bluuebunny/crossref_metadata_2025 huggingface dataset:
REVIEW: Wild Rice: Both an Ancient Grain and a Whole Grain
Authors: Timm Derek A. , Slavin Joanne L.
Published: January 2014

Wild rice (Zizania spp.) grows in shallow waters of North America and is distinct from brown and white rice (Oryza spp.). The recent trends toward gluten‐free foods and ancient grains present an opportunity for increased interest in the health benefits of wild rice. Wild rice is classified as a whole grain and typically contains 75% carbohydrate, 6.2% dietary fiber, 14.7% protein, and 1.1% lipids. Wild rice is a good source of dietary fiber and has nearly double the amount of protein of white rice. The lipid content is low; however, most of the lipids are essential omega‐6 (35.0–37.8%) and omega‐3 (20.0–31.5%) fatty acids. In addition to macronutrient content, wild rice contains phytosterol levels several times higher than white rice. Furthermore, the antioxidant activity of wild rice is 10–15 times higher than white rice. A series of rat studies in which wild rice was added to a high fat, high cholesterol diet found significant attenuation of serum free fatty acids, total cholesterol, and triglyceride levels while maintaining higher high‐density lipoprotein levels compared with a control diet. The exact explanation of the protective mechanism of wild rice is uncertain, but the dietary fiber, phytosterol, or antioxidant capacity of wild rice may be the reason for it. Current interest in whole grains and gluten‐free diets, as well as antioxidants and phytochemicals, makes wild rice an attractive grain addition to the diet.
Disease Incidence and Ascospore Dispersal from Cut Hazelnut Branches Colonized by Anisogramma anomala
Authors: Heckert S. , Pscheidt J. W. , Cluskey S. A.
Published: January 2014

Hazelnut branches bearing stromata of Anisogramma anomala cut in December (2009 and 2010) were compared with branches cut prior to bud break in March to investigate these sources of inoculum. Branches were placed into brush piles (sources). Spore traps and potted hazelnut trees were placed adjacent to each source, 6.4 m upwind and downwind, and 20 m downwind from each source. Significantly more ascospores were detected near sources of branches cut in March compared with December in 2010 however, no differences were detected between pruning treatments in 2011. Ascospore viability, as assessed by trypan blue stain, averaged 50% for both pruning times each season. Significantly more ascospores were detected 6.4 m downwind compared with 6.4 m upwind or 20 m downwind of a source both years. All potted trees exposed to branches from both pruning treatments within sources became diseased both years. The proportion of potted trees that became infected was greater for the downwind group than the upwind for both years, suggesting that ascospores were dispersed beyond the rain splash dispersal range of sources. Ascospores from diseased branches pruned in December or March remained viable, infectious and were dispersed at least 20 m downwind.
Predicting Fusarium Head Blight Epidemics with Boosted Regression Trees
Authors: Shah D. A. , De Wolf E. D. , Paul P. A. , Madden L. V.
Published: January 2014

Predicting major Fusarium head blight (FHB) epidemics allows for the judicious use of fungicides in suppressing disease development. Our objectives were to investigate the utility of boosted regression trees (BRTs) for predictive modeling of FHB epidemics in the United States, and to compare the predictive performances of the BRT models with those of logistic regression models we had developed previously. The data included 527 FHB observations from 15 states over 26 years. BRTs were fit to a training data set of 369 FHB observations, in which FHB epidemics were classified as either major (severity ≥ 10%) or non-major (severity < 10%), linked to a predictor matrix consisting of 350 weather-based variables and categorical variables for wheat type (spring or winter), presence or absence of corn residue, and cultivar resistance. Predictive performance was estimated on a test (holdout) data set consisting of the remaining 158 observations. BRTs had a misclassification rate of 0.23 on the test data, which was 31% lower than the average misclassification rate over 15 logistic regression models we had presented earlier. The strongest predictors were generally one of mean daily relative humidity, mean daily temperature, and the number of hours in which the temperature was between 9 and 30°C and relative humidity ≥ 90% simultaneously. Moreover, the predicted risk of major epidemics increased substantially when mean daily relative humidity rose above 70%, which is a lower threshold than previously modeled for most plant pathosystems. BRTs led to novel insights into the weather–epidemic relationship.
What Interval Characteristics Make a Good Categorical Disease Assessment Scale?
Authors: Chiang Kuo-Szu , Liu Shih-Chia , Bock Clive H. , Gottwald Tim R.
Published: January 2014

Plant pathologists most often obtain quantitative information on disease severity using visual assessments. Category scales have been used for assessing plant disease severity in field experiments, epidemiological studies, and for screening germplasm. The most widely used category scale is the Horsfall-Barratt (H-B) scale, but reports show that estimates of disease severity using the H-B scale are less precise compared with nearest percent estimates (NPEs) using the 0 to 100% ratio scale. Few studies have compared different category scales. The objective of this study was to compare NPEs, the H-B midpoint converted data, and four different linear category scales (5 and 10% increments, with and without additional grades at low severity [0.1, 0.5, 1.0, 2.0, 5.0, 10.0, 15.0, 20.0…100%, and 0.1, 0.5, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0…100%, respectively]). Results of simulations based on known distributions of disease estimation using the type II error rate (the risk of failing to reject H0 when H0 is false) showed that at disease severity ≤5%, a 10% category scale had a greater probability of failing to reject H0 when H0 is false compared with all other methods, while the H-B scale performed least well at 20 to 50% severity. The 5% category scale performed as well as NPEs except when disease severity was ≤1%. Both the 5 and 10% category scales with the additional grades included performed as well as NPEs. These results were confirmed with a mixed model analysis and bootstrap analysis of the original rater assessment data. A better knowledge of the advantages and disadvantages of category scale types will provide a basis for plant pathologists and plant breeders seeking to maximize accuracy and reliability of assessments to make an informed decision when choosing a disease assessment method.
A fundamental model exhibiting nonlinear oscillatory dynamics in solid oxide fuel cells
Authors: Sands J. D. , Needham D. J. , Uddin J.
Published: January 2014

In this paper, we address the phenomenon of temporal, self-sustained oscillations which have been observed under quite general conditions in solid oxide fuel cells. Our objective is to uncover the fundamental mechanisms giving rise to the observed oscillations. To this end, we develop a model based on the fundamental chemical kinetics and transfer processes which take place within the fuel cell. This leads to a three-dimensional dynamical system, which, under typical operating conditions, is rationally reducible to a planar dynamical system. The structural dynamics of the planar dynamical system are studied in detail. Self-sustained oscillations are shown to arise through Hopf bifurcations in this planar dynamical system, and the key parameter ranges for the occurrence of such oscillations are identified.
A dynamic global equilibrium in carnivoran diversification over 20 million years
Authors: Liow Lee Hsiang , Finarelli John A.
Published: January 2014

The ecological and evolutionary processes leading to present-day biological diversity can be inferred by reconstructing the phylogeny of living organisms, and then modelling potential processes that could have produced this genealogy. A more direct approach is to estimate past processes from the fossil record. The Carnivora (Mammalia) has both substantial extant species richness and a rich fossil record. We compiled species-level data for over 10 000 fossil occurrences of nearly 1400 carnivoran species. Using this compilation, we estimated extinction, speciation and net diversification for carnivorans through the Neogene (22–2 Ma), while simultaneously modelling sampling probability. Our analyses show that caniforms (dogs, bears and relatives) have higher speciation and extinction rates than feliforms (cats, hyenas and relatives), but lower rates of net diversification. We also find that despite continual species turnover, net carnivoran diversification through the Neogene is surprisingly stable, suggesting a saturated adaptive zone, despite restructuring of the physical environment. This result is strikingly different from analyses of carnivoran diversification estimated from extant species alone. Two intervals show elevated diversification rates (13–12 Ma and 4–3 Ma), although the precise causal factors behind the two peaks in carnivoran diversification remain open questions.
Population-level effects of suppressing fever
Authors: Earn David J. D. , Andrews Paul W. , Bolker Benjamin M.
Published: January 2014

Fever is commonly attenuated with antipyretic medication as a means to treat unpleasant symptoms of infectious diseases. We highlight a potentially important negative effect of fever suppression that becomes evident at the population level: reducing fever may increase transmission of associated infections. A higher transmission rate implies that a larger proportion of the population will be infected, so widespread antipyretic drug use is likely to lead to more illness and death than would be expected in a population that was not exposed to antipyretic pharmacotherapies. We assembled the published data available for estimating the magnitudes of these individual effects for seasonal influenza. While the data are incomplete and heterogeneous, they suggest that, overall, fever suppression increases the expected number of influenza cases and deaths in the US: for pandemic influenza with reproduction number, the estimated increase is 1% (95% CI: 0.0–2.7%), whereas for seasonal influenza with, the estimated increase is 5% (95% CI: 0.2–12.1%).
Between migration load and evolutionary rescue: dispersal, adaptation and the response of spatially structured populations to environmental change
Authors: Bourne Elizabeth C. , Bocedi Greta , Travis Justin M. J. , Pakeman Robin J. , Brooker Rob W. , Schiffers Katja
Published: January 2014

The evolutionary potential of populations is mainly determined by population size and available genetic variance. However, the adaptability of spatially structured populations may also be affected by dispersal: positively by spreading beneficial mutations across sub-populations, but negatively by moving locally adapted alleles between demes. We develop an individual-based, two-patch, allelic model to investigate the balance between these opposing effects on a population's evolutionary response to rapid climate change. Individual fitness is controlled by two polygenic traits coding for local adaptation either to the environment or to climate. Under conditions of selection that favour the evolution of a generalist phenotype (i.e. weak divergent selection between patches) dispersal has an overall positive effect on the persistence of the population. However, when selection favours locally adapted specialists, the beneficial effects of dispersal outweigh the associated increase in maladaptation for a narrow range of parameter space only (intermediate selection strength and low linkage among loci), where the spread of beneficial climate alleles is not strongly hampered by selection against non-specialists. Given that local selection across heterogeneous and fragmented landscapes is common, the complex effect of dispersal that we describe will play an important role in determining the evolutionary dynamics of many species under rapidly changing climate.
Prospecting and dispersal: their eco-evolutionary dynamics and implications for population patterns
Authors: Delgado M. M. , Bartoń K. A. , Bonte D. , Travis J. M. J.
Published: January 2014

Dispersal is not a blind process, and evidence is accumulating that individual dispersal strategies are informed in most, if not all, organisms. The acquisition and use of information are traits that may evolve across space and time as a function of the balance between costs and benefits of informed dispersal. If information is available, individuals can potentially use it in making better decisions, thereby increasing their fitness. However, prospecting for and using information probably entail costs that may constrain the evolution of informed dispersal, potentially with population-level consequences. By using individual-based, spatially explicit simulations, we detected clear coevolutionary dynamics between prospecting and dispersal movement strategies that differed in sign and magnitude depending on their respective costs. More specifically, we found that informed dispersal strategies evolve when the costs of information acquisition during prospecting are low but only if there are mortality costs associated with dispersal movements. That is, selection favours informed dispersal strategies when the acquisition and use processes themselves were not too expensive. When non-informed dispersal strategies evolve, they do so jointly with the evolution of long dispersal distance because this maximizes the sampling area. In some cases, selection produces dispersal rules different from those that would be ‘optimal’ (i.e. the best possible population performance—in our context quantitatively measured as population density and patch occupancy—among all possible individual movement rules) for the population. That is, on the one hand, informed dispersal strategies led to population performance below its highest possible level. On the other hand, un- and poorly informed individuals nearly optimized population performance, both in terms of density and patch occupancy.
A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification
Authors: Macqueen Daniel J. , Johnston Ian A.
Published: January 2014

Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.
Rhizobium rhizoryzae sp. nov., isolated from rice roots
Authors: Zhang Xiao-Xia , Tang Xue , Sheirdil Rizwan Ali , Sun Lei , Ma Xiao-Tong
Published: January 2014

Two strains (J3-AN59T and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59T and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus

Rhizobium

, and they were most closely related to

Rhizobium tarimense

ACCC 06128T (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59T and J3-N84 and those of recognized species of the genus

Rhizobium

were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59T and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59T and J3-N84 was 89 %, and strain J3-AN59T showed 9 % DNA–DNA relatedness to

R. tarimense

ACCC 06128T, the most closely related strain. Based on this evidence, we found that J3-AN59T and J3-N84 represent a novel species in the genus

Rhizobium

and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59T ( = ACCC 05916T = KCTC 23652T).
Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil
Authors: Dsouza Melissa , Taylor Michael W. , Ryan Jason , MacKenzie Andrew , Lagutin Kirill , Anderson Robert F. , Turner Susan J. , Aislabie Jackie
Published: January 2014

A novel bacterium, strain BrT, was isolated from gamma-irradiated soils of the Britannia drift, Lake Wellman Region, Antarctica. This isolate was rod-shaped, endospore forming, Gram-stain-variable, catalase-positive, oxidase-negative and strictly aerobic. Cells possessed a monotrichous flagellum. Optimal growth was observed at 18 °C, pH 7.0 in PYGV or R2A broth. The major cellular fatty acid was anteiso-C15 : 0 (63.4 %). Primary identified lipids included phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. Total phospholipid was 60 % (w/w) of the total lipid extract. MK-7 was the dominant isoprenoid quinone. The genomic DNA G+C content was 55.6 mol%. Based on 16S rRNA gene sequence similarity, strain BrT clusters within the genus

Paenibacillus

with similarity values ranging from 93.9 to 95.1 %. Phylogenetic analyses by maximum-likelihood, maximum-parsimony and neighbour-joining methods revealed that strain BrT clusters with

Paenibacillus daejeonensis

(AF290916),

Paenibacillus tarimensis

(EF125184) and

Paenibacillus pinihumi

(GQ423057), albeit with weak bootstrap support. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, we propose that strain BrT represents a novel species, Paenibacillus darwinianus sp. nov. The type strain is BrT ( = DSM 27245T = ICMP 19912T).
Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring
Authors: Park Sooyeon , Park Doo-Sang , Bae Kyung Sook , Yoon Jung-Hoon
Published: January 2014

A Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped or ovoid bacterial strain, designated SSK6-1T, was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK6-1T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK6-1T clustered with

Phaeobacter daeponensis

TF-218T and

Phaeobacter caeruleus

LMG 24369T, exhibiting sequence similarities of 98.6 and 98.3 %, respectively. The novel strain exhibited sequence similarities of 94.6–97.8 % to the type strains of other recognized species of the genera

Phaeobacter

and

Leisingera

. Strain SSK6-1T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids of strain SSK6-1T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain SSK6-1T was 64.6 mol% and its DNA–DNA relatedness values with

P. daeponensis

TF-218T and

P. caeruleus

were 21 and 25 %, respectively. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK6-1T is separate from recognized

Phaeobacter

species. On the basis of the data presented, strain SSK6-1T is considered to represent a novel species of the genus

Phaeobacter

, for which the name Phaeobacter aquaemixtae sp. nov. is proposed. The type strain is SSK6-1T ( = KCTC 32538T = CECT 8399T).
Chryseobacterium gallinarum sp. nov., isolated from a chicken, and Chryseobacterium contaminans sp. nov., isolated as a contaminant from a rhizosphere sample
Authors: Kämpfer Peter , Poppel Marie T. , Wilharm Gottfried , Busse Hans-Jürgen , McInroy John A. , Glaeser Stefanie P.
Published: January 2014

Two yellow-pigmented bacterial strains (100T and C26T), showing 98.4 % 16S rRNA gene sequence similarity to each other and isolated from a chicken in Germany and as a contaminant from an agar plate of a rhizosphere sample in Alabama, were studied by using a polyphasic taxonomic approach. Cells of both isolates were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequences of the two organisms with the sequences of the type strains of the most closely related species of the genus

Chryseobacterium

showed the highest sequence similarities of strains 100T and C26T to the type strains of

Chryseobacterium joostei

(respectively 97.5 and 98.2 %),

C. viscerum

(96.6, 97.8 %),

C. gleum

(97.1, 97.7 %),

C. arthrosphaerae

(97.3%, 97.7 %),

C. indologenes

(97.2, 97.7 %),

C. tructae

(96.6, 97.6 %),

C. jejuense

(97.0, 97.6 %) and

C. oncorhynchi

(96.3, 97.5 %); 16S rRNA gene sequence similarities to members of all other species of the genus

Chryseobacterium

were below 97.5 %. The fatty acid profiles of both strains consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c and iso-C17 : 0 3-OH, but also showed slight differences (absence or presence of C16 : 0 3-OH and iso-C15 : 1 F). DNA–DNA hybridizations between the two strains and between the novel strains and the type strains of

C. joostei

,

C. indologenes

,

C. jejuense

,

C. tructae

and

C. viscerum

resulted in relatedness values clearly below 70 %. These DNA–DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed that both strains 100T and C26T represent novel species, for which the names Chryseobacterium gallinarum sp. nov. (type strain 100T = LMG 27808T = CCM 8493T) and Chryseobacterium contaminans sp. nov. (type strain C26T = LMG 27810T = CCM 8492T) are proposed.
Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands
Authors: Cadillo-Quiroz Hinsby , Bräuer Suzanna L. , Goodson Noah , Yavitt Joseph B. , Zinder Stephen H.
Published: January 2014

Two mesophilic, hydrogenotrophic methanogens, designated strains SWAN1T and AL-21, were isolated from two contrasting peatlands: a near circumneutral temperate minerotrophic fen in New York State, USA, and an acidic boreal poor fen site in Alaska, USA, respectively. Cells of the two strains were rod-shaped, non-motile, stained Gram-negative and resisted lysis with 0.1 % SDS. Cell size was 0.6×1.5–2.8 µm for strain SWAN1T and 0.45–0.85×1.5–35 µm for strain AL-21. The strains used H2/CO2 but not formate or other substrates for methanogenesis, grew optimally around 32–37 °C, and their growth spanned through a slightly low to neutral pH range (4.7–7.1). Strain AL-21 grew optimally closer to neutrality at pH 6.2, whereas strain SWAN1T showed a lower optimal pH at 5.4–5.7. The two strains were sensitive to NaCl with a maximal tolerance at 160 mM for strain SWAN1T and 50 mM for strain AL-21. Na2S was toxic at very low concentrations (0.01–0.8 mM), resulting in growth inhibition above these values. The DNA G+C content of the genomes was 35.7 mol% for strain SWAN1T and 35.8 mol% for strain AL-21. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains are members of the genus

Methanobacterium

. Strain SWAN1T shared 94–97 % similarity with the type strains of recognized species of the genus

Methanobacterium

, whereas strain AL-21 shared 99 % similarity with

Methanobacterium lacus

17A1T. On the basis of phenotypic, genomic and phylogenetic characteristics, strain SWAN1T ( = DSM 25820T = JCM 18151T) is proposed as the type strain of a novel species, Methanobacterium paludis sp. nov., while strain AL-21 is proposed as a second strain of

Methanobacterium lacus

.
A study on Nim expression in Bacteroides fragilis
Authors: Leitsch David , Sóki József , Kolarich Daniel , Urbán Edit , Nagy Elisabeth
Published: January 2014

Members of the genus Bacteroides, mainly Bacteroides fragilis, can cause severe disease in man, especially after intestinal perforation in the course of abdominal surgery. Treatment is based on a small number of antibiotics, including metronidazole, which has proved to be highly reliable throughout the last 40 to 50 years. Nevertheless, metronidazole resistance does occur in Bacteroides and has been mainly attributed to Nim proteins, a class of proteins with a suggested nitroreductase function. Despite the potentially high importance of Nim proteins for human health, information on the expression of nim genes in B. fragilis is still lacking. It was the aim of this study to demonstrate expression of nim genes in B. fragilis at the protein level and, furthermore, to correlate Nim levels with the magnitude of metronidazole resistance. By the application of 2D gel electrophoresis, Nim proteins could be readily identified in nim-positive strains, but their levels were not elevated to a relevant extent after induction of resistance with high doses of metronidazole. Thus, the data herein do not provide evidence for Nim proteins acting as nitroreductases using metronidazole as a substrate, because no correlation between Nim levels and levels of metronidazole resistance could be observed. Furthermore, no evidence was found that Nim proteins protect B. fragilis from metronidazole by sequestering the activated antibiotic.
Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes
Authors: van der Sluis Renée M. , Derking Ronald , Breidel Seyguerney , Speijer Dave , Berkhout Ben , Jeeninga Rienk E.
Published: January 2014

HIV-1 transcription depends on cellular transcription factors that bind to sequences in the long-terminal repeat (LTR) promoter. Each HIV-1 subtype has a specific LTR promoter configuration, and minor sequence changes in transcription factor binding sites (TFBSs) or their arrangement can influence transcriptional activity, virus replication and latency properties. Previously, we investigated the proviral latency properties of different HIV-1 subtypes in the SupT1 T cell line. Here, subtype-specific latency and replication properties were studied in primary PHA-activated T lymphocytes. No major differences in latency and replication capacity were measured among the HIV-1 subtypes. Subtype B and AE LTRs were studied in more detail with regard to a putative AP-1 binding site using luciferase reporter constructs. c-Jun, a member of the AP-1 transcription factor family, can activate both subtype B and AE LTRs, but the latter showed a stronger response, reflecting a closer match with the consensus AP-1 binding site. c-Jun overexpression enhanced Tat-mediated transcription of the viral LTR, but in the absence of Tat inhibited basal promoter activity. Thus, c-Jun can exert a positive or negative effect via the AP-1 binding site in the HIV-1 LTR promoter, depending on the presence or absence of Tat.
Modelling and analysis of bacterial tracks suggest an active reorientation mechanism inRhodobacter sphaeroides
Authors: Rosser Gabriel , Baker Ruth E. , Armitage Judith P. , Fletcher Alexander G.
Published: January 2014

Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly-understood reorientation mechanism in the monoflagellate speciesRhodobacter sphaeroides.The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable reorientation. When rotation restarts the cell body usually points in a new direction. It has been assumed that the new direction is simply the result of Brownian rotation. We consider three variants of a self-propelled particle model of bacterial motility. The first considers rotational diffusion only, corresponding to a non-chemotactic mutant strain. A further two models also include stochastic reorientations, describing ‘run-and-tumble’ motility. We derive expressions for key summary statistics and simulate each model using a stochastic computational algorithm. We also discuss the effect of cell geometry on rotational diffusion. Working with a previously published tracking dataset, we compare predictions of the models with data on individual stopping events inR. sphaeroides. This provides strong evidence that this species undergoes some form of active reorientation rather than simple reorientation by Brownian rotation.
Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division
Authors: Grob Alice , Colleran Christine , McStay Brian
Published: January 2014

Human cell nuclei are functionally organized into structurally stable yet dynamic bodies whose cell cycle inheritance is poorly understood. Here, we investigate the biogenesis and propagation of nucleoli, sites of ribosome biogenesis and key regulators of cellular growth. Nucleolar and cell cycles are intimately connected. Nucleoli disappear during mitosis, reforming around prominent uncharacterized chromosomal features, nucleolar organizer regions (NORs). By examining the effects of UBF depletion on both endogenous NORs and synthetic pseudo-NORs, we reveal its essential role in maintaining competency and establishing a bookmark on mitotic NORs. Furthermore, we demonstrate that neo-NORs, UBF-binding site arrays coupled with rDNA transcription units, direct the de novo biogenesis of functional compartmentalized neonucleoli irrespective of their site of chromosomal integration. For the first time, we establish the sequence requirements for nucleolar biogenesis and provide proof that this is a staged process where UBF-dependent mitotic bookmarking precedes function-dependent nucleolar assembly.
(±)-trans-6,6′-Diethoxy-2,2′-[cyclohexane-1,2-diylbis(nitrilomethanylylidene)]diphenol monohydrate
Authors: Mohan Nithya , Sreejith S. S. , Sithambaresan M. , Kurup M. R. Prathapachandra
Published: January 2014

In the title hydrate, C24H30N2O4·H2O, the organic molecule adopts anEconformation with respect to the azomethine double bonds. The cyclohexane ring is in a chair conformation. The dihedral angle between benzene rings is 79.6 (2)°. Two intramolecular O—H...N hydrogen bonds are present. In the crystal, the components are linked by O–H...O hydrogen bonds and weak C—H...π interactions, generating a three-dimensional supramolecular architecture.
Tetrakis[bis(pyridin-2-yl)amine-κN2](nitrato-κO)silver(I)
Authors: Parashchenko Yuliia , Pavlishchuk Anna , Bokach Nadezhda A. , Haukka Matti
Published: January 2014

In the title complex, [Ag(NO3)(C10H9N3)4], the nitrate ligand is found to be disordered over two sets of positions, with occupancy factors of 0.473 (5) and 0.527 (5). The AgIion is located in a square-pyramidal coordination environment formed by four N atoms from four bis(pyridin-2-yl)amine ligands and one O atom from a nitrate ligand. Weak interactions between the AgIions and the nitrate anions acting in a monodentate mode [Ag...O = 2.791 (13) and 2.816 (9) Å for the major component of the nitrate ligand, and 2.865 (8) and 2.837 (8) Å for the minor component] link the complex molecules into a chain along [001]. N—H...O hydrogen bonds are observed.
Di-μ-tricyanido-tetracyanidobis[hydrotris(pyrazoylborato)]tetramethanoldiiron(III)iron(II) dimethanol disolvate
Authors: Zhang Kuirun , Sato Osamu
Published: January 2014

In the title complex, [FeIIFeIII2(C9H10BN6)2(CN)6(CH3OH)4]·2CH3OH, two [FeIII(Tp)(CN)3]−anions [Tp is hydrotris(pyrazoylborate)] are bridged by an [FeII(MeOH)4]2+cation, forming a centrosymmetric trinuclear unit. These units are connectedviaO—H...O and O—H...N hydrogen bonds involving the uncoordinated methanol solvent molecules, forming a three-dimensional network.
(Cyanido-κC)(2,2-diphenylacetamido-κ2N,O)bis(η5-pentamethylcyclopentadienyl)zirconium(IV)
Authors: Becker Lisanne , Spannenberg Anke , Arndt Perdita , Rosenthal Uwe
Published: January 2014

In the title compound, [Zr(C10H15)2(C14H12NO)(CN)], the ZrIVatom is coordinated by two pentamethylcyclopentadienyl ligands, the amidate ligandviathe N and O atoms, and an additional C[triple-bond]N ligand. The four-membered metallacycle is nearly planar (r.m.s. deviation = 0.008 Å). In the crystal, the molecules are connected into centrosymmetric dimersviapairs of N—H...N hydrogen bonds.
N-(4-Methylphenylsulfonyl)-3-nitrobenzamide
Authors: Sreenivasa S. , Nanjundaswamy M. S. , Sudha A. G. , Pampa K. J. , Lokanath N. K. , Suchetan P. A.
Published: January 2014

In the title compound, C14H12N2O5S, the dihedral angle between the aromatic rings is 86.29 (1)° and the conformation between the C=O bond of the amide group and themeta-NO2group issyn. The C—S—N—C torsion angle is −65.87 (19)° and the molecule has an L-shaped conformation. In the crystal, the molecules are connected into inversion dimers through pairs of N—H...O hydrogen bonds and C—H...O interactions formingR22(8) andR22(14) loops, respectively. The dimers are connected by further C—H...O interactions, thereby forming (100) sheets.
N-(4-Methoxybenzoyl)benzenesulfonamide
Authors: Sreenivasa S. , Nanjundaswamy M. S. , Madankumar S. , Lokanath N. K. , Suresha E. , Suchetan P. A.
Published: January 2014

In the title compound, C14H13NO4S, the dihedral angle between the aromatic rings is 69.81 (1)°; the dihedral angle between the planes defined by the S—N—C=O segment of the central chain and the sulfonyl benzene ring is 74.91 (1)°. In the crystal, the molecules are linked by weak N—H...O hydrogen bonds intoC(4) chains running along [100]. The molecules in adjacent chains are linked by weak C—H...O interactions, generatingR22(16) dimeric pairs. Weak C—H...π interactions connect the double chains into (001) sheets.
Understanding the elements of a digital library project plan: part 1
Authors: Cervone H. Frank
Published: January 2014

Purpose

This, the first of a two‐part article, aims to provide an overview of the elements necessary to develop an effective project plan for digital library projects.

Design/methodology/approach

The paper takes the form of a review and summarization of the literature and thinking in project management applied to the digital library context.

Findings

It is found that there are many different approaches to creating a digital library project plan, but five basic elements are essential for developing an effective digital library project plan.

Originality/value

This article provides a succinct synopsis and checklist for creating a digital library project plan.
Are drug arrests a valid measure of drug use? A time series analysis
Authors: Moffatt Steve , Wan Wai‐Yin , Weatherburn Don
Published: January 2014

Purpose

The purpose of this paper is to determine whether trends in arrests for heroin, amphetamine‐type substances (ATS) and cocaine can be used as indicators of trends in the use of these drugs.

Design/methodology/approach

The question was addressed using ARIMA models to analyse the relationship between arrests and emergency department (ED) admissions for narcotics, amphetamine type substances (ATS) and cocaine.

Findings

Strong positive correlations were found for the narcotics and cocaine series between arrests and EDs in the same month (contemporaneous correlation) and between arrests in the current month and overdoses in earlier months (lagged correlation). The contemporaneous correlation between ATS arrests and EDs was slightly less strong than the lagged correlations at two and four months. A jump in ATS EDs, was followed by a jump in arrests in the same month and then two and four months later.

Practical implications

Arrests for narcotics use/possession, ATS use/possession and cocaine use/possession may in some circumstances provide useful intelligence about drug trends and/or a basis for evaluating the impact of police drug law enforcement activity on the use of narcotics, ATS and cocaine when other stronger measures of drug use are not available.

Originality/value

Efforts to evaluate local drug law enforcement activity on illicit drug use have been hampered by poor measures of trends in illicit drug use at small area levels. This is the only study the authors are aware of that has examined the long‐term relationship between illicit drug arrests and emergency department admissions for illicit drug use.
Transparency in pricing and its effect on perceived price fairness
Authors: L. Ferguson Jodie , Scholder Ellen Pam
Published: January 2014

Purpose

– This research aims to examine the effects of transparency in pricing (i.e. disclosure of a price increase and extent of explanation) on perceived price fairness when a firm increases price.

Design/methodology/approach

– US adult consumer panelists participated in two online experiments.

Findings

– Consumers perceive a firm's price increase as more fair when the firm discloses the increase itself as compared to an outside source disclosing it. For a small price increase, a limited explanation was perceived as more fair; for a larger price increase, a more detailed aligned cost explanation was perceived as more fair.

Research limitations/implications

– Firms who must raise prices may increase consumer perceptions of price fairness by disclosing the price increase and providing an appropriate explanation matched to the size of the increase.

Originality/value

– This research focuses on the effects of being more transparent about pricing in the case of a price increase. Perceived price fairness is affected by who discloses the price increase, the amount of the price increase and the extent to which reasons are revealed and aligned with the firm's costs.
Sales training: comparing multinational and domestic companies
Authors: M. Attia Ashraf , Asri Jantan M. , Atteya Nermine , Fakhr Rana
Published: January 2014

Purpose

– The purpose of this paper is to examine similarities and differences of current state of initial sales training practices of both domestic and multinational corporations (MNCs) in Egypt. This paper begins by reviewing the cross-cultural sales training research and developing hypotheses.

Design/methodology/approach

– A methodology section follows, including measurement instruments, sample and data collection, and validity and reliability measures. The data were collected from sales managers, marketing managers, and sales supervisors.

Findings

– Results reveal that MNCs differ significantly from their domestic counterparts in the following sales training phases: needs determination, objective setting, program methods, program contents, and training evaluation.

Research limitations/implications

– In-depth discussion, managerial implications, and suggestions for future research are provided.

Originality/value

– There has been very limited research published on sales training practices in the Middle East (Yaseen and Khanfar, 2009) and Egypt in particular (e.g. Attia and Honeycutt, 2012; Honeycutt et al., 2001). This research sheds further highlights on sales training practices in Egypt and adds in filling in the gap in sales training literature by addressing sales training in Egypt.
Density dependence, precipitation and biological control agent herbivory influence landscape‐scale dynamics of the invasive Eurasian plant Linaria dalmatica
Authors: Weed Aaron S. , Schwarzländer Mark
Published: January 2014

Resource availability and natural enemies are among the most commonly cited mechanisms affecting competitive ability of invasive plants, but their simultaneous effects on plant dynamics are seldom evaluated in the field. Understanding how endogenous and exogenous factors affect invasive plant abundance is essential when evaluating the impact of classical weed biological control agents because misinterpretations of the mechanisms regulating plant demography may bias inference of herbivore impact.

In this study, we report results from a citizen‐science monitoring programme initiated to evaluate the effects of the stem‐mining weevil Mecinus janthiniformis on the Eurasian invasive weed Dalmatian toadflax Linaria dalmatica. We used a discrete model of population dynamics to evaluate the relative importance of endogenous and exogenous processes affecting changes in ramet density of L. dalmatica at 38 spatially replicated sites in Idaho, USA.

Analysis of per‐capita population growth rates based on ramet density indicated the presence of direct density dependence, which was most likely due to intraspecific competition. Changes in ramet density were not influenced by the abundance of the resident plant community.

Precipitation had a strong, positive effect on ramet density of L. dalmatica, while the abundance of M. janthiniformis had a weaker, but significant, negative effect after accounting for the density dependence. There was no support for an interactive effect between precipitation and herbivory.

Synthesis and applications. Our results indicate that biological control is an important factor affecting weed population growth at the landscape scale, but they also suggest that biological control impact may vary considerably on local infestations due to site‐specific variation in rainfall and density‐dependent processes. We recommend that invasive plant management strategies integrate precipitation and biological control agent monitoring into their programmes to estimate expected biological control efficacy. Alternative control methods should be prioritized in areas where herbivore impact is expected to be low.
Staying ‘in the zone’ but not passing the ‘point of no return’: embodiment, gender and drinking in mid‐life
Authors: Lyons Antonia C. , Emslie Carol , Hunt Kate
Published: January 2014

Public health approaches have frequently conceptualised alcohol consumption as an individual behaviour resulting from rational choice. We argue that drinking alcohol needs to be understood as an embodied social practice embedded in gendered social relationships and environments. We draw on data from 14 focus groups with pre‐existing groups of friends and work colleagues in which men and women in mid‐life discussed their drinking behaviour. Analysis demonstrated that drinking alcohol marked a transitory time and space that altered both women's and men's subjective embodied experience of everyday gendered roles and responsibilities. The participants positioned themselves as experienced drinkers who, through accumulated knowledge of their own physical bodies, could achieve enjoyable bodily sensations by reaching a desired level of intoxication (being in the zone). These mid‐life adults, particularly women, discussed knowing when they were approaching their limit and needed to stop drinking. Experiential and gendered embodied knowledge was more important in regulating consumption than health promotion advice. These findings foreground the relational and gendered nature of drinking and reinforce the need to critically interrogate the concept of alcohol consumption as a simple health behaviour. Broader theorising around notions of gendered embodiment may be helpful for more sophisticated conceptualisations of health practices.
Alkaptonuric ochronosis: a clinical study from Ardabil, Iran
Authors: Azami Ahad , Maleki Nasrollah , Tavosi Zahra
Published: January 2014

Objective

Ochronosis is a term used to describe pigment deposition that occurs in the connective tissues of patients with alkaptonuria, an autosomal recessive disorder that results from a deficiency of homogentisic acid oxidase. Brown or blue‐gray discoloration of the skin may be seen on the axillary and inguinal areas, face, palms or soles. In addition, blue‐black discoloration can be apparent on skin overlying cartilage in which the pigment is deposited, such as the ears. The sclerae are also typically involved. The cheapest screening test to perform prior to expensive lab tests is the urine oxidation test: having it standing in light for a period of 24 h when suspicion has risen.

Methods

Retrospective analysis of patients with ochronotic arthropathy seen between September 2011 to September 2013 was carried out.

Results

Seven patients (four male, three female) with ochronotic arthropathy were seen, their mean age was 46.1 years. All patients had bluish‐black pigmentations of the ear cartilage and sclera. Spondylosis was seen in all, whereas peripheral arthritis was present in five patients. Moderate aortic insufficiency and calcification of the aortic valve was detected in one male patient. Urine screening for homogentisic acid was positive in all seven patients.

Conclusion

Alkaptonuria is a rare autosomal recessive disorder of the metabolism caused by deficiency of homogentisic acid oxidase. It is suggested that more widespread screening should be undertaken in order to assess the true incidence of the disorder.
Relationship of cultural values to counterproductive work behaviour: The mediating role of job stress
Authors: Smithikrai Chuchai
Published: January 2014

The purposes of this study were to investigate how cultural values are related to counterproductive work behaviour (CWB), and to examine whether individuals' job stress acts as a mediator between cultural types and CWB. Using an anonymous questionnaire survey, the sample was comprised of 440 employees working in government institutes and private sectors in Thailand. The results show that job stress not only has a direct relationship to CWB, but also partially mediates the relationship between cultural values and CWB. The strong mediating links were between horizontal collectivism and CWB and between vertical individualism and CWB.
The Architecture of Collective Intimacy: Masonic Friendships as a Model for Collective Attachments
Authors: Kaplan Danny
Published: January 2014

Despite a growing recognition that interpersonal friendship informs wider forms of solidarity, there is little systematic analysis as to how community members extend the logic of friendship and intimacy to broader organizational and societal context. Masonic organizational practices provide a useful model for this inquiry. Drawing on an ethnographic study of contemporary Israeli Freemasonry, I examine the intersections of interpersonal, public, and collective intimacy in members’ ritual activities and everyday life. The juxtaposition of mundane sociability and Masonic sacred rituals serves to rescale the distance between interpersonal friendship and communal solidarity. As members take on the roles of citizen, bureaucrat, priest, and president concomitantly, they partly collapse the distinctions between personal and collective ties, between the familiar and the revered. These intersections of intimacy are offered as a programmatic research strategy to study how institutionalized patterns of sociability inform civic and national attachments.