Shao Yunpeng , Su Lan , Zhou Yin , Sun Xiulian
Published: April 2014

Revealing the interactions among cypovirus proteins would facilitate our understanding of the replication and assembly of this virus. In the present study, interactions among proteins encoded by the 10 segments of Dendrolimus punctatus cypovirus (DpCPV) were identified using yeast two-hybrid (Y2H) and far-Western blotting assays. In total, 24 pairs of interactions were detected. Twelve pairs of one-direction interactions, four pairs of binary interactions and four pairs of self-associations were identified in the Y2H assays. Another four pairs of interactions were identified by far-Western blotting. The interactions between the methyltransferase domain of the turret protein (VP3) and VP4 as well as between polyhedrin and VP4 were further confirmed by far-Western blotting and pull-down assays, respectively. In addition, immunogold labelling showed that the A-spike of DpCPV is formed by VP4. In conclusion, we obtained a protein–protein interaction network of DpCPV and showed that its A-spike is formed by VP4 encoded by genomic segment 6.
Relationship between genotypes and serotypes of genogroup 1 recoviruses: a model for human norovirus antigenic diversity
Authors: Farkas Tibor , Lun Cindy Wong Ping , Fey Brittney
Published: April 2014

Human norovirus (NoV) research greatly relies on cell culture-propagable surrogate caliciviruses, including murine NoVs and the prototype ‘recovirus’ (ReCV), Tulane virus. However, the extreme biological diversity of human NoVs cannot be modelled by a uniform group of viruses or single isolate. Based on a diverse group of recently described ReCVs, a more advanced model reflecting human NoV biological diversity is currently under development. Here, we have reported the genotypic and serotypic relationships among 10 G1 ReCV isolates, including Tulane virus and nine other recent cell culture-adapted strains. Based on the amino acid sequences of virus capsid protein, VP1, and classification constraints established for NoVs, G1 ReCVs were separated into three genotypes, with variable organization of the three open reading frames. Interestingly, cross-neutralization plaque assays revealed the existence of four distinct serotypes, two of which were detected among the G1.2 strains. The amino acid (aa) difference between the two G1.2 ReCV serotypes (12%) was less than the minimum 13 % difference established between NoV genotypes. Interestingly, one of the G1.3 ReCVs was equally neutralized by antisera raised against the G1.3 (6 % aa difference) and G1.1 (25 % aa difference) representative strains. These results imply the existence of a large number of human NoV serotypes, but also shared cross-neutralization epitopes between some strains of different genotypes. In conclusion, the newly developed ReCV surrogate model can be applied to address biologically relevant questions pertaining to enteric CV diversity.
Recombinant bovine respiratory syncytial virus with deletion of the SH gene induces increased apoptosis and pro-inflammatory cytokines in vitro, and is attenuated and induces protective immunity in calves
Authors: Taylor Geraldine , Wyld Sara , Valarcher Jean-Francois , Guzman Efrain , Thom Michelle , Widdison Stephanie , Buchholz Ursula J.
Published: April 2014

Bovine respiratory syncytial virus (BRSV) causes inflammation and obstruction of the small airways, leading to severe respiratory disease in young calves. The virus is closely related to human (H)RSV, a major cause of bronchiolitis and pneumonia in young children. The ability to manipulate the genome of RSV has provided opportunities for the development of stable, live attenuated RSV vaccines. The role of the SH protein in the pathogenesis of BRSV was evaluatedin vitroandin vivousing a recombinant (r)BRSV in which the SH gene had been deleted. Infection of bovine epithelial cells and monocytes with rBRSVΔSH,in vitro, resulted in an increase in apoptosis, and higher levels of TNF-α and IL-1β compared with cells infected with parental, wild-type (WT) rBRSV. Although replication of rBRSVΔSH and WT rBRSV,in vitro, were similar, the replication of rBRSVΔSH was moderately reduced in the lower, but not the upper, respiratory tract of experimentally infected calves. Despite the greater ability of rBRSVΔSH to induce pro-inflammatory cytokines,in vitro, the pulmonary inflammatory response in rBRSVΔSH-infected calves was significantly reduced compared with that in calves inoculated with WT rBRSV, 6 days previously. Virus lacking SH appeared to be as immunogenic and effective in inducing resistance to virulent virus challenge, 6 months later, as the parental rBRSV. These findings suggest that rBRSVΔSH may be an ideal live attenuated virus vaccine candidate, combining safety with a high level of immunogenicity.
Protected Polymorphisms and Evolutionary Stability of Patch-Selection Strategies in Stochastic Environments
Authors: Evans Steven N. , Hening Alexandru , Schreiber Sebastian J.
Published: April 2014

We consider a population living in a patchy environment that varies stochastically in space and time. The population is composed of two morphs (that is, individuals of the same species with different genotypes). In terms of survival and reproductive success, the associated phenotypes differ only in their habitat selection strategies. We compute invasion rates corresponding to the rates at which the abundance of an initially rare morph increases in the presence of the other morph established at equilibrium. If both morphs have positive invasion rates when rare, then there is an equilibrium distribution such that the two morphs coexist; that is, there is a protected polymorphism for habitat selection. Alternatively, if one morph has a negative invasion rate when rare, then it is asymptotically displaced by the other morph under all initial conditions where both morphs are present. We refine the characterization of an evolutionary stable strategy for habitat selection from [Schreiber, 2012] in a mathematically rigorous manner. We provide a necessary and sufficient condition for the existence of an ESS that uses all patches and determine when using a single patch is an ESS. We also provide an explicit formula for the ESS when there are two habitat types. We show that adding environmental stochasticity results in an ESS that, when compared to the ESS for the corresponding model without stochasticity, spends less time in patches with larger carrying capacities and possibly makes use of sink patches, thereby practicing a spatial form of bet hedging.
(μ2-2-Methoxyethanol-κ3O1:O1,O3)(2-methoxyethanol-κO1)tris(μ2-3,4,5,6-tetrafluoro-o-phenylene-κ2C1:C2)trimercury(II)
Authors: Castañeda Raúl , Draguta Sergiu , Yakovenko Andrey , Fonari Marina , Timofeeva Tatiana
Published: April 2014

In the title compound, [Hg3(C6F4)3(C3H8O2)2], two O atoms from one 2-methoxyethanol ligand and one O atom from the second 2-methoxyethanol ligand coordinate three HgIIatoms [Hg—O = 2.765 (7)–2.890 (8) Å] in the trimeric organomercurial Lewis acid (o-C6F4Hg)3. The hydroxy groups are involved in formation of intra- and intermolecular O—H...O hydrogen bonds; the latter link two molecules into centrosymmetric dimers. An extensive net of weak intermolecular C—H...F interactions further consolidates the crystal packing.
N,N,N′-Trimethyl-N′′-(4-nitrophenyl)-N′-phenylguanidine
Authors: Tiritiris Ioannis , Frey Wolfgang , Kantlehner Willi
Published: April 2014

The C—N bond lengths in the guanidine unit of the title compound, C16H18N4O2, are 1.298 (2), 1.353 (2) and 1.401 (3) Å, indicating double- and single-bond character. The N—C—N angles are 115.81 (16), 118.90 (18) and 125.16 (18)°, showing a deviation of the CN3plane from an ideal trigonal–planar geometry. In the crystal, C—H...O hydrogen bonds are observed between the methyl- and aromatic-H atoms and nitro-O atoms. One H atom of the phenyl ring and of the NMe2group associate with the O atoms of the nitro group, giving chains along thea-andb-axis directions. Cross-linking of these two chains results in a two-dimensional network alongbc.
2-[1-(4-Bromophenyl)-2-nitroethyl]hexanoic acid
Authors: Zhang Yanpeng , Zhang Can , Xia Ai-Bao
Published: April 2014

In the crystal structure of the title compoud, C14H18BrNO4, molecules are linked by a strong O—H...O hydrogen bond and weaker C—H...O interactions. The benzene ring makes dihedral angles of 3.67 (3) and 72.63 (3)° with the carboxylic acid group and the nitro group, respectively.
Trichlorido(1-ethylpiperazin-1-ium)cobalt(II)
Authors: Dhieb Abdelhamid Chiheb , Janzen Daron E. , Rzaigui Mohamed , Smirani Sta Wajda
Published: April 2014

In the title complex, [Co(C6H15N2)Cl3], the Co2+ion is coordinated in a distorted tetrahedral fashion by three chloride ions and one N atom of the piperazine ring; the ring adopts a chair conformation with the N—Co and N—CEtbonds in equatorial orientations. In the crystal, molecules are connected by N—H...Cl hydrogen bonds, generating (10-1) sheets.
1:1 Co-crystal of 4,4′-(ethene-1,2-diyl)dipyridin-1-ium sulfate and hexaaquairon(II) sulfate monohydrate
Authors: Yang Dan , Yang Fei-Lin
Published: April 2014

In the title hydrated double salt, 4,4′-(ethene-1,2-diyl)dipyridin-1-ium hexaaquairon(II) bis(sulfate) monohydrate, (C12H12N2)[Fe(H2O)6](SO4)2·H2O, the FeIIcation is coordinated by six water molecules in a slightly distorted octahedral geometry; the two pyridine rings of the 4,4′-(ethene-1,2-diyl)dipyridin-1-ium cation are twisted to each other by a dihedral angle of 11.84 (10)°. In the crystal, the cations, sulfate anions and water molecules of crystallization are linked by O—H...O, N—H...O and weak C—H...O hydrogen bonds, forming a three-dimensional supramolecular network.
5-Bromo-2,7-dimethyl-3-(4-methylphenylsulfonyl)-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: April 2014

In the title compound, C17H15BrO3S, the dihedral angle between the mean planes of the benzofuran and 4-methylphenyl rings is 76.43 (5)°. In the crystal, molecules are linkedviapairs of C—H...O hydrogen bonds into inversion dimers that are further linked by Br...Br [3.6517 (4) Å] contacts about inversion centers into supramolecular sheets that lie parallel to (111).
(E)-3-(Oxolan-2-ylidene)-1-phenylpyrrolidine-2,5-dione
Authors: Shao Ying , Xia Yong-An , Wu Zhu-Hong , Liu Xiao-Long
Published: April 2014

In the title compound, C14H13NO3, the dihedral angles between the central pyrrolidine ring and the pendant tetrahydrofuran and phenyl rings are 5.34 (18) and 58.99 (17)°, respectively. The tetrahydrofuran ring is almost planar (r.m.s. deviation = 0.008 Å). In the crystal, molecules are linked by C—H...O interactions, generating a three-dimensional network.
(5-Fluoro-4′-methylbiphenyl-3-yl)(2,4,6-trimethylphenyl)iodonium trifluoromethanesulfonate
Authors: Shao Ying , Liu Xiao-Long , Wu Zhu-Hong , Xia Yong-An
Published: April 2014

In the title molecular salt, C22H21FI+·CF3SO3−, the dihedral angle between the rings of the biphenyl group is 65.6 (1)°. The ring of the mesitylene group is inclined to the fluorobenzene ring at an angle of 86.1 (3)° and the C—I—C bond angle is 97.0 (2)°. In the crystal, extremely short I...O contacts of 2.862 (5) and 2.932 (5) Å occur, due to the strong electrostatic interactions between the I atom and two adjacent trifluoromethanesulfonate counter-ions. There are also C—H...F and C—H...π interactions present: together with the I...O bonds, these result in a three-dimensional network.
3,4-Difluoro-2-hydroxybenzoic acid
Authors: Ravi Kiran Bhaskarachar , Palakshamurthy Bandrehalli Siddagangaiah , Vijayakumar Giriyapura R. , Bharath Hebbur Shivamurthy
Published: April 2014

In the title compound, C7H4F2O3, an intramolecular O—H...O hydrogen bond is observed. In the crystal, inversion dimers linked by pairs of O—H...O hydrogen bonds generateR22(8) ring motifs. These dimers are linked by C—H...O and C—H...F hydrogen bonds, forming sheets lying parallel to (30-1). The sheets are linked by aromatic π–π stacking interactions [inter-centroid distance = 3.7817 (9) Å], forming a three-dimensional structure.
Diethyl 4-oxo-4H-[1,4′-biquinoline]-3,3′-dicarboxylate
Authors: Ishikawa Yoshinobu , Yoshida Nanako
Published: April 2014

In the title molecule, C24H20N2O5, the quinoline and quinolinone moieties are practically perpendicular to each other, forming a dihedral angle of 89.06 (3)°. In the crystal, each moiety forms coplanar π-stacked couples with the respective inversion equivalents. The quinolinone moieties overlap with their benzene rings with a centroid–centroid separation of 3.641 (2) Å, whereas the quinoline moieties overlap with their pyridine rings with a separation of 3.592 (2) Å. The resulting supramolecular chains propargate along [101].
{(3aR,5S,6R,6aR)-5-[(R)-1,2-Dihydroxyethyl]-2,2-dimethyltetrahydrofuro[2,3-d][1,3]dioxol-6-yl}methyl methanesulfonate
Authors: Rjabovs Vitālijs , Mishnev Anatoly , Kiselovs Glebs , Turks Māris
Published: April 2014

In the title compound, C11H20O8S, the furanose ring has a pseudorotation phase angle equal to 31.3° and assumes a3T4conformation, with deviations of 0.297 (4) and −0.152 (4) Å for the corresponding C atoms. The dioxolane ring adopts an envelope conformation. One of the O atoms is at the flap and deviates from the least-squares plane formed by the other four ring atoms by 0.405 (2) Å. The dihedral angle between the planar fragments of the rings is 63.53 (8)°. In the crystal, molecules are associated into sheets perpendiculer to thebaxis by means of O—H...O hydrogen bonds. A few weak C—H...O interactions are also observed.
Boundary practices at incident sites
Authors: Kvarnlöf Linda , Johansson Roine
Published: April 2014

Purpose

– Incident sites can be described as the joint work site of the emergency services, where one of their challenges is to interact with the public. The purpose of this paper is to study how this interaction is structured by the emergency personnel's jurisdictional claims.

Design/methodology/approach

– This paper rests upon qualitative method and in-depth interviews. In total, 28 people have been interviewed, out of which 13 are emergency personnel and 15 are unaffiliated volunteers. The interview material has been analysed qualitatively and thematically by the authors.

Findings

– The findings show that the interaction between emergency personnel and unaffiliated volunteers can be described in terms of three different boundary practices: cordoning off, division of labour and conversation, varying in degrees of inclusion and exclusion. The result shows that the emergency personnel's relationship to volunteers is ambivalent, as they are both seen as an uncertain element at the incident site in need of control and as a valuable source of information.

Originality/value

– While most other studies have been focusing on the interaction between emergency organizations, the authors have investigated the interaction between emergency organizations and a group previously unstudied: unaffiliated volunteers. While sociologists in the field of boundary work normally describe boundary practices in terms of negotiation, sympathizing with the concept of negotiated order, the results point to the fact that boundaries are not necessarily a subject for negotiation.