bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells
Authors: Roy Sobhan , Ly Dalam , Li Nan-Sheng , Altman John D. , Piccirilli Joseph A. , Moody D. Branch , Adams Erin J.
Published: October 2014

Significance

Mycobacterium tuberculosisinfects more than one-third of humans yet no effective vaccine exists. This study shows how a subset of αβ T cells targetsM. tuberculosislipid antigens that are presented by the MHC molecule CD1c. In contrast to many T cells that recognize CD1d, these αβ T cells express diverse T-cell receptors and have differing footprints on CD1c during lipid recognition. This study also shows that some CD1c-specific αβ T cells are exquisitely specific for the lipid presented, whereas others have a more promiscuous reactivity, demonstrating that the αβ T-cell response to CD1c lipid presentation is diverse and adaptable. These data may provide additional resources for development of MHC-independent vaccines againstM. tuberculosis.
How Body Size and Food Availability Influence First‐Winter Growth and Survival of a Stocked Piscivore
Authors: Kallis Jahn L. , Marschall Elizabeth A.
Published: October 2014

The first winter of life can play an important role in the success of age‐0 fishes. First‐winter survival is often size dependent, with larger fish exhibiting higher survival than small fish. Cohorts of age‐0 saugeye female Walleye Sander vitreus × male Sauger S. canadensis stocked into Ohio reservoirs exhibit overwinter shifts toward larger body sizes; however, it is unclear whether growth, size‐dependent mortality, or size‐dependent emigration underlie this phenomenon. Saugeye may experience low prey availability during the overwinter period, making them especially vulnerable to starvation. Furthermore, survivors emerging from winter in poor energetic condition may experience reduced spring foraging success and growth. We used a combination of overwinter PIT tag studies in the field and overwinter outdoor pool experiments to understand these direct and indirect effects of winter on survival and size distributions of cohorts of saugeye. Using PIT tags to allow us to track growth of individuals in reservoirs, we found that saugeye of all sizes increased in length over winter, there was no evidence of size‐dependent overwinter mortality, and rates of emigration out of the reservoir were greater for large saugeye than small saugeye. Thus, only growth rate, and not mortality or emigration biased toward small fish, can explain the observed overwinter shift in size distributions. In pool experiments, we found no direct effects of winter on survival, even in the complete absence of food, and no negative consequences of starvation over the winter on the ability of saugeye to resume feeding in the spring. Our results suggest that shifts in size distributions of first‐year cohorts over winter are driven by growth rather than mortality. Neither direct effects of first winter on survival nor indirect effects mediated through effects of starvation on future foraging ability are important in recruitment success of saugeye in Ohio reservoirs.

Received March 18, 2014; accepted June 30, 2014
Thermal Performance of Three Rainbow Trout Strains at Above‐Optimal Temperatures
Authors: Hartman Kyle J. , Porto Michael A.
Published: October 2014

Studies have predicted declines in trout habitat of over 50% given projected climate warming scenarios. Therefore, knowledge of the performance of trout strains at elevated temperature is critical for management of trout fisheries and trout strains under climate change. Our objectives were to compare the performance of three strains of Rainbow Trout Onchorynchus mykiss at elevated temperatures. We compared growth, consumption, and feed efficiency at 20°C and 22°C, and critical thermal maxima (CTM) among the strains. The Case Western strain is registered as a warm‐tolerant strain with the National Fish Strain Registry, and it did achieve a significantly higher CTM (31.29°C) than the Kamloops (31.14°C) but not the Wytheville (31.20°C) strain. Such small differences are likely not biologically significant. While the CTM of the Case Western strain was higher than that of the Kamloops, the Case Western strain consistently performed poorer than the other strains in feeding and growth experiments at 20°C and 22°C. Our results add to the growing body of literature suggesting that differences in thermal performance do exist between strains of trout. While there is debate about whether these differences are due to evolutionary adaptation to local environmental conditions or phenotypic plasticity, the differences being found in thermal performance of trout suggests future research aimed at improving thermal performance via thermal testing and selective breeding may yield stock with improved tolerance and growth at warmer temperatures.

Received April 17, 2014; accepted June 24, 2014
An unlikely bulwark of Sovietness: cross-border travel and Soviet patriotism in Western Ukraine, 1956–1985
Authors: Wojnowski Zbigniew
Published: October 2014

Focusing on the development of travel between the borderlands of Ukraine and Soviet satellite states in Eastern Europe, this article explores what it meant to be Soviet outside the Russian core of the USSR between the mid-1950s and the mid-1980s. The cautious opening of the Soviet border was part of a larger attempt to find fresh sources of popular support and enthusiasm for the regime's “communist” project. Before the Prague Spring of 1968 in particular, official policies and narratives of travel thus praised local inhabitants who crossed the Soviet border for supposedly overcoming age-old hatreds to build a brighter future in Eastern Europe. By the 1970s, however, smuggling and cultural consumption discredited the idea of “internationalist friendship.” This encouraged residents of Ukraine to speak and write about the continuing importance of the Soviet border. The very idea of Sovietness was defined in national terms, as narratives of travel emphasized that Soviet citizens were inherently different from ethno-national groups in the people's democracies. Eastern Europe thus emerged as an “other” that highlighted the Soviet character of territories incorporated into the USSR after 1939, helping to obscure western Ukraine's troubled past and leading to the emergence of new social hierarchies in the region.
Increasing Juvenile Coho Salmon Densities during Early Recolonization Have Not Affected Resident Coastal Cutthroat Trout Growth, Movement, or Survival
Authors: Buehrens T. W. , Kiffney P. , Pess G. R. , Bennett T. R. , Naman S. M. , Brooks G. , Quinn T. P.
Published: October 2014

The process of salmon colonization in the upper Cedar River and Rock Creek, Washington, following the installation of a fish ladder at Landsburg Diversion Dam in 2003, offered an opportunity to measure the effects of interspecific interactions on the dynamics of resident fish populations. Rapid recolonization by Coho Salmon Oncorhynchus kisutch provided a natural experiment to determine the influence of Coho Salmon densities on the growth, movement, and survival of resident Coastal Cutthroat Trout O. clarkii clarkii relative to other abiotic and biotic factors such as habitat quality, environmental conditions, and conspecific density. During 14 seasonal sampling events from 2005 to 2009, we PIT-tagged 1,851 and recaptured 394 Cutthroat Trout in Rock Creek, collected habitat data, enumerated fish populations, and monitored fish movements with PIT tag antenna arrays. Trout growth varied significantly among seasons and was greatest during spring and early summer. Mean juvenile Coho Salmon density in summer and fall increased eightfold from 0.04 to 0.32 and from 0.08 to 0.68 fish/m2, respectively, approaching levels seen in established populations, but did not explain variation in trout growth, movement, or survival. Summer growth of trout parr and fry were both negatively correlated with the density of conspecifics but were positively correlated with total salmonid density. Additionally, trout parr growth was positively correlated with stream discharge, whereas trout fry growth was negatively correlated with initial size and declined during the course of the study. However, abiotic and biotic explanatory variables accounted for little of the variation in trout growth, movement, and survival, suggesting that a great deal of individual variation exists. Overall, trout were largely unaffected by Coho Salmon colonists despite large increases in juvenile Coho Salmon density, though this may change if salmon populations continue to grow.

Received October 18, 2013; accepted May 5, 2014
Adfluvial Life History in Spring Chinook Salmon from Quartzville Creek, Oregon
Authors: Romer Jeremy D. , Monzyk Fred R.
Published: October 2014

Through spawning ground and snorkel surveys, we confirmed the presence of adfluvial spring Chinook Salmon Oncorhynchus tshawytscha in a tributary upstream from a high-head dam in the upper Willamette River in northwest Oregon. Spring Chinook Salmon previously had been extirpated above the dam but juvenile hatchery fish were released in the reservoir in subsequent years. In 2012, we recovered six carcasses of adfluvial Chinook Salmon adults, identified nine live adults, and recorded nine redds. Analyses of scales from carcasses revealed those fish were ages 5–6. Otolith microchemistry from an unmarked adult female Chinook Salmon did not indicate ocean residence, and no hatchery thermal marks were observed, suggesting this fish was the progeny of adfluvial adults. In 2013, we observed one live, unclipped adult and three juvenile Chinook Salmon. We conclude that adfluvial spring Chinook Salmon exist in Green Peter Reservoir and successfully reproduce. This is the first documentation of adfluvial Chinook Salmon in Oregon, and this unusual life history should be considered in the context of research, monitoring, and recovery actions pertaining to ongoing reintroduction programs for threatened Willamette River spring Chinook Salmon above dams.

Received February 21, 2014; accepted May 7, 2014
Evaluating the Accuracy and Precision of Multiple Abundance Estimators Using State-Space Models: A Case Study for a Threatened Population of Chinook Salmon in Johnson Creek, Idaho
Authors: Chasco Brandon E. , Ward Eric J. , Hesse Jay A. , Rabe Craig , Kinzer Ryan , Vogel Jason L. , Orme Rick
Published: October 2014

Over the last century, Chinook Salmon Oncorhynchus tshawytscha populations in the Pacific Northwest have experienced dramatic declines, leading to many of them being listed as threatened under the Endangered Species Act. The abundance of these threatened populations relative to the thresholds for delisting remains the primary metric for assessing recovery, yet determining the true population abundances from multiple survey types with unknown levels of accuracy and precision remains difficult. The abundance of the spring–summer Chinook Salmon population in Johnson Creek, Idaho, has been measured using a mark–recapture survey and three different redd count surveys (RCSs) that vary temporally and spatially. Using a state-space model, we determined the accuracy and precision of each survey type by decoupling the observation error of the survey from the process error describing the annual variability in the true population abundance. We then extended the results of the model to determine the risk of managers’ incorrectly delisting the population (a type I error) or incorrectly keeping it listed (a type II error). Finally, we show that salmon managers with data-limited populations (primarily those with only single-pass index RCSs) might use the results of our risk analysis to determine whether expanding survey efforts to minimize management risks is appropriate when they are confronted with dwindling financial resources. For example, we determined that although both the multiple-pass extended RCS (CV = 0.06) and mark–recapture surveys (CV = 0.14) provide unbiased estimates of salmon abundance in Johnson Creek, the mark–recapture study can have annual costs that are 30–100 times greater. Managers may determine that directing research funds toward acquiring information unique to weir-based mark–recapture surveys (i.e., migration timing, good genetics samples, etc.) may not be justified for all populations.

Received October 7, 2013; accepted March 5, 2014
Effect of Fishing Success on Angler Satisfaction on a Central Oregon Rainbow Trout Fishery: Implications for Establishing Management Objectives
Authors: McCormick Joshua L. , Porter Timothy K.
Published: October 2014

Understanding the relationship between fish populations, fishing success, and angler satisfaction is critical for effective fisheries management. Our objectives were to quantify angler satisfaction in a fishery for Rainbow Trout Oncorhynchus mykiss in central Oregon and examine the factors influencing angler satisfaction. Multinomial logistic regression models were used to determine the effect of several variables, including fishing success, on angler satisfaction. Measures of fishing success were present in all of the top candidate models. The probability of an increase in angler satisfaction rating was positively related to mean length and number of fish caught per hour. However, younger anglers tended to have higher satisfaction ratings at lower mean length and catch rates of fish than did older anglers. These models provided information on the expected percentage of anglers that will be satisfied given the average length of fish caught and the number of fish caught per hour. These results can be used to establish quantitative, measurable, management objectives that will satisfy desired percentages of anglers and lead to more effective fisheries management.

Received February 9, 2014; accepted May 27, 2014
Integration of Auxiliary Information in Statistical Catch-at-Age (SCA) Analysis of the Saginaw Bay Stock of Walleye in Lake Huron
Authors: Fielder David G. , Bence James R.
Published: October 2014

Estimates of mortality rates and abundance for the Saginaw Bay stock of Walleye Sander vitreus has traditionally been performed with an analysis of tag returns using a Brownie-style analysis. An estimation approach that more fully accounted for sources of exploitation in addition to the recreational fishery in Saginaw Bay and inclusive of the rest of Lake Huron was needed. We developed a statistical catch-at-age model to accomplish this and evaluated four versions including three different treatments of natural mortality (M): a constant value, age-based M values, and time-varying M values. Deviance information criterion model selection procedures indicated that an age-based M model version was optimal. We also evaluated an integrated version that incorporated tag returns as auxiliary information for the recreational component. In this case, model selection was based on conformity between observed and predicted data and model convergence. The integrated version was ruled out due to poor agreement of the observed and predicted values and predictions of abundance that were not reflected by the fisheries. We concluded that the component of the population used for tagging may exhibit dynamics that differ from the rest of the stock. Total annual mortality of Walleyes was greatest for older ages in all fisheries and ranged from 32% for age-2 fish to 39% for fish of ages 10 and older. The recreational fishery accounted for the majority of fishing mortality, but the commercial trap-net fishery in the main basin of Lake Huron and bykill from other trap nets in the bay accounted for proportionally greater fishing mortality of younger ages of fish. Abundance peaked in 2007 at 4 million Walleyes age2 and older, but estimates indicated a previous period of high abundance in the late 1980s, forcing the reconsideration of the past stock as depressed and dependent on stocking.

Received January 8, 2014; accepted June 11, 2014
Low-Cost Restoration Techniques for Rapidly Increasing Wood Cover in Coastal Coho Salmon Streams
Authors: Carah Jennifer K. , Blencowe Christopher C. , Wright David W. , Bolton Lisa A.
Published: October 2014

Like many rivers and streams in forests of the Pacific Northwest, California north coast rivers and streams have been depleted of downed wood through timber harvest and direct wood removal. Due to the important role of wood in creating and maintaining salmonid habitat, wood augmentation has become a common element of stream restoration. Restoration efforts in North America often focus on building anchored, engineered wood structures at the site scale; however, these projects can fail to meet restoration goals at the watershed scale, do not closely mimic natural wood loading processes or dynamics, and can be expensive to implement. For critically imperiled populations of Coho Salmon Oncorhynchus kisutch in California, there is a strong impetus to achieve as much habitat restoration as possible in priority watersheds in the shortest time and with limited resources, so cost-efficient techniques are necessary. In this multi-site project, we investigated unanchored techniques for wood loading to evaluate cost and contribution to salmonid habitat in Mendocino County, California. Over a period of 6 years, 72.4 km of stream were treated with 1,973 pieces of strategically placed wood. We found that unanchored wood loading techniques were much less costly than commonly used anchored techniques, reliably improved habitat, and retained wood at high rates (mean = 92%) in small- to moderate-sized streams, at least over the short term (<6 years). The average cost of design and construction for the unanchored projects was US$259 per log, equivalent to 22% of the cost associated with the anchored wood augmentation methods examined here. Our results suggest that this unanchored wood loading approach has the potential to increase the pace and scale at which wood augmentation projects are implemented in the Pacific Northwest and beyond.

Received January 22, 2014; accepted June 25, 2014
Validation of Annuli Formation in Pectoral Fin Rays from Shovelnose Sturgeon in the Lower Platte River, Nebraska
Authors: Rugg M. L. , Hamel M. J. , Pegg M. A. , Hammen J. J.
Published: October 2014

Fish age is commonly estimated by counting bands on calcified structures. Age estimates are used to calculate information on population dynamics such as growth, mortality, and recruitment. Pectoral fin rays are the most frequently used structure to age sturgeon species, yet little work has been done to validate annuli formation. We collected Shovelnose Sturgeon Scaphirhynchus platorynchus monthly from the lower Platte River, Nebraska, during 2011 and 2012 and removed the leading, left pectoral fin ray from each fish captured. We used marginal increment analysis to assess the validity of annual deposition of growth marks on pectoral fin rays. There were two complete cycles of increasing and decreasing increment values between March and November within each year. Mean marginal increments showed minimal peaks in March, July, and October followed by a decrease in increment length during April, September, and November. However, mean marginal increments were similar between months in both years. These results suggest there is no discernible pattern in growth ring deposition for Shovelnose Sturgeon in the lower Platte River and that their use for age and growth analyses would likely lead to biased estimates. Inaccuracies in age assignment can lead to errors when calculating population dynamic parameters and, ultimately, misguided management decisions. We recommend that alternate methods for estimating the ages of Shovelnose Sturgeon be explored.

Received February 25, 2014; accepted July 4, 2014
Indian South Africans and the Black Consciousness Movement under apartheid
Authors: Desai Ashwin
Published: October 2014

In the late 1960s, “non-White” university students marched out of the white dominated but, at that stage, still multiracial, National Union of South African Students. They formed the South African Students Organisation (SASO) and began formulating an ideology called Black Consciousness. At its heart, the Black Consciousness Movement (BCM) called for the unity of South Africa’s oppressed, which they defined as African, Coloured and Indian. Those who were not students found a home in the Black People’s Convention. Many students of Indian origin joined SASO and played leading roles in the development of the BCM. This article traces these developments, paying particular attention to Indian women, seeking to understand their motivations in joining the movement, and record their experiences inside the BCM. Their story has to date been largely ignored, primarily because the Indian male members of BCM who stood trial and went to Robben Island during this period have tended to overwhelm the narrative, and in more recent times, the post-apartheid liberation story has been dominated by the journey of the African National Congress.
Transnational locality: Diasporas and indentured South Asians
Authors: Reddy Movindri
Published: October 2014

This article investigates why Diasporas are often considered threatening to state security, especially during periods of national or international uncertainty. The central argument is that this perception can best be understood if they are seen as inhabiting atransnational locality, a space that encapsulates both their indigenization and transnationality. In other words, it is limiting to view Diasporas in terms of a home–host trope; this relies on a stateto- state structural analysis that elides the complex identities associated with Diasporas and the abiding perception that they are a threat. What is distinctive about Diasporas is that they are indigenized over time (Creolized, hybridized), but they retain a transnational identity that is associated with a perceived homeland (real or imagined). While they are insiders in the nation-state, they are also outsiders in all states – they reside in a transnational locality that is rooted, but also removed. The article relies on empirical evidence from the Indian indentured diaspora in Fiji and South Africa. It is proposed that the transnationality intrinsic to their diaspora identities not onlymarksthem “Indian”, but also alienates them from other national ethnic groups and from India.
Where did it come from, where do you go? Direction sources influence navigation decisions during spatial uncertainty
Authors: Brunyé Tad T. , Gagnon Stephanie A. , Gardony Aaron L. , Gopal Nikhil , Holmes Amanda , Taylor Holly A. , Tenbrink Thora
Published: October 2014

Previous research on route directions largely considers the case when a knowledgeable route-giver conveys accurate information. In the real world, however, route information is sometimes inaccurate, and directions can lead navigators astray. We explored how participants respond to route directions containing ambiguities between landmarks and turn directions, forcing reliance on one or the other. In three experiments, participants read route directions (e.g., To get to the metro station, take a right at the pharmacy) and then selected from destinations on a map. Critically, in half of the trials the landmark ( pharmacy) and turn ( right) directions were conflicting, such that the participant had to make a decision under conditions of uncertainty; under these conditions, we measured whether participants preferentially relied upon landmark- versus direction-based strategies. Across the three experiments, participants were either provided no information regarding the source of directions (Experiment 1), or told that the source of directions was a GPS device (Experiment 2), or a human (Experiment 3). Without information regarding the source of directions, participants generally relied on landmarks or turn information under conditions of ambiguity; in contrast, with a GPS source participants relied primarily on turn information, and with a human source on landmark information. Results were robust across gender and individual differences in spatial preference. We discuss these results within the context of spatial decision-making theory and consider implications for the design and development of landmark-inclusive navigation systems.
Perspectives for change in Tunisia, Egypt and Syria: the military factor and implications of previous authoritarian regimes
Authors: Battera Federico
Published: October 2014

This article argues that differences in Arab authoritarian regimes were mainly linked to the relationship between the state, the political party in power and the military. By exploring such differences in Tunisia, Egypt and Syria prior to the 2011 crisis, they are explained in the context of the political changes that ensued in the wake of the crisis. How the army played the dual role of instigating change while impeding it at crucial points in the transitional process is described. The mutual lack of autonomy between the state, the party and the military appears to have been a key factor in impeding change, whereas a clear separation of the functions of these institutions was more likely to enable political change to come about.
Female labour participation and pay equity in Arab countries: commonalities and differences
Authors: Sidani Yusuf M. , Feghali Tony
Published: October 2014

While there is a common belief that female labour indicators in Arab countries demonstrate a problematic situation, little is understood about the varieties within countries in that region. This paper attempts to draw a segmentation of the Arab world to show how different countries differ in this regard. It looks at two specific measures: the level of female participation as a percentage of male participation (FPM), and the female earned income to male income (FIM). Statistics from 20 Arab countries generated four clusters in which those countries are classified. Female labour indicators in most countries in the Arab world show similar patterns found in other countries in their stage of development. This confirms earlier research that indicates that women’s labour participation decreases as societies move away from agriculture into manufacturing, services and industry. Only four countries are identified as outliers whose labour indicators can be understood within the context of the cultural values that dominate. The implications are discussed and individual research on female labour within each Arab country is invited.
GSK3 and Polo-like kinase regulate ADAM13 function during cranial neural crest cell migration
Authors: Abbruzzese Genevieve , Cousin Hélène , Salicioni Ana Maria , Alfandari Dominique
Published: October 2014

ADAMs are cell surface metalloproteases that control multiple biological processes by cleaving signaling and adhesion molecules. ADAM13 controls cranial neural crest (CNC) cell migration both by cleaving cadherin-11 to release a promigratory extracellular fragment and by controlling expression of multiple genes via its cytoplasmic domain. The latter activity is regulated by γ-secretase cleavage and the translocation of the cytoplasmic domain into the nucleus. One of the genes regulated by ADAM13, the protease calpain8, is essential for CNC migration. Although the nuclear function of ADAM13 is evolutionarily conserved, it is unclear whether the transcriptional regulation is also performed by other ADAMs and how this process may be regulated. We show that ADAM13 function to promote CNC migration is regulated by two phosphorylation events involving GSK3 and Polo-like kinase (Plk). We further show that inhibition of either kinase blocks CNC migration and that the respective phosphomimetic forms of ADAM13 can rescue these inhibitions. However, these phosphorylations are not required for ADAM13 proteolysis of its substrates, γ-secretase cleavage, or nuclear translocation of its cytoplasmic domain. Of significance, migration of the CNC can be restored in the absence of Plk phosphorylation by expression of calpain-8a, pointing to impaired nuclear activity of ADAM13.
Microvascular Free Flap for Total Eyelid Reconstruction With a Visually Useful Eye
Authors: Ghadiali Larissa K. , Patel Payal , Levine Jamie P. , Gold Katherine G. , Lisman Richard D.
Published: October 2014

Total eyelid loss, full thickness loss of the upper and lower eyelids, is uncommon and surgically challenging. Eyelid reconstruction after such injuries can be further complicated by loss of adjacent tissue. When tissue for local flaps is unavailable, free flaps must be considered. Few cases of total eyelid reconstruction via microvascular free flap have been reported, especially with an intact globe and good visual acuity. In this report, we describe the use of a microvascular free flap based on the radial artery for total eyelid reconstruction in a patient with an intact globe and useful visual acuity.
From induction to conduction: how intrinsic transcriptional priming of extrinsic neuronal connectivity shapes neuronal identity
Authors: Russ Jeffrey B. , Kaltschmidt Julia A.
Published: October 2014

Every behaviour of an organism relies on an intricate and vastly diverse network of neurons whose identity and connectivity must be specified with extreme precision during development. Intrinsically, specification of neuronal identity depends heavily on the expression of powerful transcription factors that direct numerous features of neuronal identity, including especially properties of neuronal connectivity, such as dendritic morphology, axonal targeting or synaptic specificity, ultimately priming the neuron for incorporation into emerging circuitry. As the neuron's early connectivity is established, extrinsic signals from its pre- and postsynaptic partners feedback on the neuron to further refine its unique characteristics. As a result, disruption of one component of the circuitry during development can have vital consequences for the proper identity specification of its synaptic partners. Recent studies have begun to harness the power of various transcription factors that control neuronal cell fate, including those that specify a neuron's subtype-specific identity, seeking insight for future therapeutic strategies that aim to reconstitute damaged circuitry through neuronal reprogramming.
A note on improved
F
-expansion method combined with Riccati equation applied to nonlinear evolution equations
Authors: Islam Md. Shafiqul , Khan Kamruzzaman , Akbar M. Ali , Mastroberardino Antonio
Published: October 2014

The purpose of this article is to present an analytical method, namely the improved
F
-expansion method combined with the Riccati equation, for finding exact solutions of nonlinear evolution equations. The present method is capable of calculating all branches of solutions simultaneously, even if multiple solutions are very close and thus difficult to distinguish with numerical techniques. To verify the computational efficiency, we consider the modified Benjamin–Bona–Mahony equation and the modified Korteweg-de Vries equation. Our results reveal that the method is a very effective and straightforward way of formulating the exact travelling wave solutions of nonlinear wave equations arising in mathematical physics and engineering.
A gradient field defeats the inherent repulsion between magnetic nanorods
Authors: Gu Yu , Burtovyy Ruslan , Custer John , Luzinov Igor , Kornev Konstantin G.
Published: October 2014

When controlling the assembly of magnetic nanorods and chains of magnetic nanoparticles, it is extremely challenging to bring them together side by side while keeping a desired spacing between their axes. We show that this challenge can be successfully resolved by using a non-uniform magnetic field that defeats an inherent repulsion between nanorods. Nickel nanorods were suspended in a viscous film and a non-uniform field was used to control their placement. The in-plane movement of nanorods was tracked with a high-speed camera and a detailed image analysis was conducted to quantitatively characterize the behaviour of the nanorods. The analysis focused on the behaviour of a pair of neighbour nanorods, and a corresponding dynamic model was formulated and investigated. The complex two-dimensional dynamics of a nanorod pair was analysed analytically and numerically, and a phase portrait was constructed. Using this phase portrait, we classified the nanorod behaviour and revealed the experimental conditions in which nanorods could be placed side by side. Dependence of the distance between a pair of neighbour nanorods on physical parameters was analysed. With the aid of the proposed theory, one can build different lattices and control their spacing by applying different field gradients.
Epilithonimonas ginsengisoli sp. nov., isolated from soil of a ginseng field
Authors: Hoang Van-An , Kim Yeon-Ju , Ponnuraj Shree Priya , Nguyen Ngoc-Lan , Hwang Kyu-Hyon , Yang Deok-Chun
Published: October 2014

A novel Gram-staining-negative, rod-shaped bacterium, designated DCY78T, was isolated from soil of a ginseng field in Yeon-cheon province (38° 04′ 00″ N 126° 57′ 00″ E), Republic of Korea. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY78T belonged to the genus

Epilithonimonas

and was most closely related to

Epilithonimonas lactis

DSM 19921T (98.5 % sequence similarity) and

Epilithonimonas tenax

DSM 16811T (97.8 %). Growth occurred at 10–30 °C with an optimum temperature of 28 °C. The pH range for growth was pH 5.5–8.0. The major polar lipids were found to be phosphatidylethanolamine three unidentified amino lipids and one unidentified polar lipid. The only predominant quinone was MK-6. The major polyamines were sym-homospermidine and spermidine. The major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content was 37.9 mol%. On the basis of the phenotypic and genotypic analysis, the isolate is classified as representative of a novel species in the genus

Epilithonimonas

, for which the name Epilithonimonas
ginsengisoli is proposed. The type strain is DCY78T ( = KCTC 32174T = JCM 19896T).
Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil
Authors: Kumar Roshan , Dwivedi Vatsala , Nayyar Namita , Verma Helianthous , Singh Amit Kumar , Rani Pooja , Rao D. L. N. , Lal Rup
Published: October 2014

Strain RK1T, a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium was isolated from a hexachlorocyclohexane (HCH) dumpsite, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RK1T belongs to the family

Sphingobacteriaceae

and showed highest sequence similarity to

Parapedobacter koreensis

Jip14T (95.63 %). The major cellular fatty acids of strain RK1T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c), iso-C15 : 0 3-OH and C16 : 0. The major respiratory pigment and polyamine of RK1T were menaquinone (MK-7) and homospermidine, respectively. The main polar lipids were phosphatidylethanolamine and sphingolipid. The G+C content of the DNA was 44.5 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly demonstrated that strain RK1T represents a novel species of the genus

Parapedobacter

, for which the name Parapedobacter
indicus sp. nov. is proposed. The type strain is RK1T ( = DSM 28470T = MCC 2546T).
Interactions of uroseptic Escherichia coli with renal (A-498) and gastrointestinal (HT-29) cell lines
Authors: Vollmerhausen Tara L. , Woods Jasmine L. , Faoagali Joan , Katouli Mohammad
Published: October 2014

We investigated the ability of Escherichia coli isolated from septic patients with urinary tract infection (UTI) to translocate through the gastrointestinal (GI) tract of the same patients using cell-culture models. Forty-seven hospitalized patients with urosepsis were included in this study. E. coli was isolated from their urine and blood (total 94 isolates) and investigated for genetic relatedness and interaction with the cell lines A-498 and HT-29. An initial comparison of the strains isolated from urine and blood showed that 44 out of 47 patients (94 %) had identical strains in their blood and urine. The blood isolates adhered to both cell lines, although their rate of adherence to A-498 cells was significantly higher than that to HT-29 cells (5.8±3.8 per cell vs 2.8±1.9; P<0.0001). The rate of translocation in A-498 cells was also significantly higher after 120 min (8.7×105 vs 2.9×105; P = 0.0006). Three non-identical blood isolates were unable to translocate in HT-29 cells, indicating that host immune factors might be more important than bacterial ability to translocate the GI epithelium in these patients. Our data showed that blood isolates from uroseptic patients are able to adhere to and translocate through both cell lines. This suggests that E. coli in patients with UTI may translocate from either the GI tract or the urinary tract, hence questioning the assumption that the urinary tract is the only source of septicaemia in these patients.
RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing
Authors: Gupta Vikas , Estrada April D. , Blakley Ivory , Reid Rob , Patel Ketan , Meyer Mason D. , Andersen Stig Uggerhøj , Brown Allan F. , Lila Mary Ann , Loraine Ann E.
Published: October 2014

Background

Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable breeding berry varieties with enhanced health benefits.

Results

Toward this end, we annotated a draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grapeVitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic.

Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up and down regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3’ end formation.

Conclusions

We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry. RNA-Seq data are freely available for visualization in Integrated Genome Browser, and analysis code is available from the git repository athttp://bitbucket.org/lorainelab/blueberrygenome.
Analysis of road transport energy consumption and emissions: a case study
Authors: Franco Sainu , Ravibabu Mandla Venkata
Published: October 2014

Purpose

– The purpose of this study is to examine the growing energy consumption pattern and emissions due to increasing vehicular density in the Vellore district. The transport demand in Indian cities has increased substantially over the past few years. Increasing household incomes and economic development in cities have added to this growing demand.

Design/methodology/approach

– The growth of Vellore town currently is such that in a short period of time, the development is likely to engulf the entire district as one big city, as it happened for Chennai. It is at a transitional stage where it is possible to bring about certain policy changes to prevent the catastrophic effects of urbanization. To test the objectives of the study, statistical and mathematical tools such as mean, coefficient of variation, correlation and regression models are used. Growth of vehicle population in Tamil Nadu in general and Vellore in particular are analyzed by computing the percentage rate of change and trend rate of growth.

Findings

– A study of the past four years shows a tremendous growth in the number of two-wheelers, while the number of buses has declined. The study also shows that public transport fuel consumption is < 20 per cent of the overall fuel consumption. The emission of all greenhouse gases is rising and it shows a linear growth. The increase in emission of CO2 is most alarming.

Research limitations/implications

– The diversity of sources that have been combined together implies a consequent reduction in accuracy. Data from different sources had different geographical boundaries (state, district, region and country). Thus, the data had to be translated to the relevant geographical area by using proportionality ratio. This manipulation does impact on the accuracy of the used data.

Practical implications

– This article provides a framework that can inform decisions makers on consequences in the absence of timely intervention and policy changes.

Originality/value

– Road transport is an inherently complex sector as it deals with a very large number of individual vehicles and factors of influence. The findings have implications for government in general and policy-makers in particular. This article puts together data of a particularly vulnerable region at a time when policy changes could bring about lasting beneficial effects. This region has not been included in any previous research.
Regional cost sharing in expansions of electricity transmission grids
Authors: Nylund Hans
Published: October 2014

Purpose

– The purpose of this paper is to analyse how the regional effects of expansion can be managed under the constraints of voluntary cooperation. This paper studies international cooperation on electricity transmission expansions in a region of countries that shares a joint electricity infrastructure.

Design/methodology/approach

– Cooperative game theory and the partition-function form were applied in combination with benefit–cost ratios to model and analyse the incentives to cooperate under different cost allocation rules. Empirical background was provided by a case study of a transmission investment agreement made on the Nordic electricity market.

Findings

– Both cost sharing and the composition of expansion plans were identified as ways of reaching regional agreements. It was found that agreements based on proportional division of costs in relation to benefits were the best choice for voluntary cooperation.

Research limitations/implications

– The study did not analyse the effects or relevance of surplus sharing in addition to that implied by cost sharing, nor has it studied the regulatory and legal requirements for implementing side-payments between countries in grid expansions. These issues could benefit from more study.

Practical implications

– The results are relevant for the development of international cooperation on grid expansions and as an input to regulations and policies aimed at promoting regional perspectives, in particular for the case of a single internal energy market in Europe.

Originality/value

– The paper contributes with an analysis of incentives for transmission expansions in a multinational environment subject to voluntary provision and a lack of supranational authorities with decision power.
Analysis of machinery breakdowns in power plants fed by biomass and MSW
Authors: De Antonellis Stefano , De Antonellis Mario
Published: October 2014

Purpose

– The aim of the study is to identify main failure phenomena and to evaluate reparation costs, reparation time, loss of profit and their relationship with power plant and faulty components age. In this work, several machinery breakdowns occurred in thermal power plants fed by solid biomass, biodiesel, biogas and municipal solid waste, have been investigated. In the period between 2004 and 2012, 23 faults have been analyzed.

Design/methodology/approach

– Each fault has been classified considering: power plant technical specifications, type of damage, reparation cost, reparation time and loss of profit (when data are available). The whole data have been, therefore, compared to find out significant information.

Findings

– It has been pointed out that relevant property damages are mainly caused by old components failure. In addition, the loss of profit is generally much higher than the property damage (six times on average basis).

Originality/value

– The study provides useful information that can be of interest for personnel of energy utilities, banks and insurance companies in managing power plants risks and in planning the availability of energy services.
Spanning information behaviour across the stages of a learning task
Authors: Heinström Jannica , Sormunen Eero , Kaunisto-Laine Sarita
Published: October 2014

Purpose

– The purpose of this paper is to explore the role of personality (intellectual curiosity, conscientiousness and negative emotionality) and approach to studying (deep, strategic and surface) on students’ learning-related information behaviour in inquiry tasks.

Design/methodology/approach

– Data were collected from 219 senior high school students with the use of three questionnaires.

Findings

– The findings showed that students’ individual traits influenced different aspects of their learning-related information behaviour from information need to information use.

Research limitations/implications

– The results were based on survey data. Reliability issues with the scales are discussed. In future research qualitative data would enrich the understanding of the phenomena.

Practical implications

– The results are informative for teachers and librarians who guide students in inquiry tasks.

Originality/value

– The study spanned learning-related information behaviour across the whole inquiry process: from task construction through task performance to task completion. The findings showed that individual traits were particularly influential at the task completion stage, that is on information use.
The Information School at the University of Sheffield, 1963-2013
Authors: Benson Melanie T. , Willett Peter
Published: October 2014

Purpose

– The purpose of this paper is to describe the historical development of library and information science (LIS) teaching and research in the University of Sheffield's Information School since its founding in 1963.

Design/methodology/approach

– The history is based on published materials, unpublished school records, and semi-structured interviews with 19 current or ex-members of staff.

Findings

– The School has grown steadily over its first half-century, extending the range of its teaching from conventional programmes in librarianship and information science to include cognate programmes in areas such as health informatics, information systems and multi-lingual information management.

Originality/value

– There are very few published accounts of the history of LIS departments.
Successful treatment of angioma serpiginosum using a novel 532 nm potassium titanyl phosphate (KTP) laser
Authors: Rho Nark Kyoung , Kim Hyree , Kim Hei Sung
Published: October 2014

Angioma serpiginosum (AS) is a rare, benign, vascular disorder comprising non‐blanchable punctate red to purple lesions in a gyrate or serpiginous configuration. We report a case of a 38‐year‐old woman with a red colored eruption on her chest which was present since puberty. A novel 532 nm potassium‐titanyl phosphate (KTP) laser (Excel V, Cutera Inc., Brisbane, CA, USA) was applied which resulted in near complete resolution after two sessions of treatment.