bluuebunny/crossref_metadata_2025 huggingface dataset:
OPTIMAL TAXATION AND SOCIAL NETWORKS
Authors: Arbex Marcelo , O'Dea Dennis
Published: June 2013

We study optimal taxation when jobs are found through a social network. The network determines employment, which workers may influence by engaging in social activities. The network parameters play an important role in determining the economy's employment level and the optimal income tax. The optimal labor income tax depends on both the traditional intensive margin of labor supply and a new extensive margin that depends on the structure of the social network. Social activities that promote social connections are instrumental to acquiring job information; taxation thus discourages both social activities and labor supply, reducing employment. Labor taxes vary positively with labor supply and negatively with employment. When networking is absent, taxes are higher and the economy's employment rate is lower. The optimal capital tax rate is zero, independent of labor market frictions. Social networking reduces job search frictions and is welfare-enhancing.
Alcohol During Pregnancy from 1985 to 2005: Prevalence and High Risk Profile
Authors: Pfinder Manuela , Feldmann Reinhold , Liebig Stefan
Published: June 2013

Aims: This study aimed 1. to examine the prevalence of German children born with prenatal alcohol exposure (PAE) from 1985 to 2005, and asked 2. whether it differed on levels of socioeconomic status (SES) and 3. whether there are differences between abstainers and drinkers during pregnancy in regard to physical, behavioural and sociodemographic features. Methods: 16 978 German mothers, enrolled in the German Health Interview and Examination Survey (KiGGS) were studied. Results: Between 1985 and 2005 13.5 percent of the children were born with PAE. No stable decrease was found over time. Over 20 years, the prevalence of children born with PAE was highest in the upper class. Drinkers differed from abstainers in regard to physical, behavioural and sociodemographic characteristics. High SES women were on a higher risk of alcohol intake during pregnancy. Conclusions: The prevalence of children born with PAE over time indicates that alcohol intake during pregnancy needs further interventions and prevention as no long-lasting decrease was found in the years from 1985 to 2005. Alcohol intake during pregnancy was and still is an issue in women from the upper class. Future research should therefore aim to explain the social gradient.
Mineralocorticoid receptors modulate vascular endothelial function in human obesity
Authors: Hwang Moon-Hyon , Yoo Jeung-Ki , Luttrell Meredith , Kim Han-Kyul , Meade Thomas H. , English Mark , Segal Mark S. , Christou Demetra D.
Published: June 2013

Obesity increases linearly with age and is associated with impaired vascular endothelial function and increased risk of cardiovascular disease. MRs (mineralocorticoid receptors) contribute to impaired vascular endothelial function in cardiovascular disease; however, their role in uncomplicated human obesity is unknown. Because plasma aldosterone levels are elevated in obesity and adipocytes may be a source of aldosterone, we hypothesized that MRs modulate vascular endothelial function in older adults in an adiposity-dependent manner. To test this hypothesis, we administered MR blockade (eplerenone; 100 mg/day) for 1 month in a balanced randomized double-blind placebo-controlled cross-over study to 22 older adults (ten men, 55–79 years) varying widely in adiposity [BMI (body mass index): 20–45 kg/m2], but who were free from overt cardiovascular disease. We evaluated vascular endothelial function [brachial artery FMD (flow-mediated dilation)] via ultrasonography) and oxidative stress (plasma F2-isoprostanes and vascular endothelial cell protein expression of nitrotyrosine and NADPH oxidase p47phox) during placebo and MR blockade. In the whole group, oxidative stress (P>0.05) and FMD did not change with MR blockade (6.39±0.67 compared with 6.23±0.73%; P=0.7). However, individual improvements in FMD in response to eplerenone were associated with higher total body fat (BMI: r=0.45, P=0.02; and dual-energy X-ray absorptiometry-derived percentage body fat: r=0.50, P=0.009) and abdominal fat (total: r=0.61, P=0.005; visceral: r=0.67, P=0.002; and subcutaneous: r=0.48, P=0.03). In addition, greater improvements in FMD with eplerenone were related to higher baseline fasting glucose (r=0.53, P=0.01). MRs influence vascular endothelial function in an adiposity-dependent manner in healthy older adults.
Proteomic analysis during capsicum ripening reveals differential expression of ACC oxidase isoform 4 and other candidates
Authors: Aizat Wan M. , Able Jason A. , Stangoulis James C. R. , Able Amanda J.
Published: June 2013

Capsicum (Capsicum annuum L.) is categorised as a non-climacteric fruit that exhibits limited ethylene production during ripening and the molecular mechanisms associated with this process are poorly understood. A proteomic approach was used to identify the differentially expressed proteins during various ripening stages (Green (G), Breaker Red 1 (BR1) and Light Red (LR)) and the genes associated with their synthesis. From 2D gel electrophoresis (2DGE), seven protein spots were identified as selectively present either in G or BR1 and are involved in carbon metabolism, colour and fruit development, protein synthesis and chaperones or biosynthesis of amino acids and polyamines. One candidate of interest, 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) is known to be involved in ethylene biosynthesis and was only present in BR1 and is related to the tomato ACO isoform 4 (LeACO4) and hence named CaACO4. CaACO4 RNA expression as well as total ACO protein expression in multiple stages of ripening (G, Breaker (B), BR1, Breaker Red 2 (BR2), LR and Deep Red (DR)) corresponded to the 2DGE protein spot abundance in breaker stages. Our findings highlight the involvement of the ethylene pathway in non-climacteric fruit ripening.
Changing relative abundance and behaviour of silky and grey reef sharks baited over 12 years on a Red Sea reef
Authors: Clarke C. R. , Lea J. S. E. , Ormond R. F. G.
Published: June 2013

There is a lack of studies on how provisioning may influence shark numbers and behaviour. The effects of long-term provisioning were investigated at a Red Sea reef, where both grey reef shark (Carcharhinus amblyrhynchos) and silky shark (Carcharhinus falciformis) occurred. Initially, grey reef sharks outnumbered silky sharks, but over 6 years, silky shark numbers increased almost 20-fold, whereas grey-reef sightings decreased >90%. Following this, silky-shark sightings also declined considerably (>80%). It is suggested that these declines could relate to local overfishing. Many silky sharks were identified individually through distinctive markings or conventional tagging. Some individual silky sharks were recorded regularly over 2 years or more, but most appeared to be transient visitors. Sighting records indicated that provisioning extended the residency of transient individuals. If visiting silky sharks were drawn from a larger regional population, this would explain both their initial accumulation and why, to begin with, sightings were sustained despite local fishing pressure. Conversely, the site fidelity typical of grey reef sharks would have made them more susceptible to local depletion. Silky sharks were recorded as behaving more boldly when present in greater numbers, but the decline in grey reef sharks appears to be unrelated to the initial increase in the numbers of silky shark.
Deep-water red coral from the island of Sardinia (north-western Mediterranean): a local example of sustainable management
Authors: Follesa Maria Cristina , Cannas Rita , Cau Alessandro , Pedoni Claudia , Pesci Paola , Cau Angelo
Published: June 2013

Since 1979, red coral harvesting in Sardinia has been regulated by regional laws. The regulations, including a minimum take size of 10-mm basal diameter, were imposed to limit and control harvesting. Our study indicated that >75% of the red coral colonies harvested in 2007–08 in the north-western coast were above the legal minimum size for exploitation. Moreover, extensive surveys with remotely operated vehicles allowed us to document the real structure of wild populations. Large colonies (>10 mm) represented a big portion of the population (~38% of the total), suggesting that harvesting effort did not affect yet the maximum size of colonies. All these results seem to be confirmed by the application of the model of Beverton and Holt. This model shows that the fishery of red coral in Sardinia reaches its maximum yield at an age at first capture of 20 years, an age significantly lower than the average age of 30 years calculated for the colonies actually harvested in the Sardinian coast. Our data confirmed that the measures enacted in the Sardinian regulations provide for an adequate management of this resource and, in addition, can represent a guideline for other countries that still lack a valid management plan.
Environmental influences on the larval recruitment dynamics of snapper, Chrysophrys auratus (Sparidae)
Authors: Sim-Smith Carina J. , Jeffs Andrew G. , Radford Craig A.
Published: June 2013

Recruitment success in demersal fish species that settle in estuaries after a pelagic larval duration in coastal waters is dependent on (1) abiotic and biotic variables that promote good survival, and (2) local environmental conditions that facilitate and direct the transport of larvae to settlement habitats. In the present study, we described the patterns of larval abundance, pelagic larval duration and settlement of a commercially important sparid, Chrysophrys auratus, in northern New Zealand over 2 years, and investigated the relationships among pelagic larval duration or daily settler abundance and various environmental variables. Pelagic larval duration varied from 17 to 33 days and the successful spawning period that produced settled juveniles varied from 29 to 109 days among our four sites. For 91% of fish captured, the average temperature during the pelagic larval duration was >18°C. Significant correlations between daily settler abundance and environmental variables varied among sites and between years; however, temperature, tidal range and on-shore winds were most strongly correlated with settlement, explaining up to 38% of the variability in settler abundance. The present results suggested that, in some locations, high water temperatures, large tides and on-shore winds are likely to increase recruitment success in C. auratus.
Is stocking barramundi (Lates calcarifer) in north-eastern Queensland a threat to aquatic biodiversity?
Authors: Russell D. J. , Thuesen P. A. , Thomson F. E. , Power T. N.
Published: June 2013

The stocking of predators can have significant consequences on recipient aquatic ecosystems. We investigated some potential ecological impacts of stocking a predatory fish (Lates calcarifer) into a coastal river and a large impoundment in north-eastern Australia. L. calcarifer was mostly found in slower-moving, larger reaches of the river or in the main body of the impoundment where there was abundant suitable habitat. In the tidally influenced freshwater reaches of the coastal river, L. calcarifer predominately consumed aytid and palaemonid shrimp that were associated with local macrophyte beds or littoral grasses. In this area the diets of juvenile stocked and wild L. calcarifer were similar and stocked fish displayed a high degree of site fidelity. Further upstream in the river, away from tidal influence, and in the impoundment, fish were the main prey item. Cannibalism was uncommon and we suggest that, at the current stocking densities, there was little dietary evidence of predatory impacts from L. calcarifer on species of conservation concern. We caution against introducing novel predatory species such as L. calcarifer in or near areas that are outside their natural range and are known to support rare, threatened or endangered species.
Combustion of eucalyptus bark firebrands in varying flow incidence and velocity conditions
Authors: Almeida Miguel , Viegas D. X. , Miranda A. I.
Published: June 2013

To validate the use of the combustion laws of embers that can be potential sources of spot fires, namely mass loss prediction laws determined in fixed or pure static conditions to changing flow or particle orientation properties, a series of tests in which these parameters were changed during particle combustion were performed. Hollow cylindrical pieces of bark of eucalyptus trees (Eucalyptus globulus Labill.) burning from one extremity to the other in a vertical flow were tested. It was found that ember combustion in varying conditions of flow velocity or incident flow direction (dynamic or quasistatic conditions) was quite different from that observed in pure static tests for the same values of the reference parameters, indicating that the combustion laws for pure static conditions are not applicable in cases where an ember is immersed in a varying flow. It was found that mass loss coefficients depend not only on the flow velocity and flow particle incidence, but also on the sign and magnitude of variation of these parameters. Mass loss coefficients obtained in pure static conditions were usually a lower limit of the corresponding parameter for dynamic and quasistatic conditions. It was concluded that significant errors can be committed when using common experimental static-condition parameters to predict maximum spotting distance in real situations in which the flow conditions vary continuously.
Market value of restocking and landscape in red-legged partridge hunting: a study based on advertisements
Authors: Díaz-Fernández Silvia , Arroyo Beatriz , Vióuela Javier , Patióo-Pascumal Isabel , Riera Pere
Published: June 2013

Context In Spain, the release of farm-reared partridges to hunt is increasingly used, despite being thought to affect sustainability of wild stocks and to reduce the need of natural habitats for game. Aims To explore the market value as a possible incentive for current management, we evaluated within a segment of the red-legged partridge hunting market whether the use of farm-reared birds (as opposed to wild stock) or the naturalisation of landscapes are affecting the hunt market price. Methods We considered estates that sell individual hunting days and contacted buyers through advertisements. We gathered all advertisements for the 2010 season in four top hunting magazines and two websites, and conducted a telephone survey to record price and associated characteristics of hunts. We looked for relationships between price and the characteristics of sold hunts, using general linear models. Key results Hunts varied largely in price, but neither restocking nor naturalisation of the landscape explained price variation, at least within our sample of estates. The absence of price difference between wild or released partridges could be reflecting the current difficulty to distinguish both kinds of products in the market. Conclusions Market forces alone might not be promoting the public interest of the sustainable use of wild stocks versus industrial hunting based on farm-reared birds. Implications If promoting conservation and sustainable use of wild stocks is considered a major goal of official institutions in charge of biodiversity conservation and game management, they should promote reliable ways of identifying estates selling wild or restocked partridges, and they should also evaluate benefits and costs associated with hunting farm-reared birds relative to wild birds, so as to help internalise these costs and benefits if necessary. A study of the determinants of hunter demands would also help explain variation in supply and market prices.
Microsatellite Analysis of Population Structure in Alaska Eulachon with Application to Mixed‐Stock Analysis
Authors: Flannery Blair G. , Spangler Robert E. , Norcross Brenda L. , Lewis Cara J. , Wenburg John K.
Published: June 2013

Estimation of genetic population structure, diversity, and effective population size (Ne) is important for defining meaningful conservation units and assessing genetic health. Recent conservation concerns in Alaska have highlighted the need for research on Eulachon Thaleichthys pacificus, a species about which relatively little is known. Therefore, genetic variation was assayed at 14 microsatellite loci to investigate the genetic population structure of Alaska Eulachon. This analysis revealed a low degree of genetic divergence (GST = 0.005) that is structured by broad‐scale northern and southern geographic regions. Overall, there is a significant correlation between genetic and geographic distances, suggesting that gene flow is geographically restricted and follows an isolation‐by‐distance (IBD) model. However, closer analysis reveals an absence of IBD within regions and that gene flow is primarily restricted by the geographic distance between regions, a pattern that better approximates the hierarchical island model. Gene flow is likely restricted between regions by a biogeographical barrier (i.e., the Alexander Archipelago). Alaska Eulachon have high levels of genetic diversity and relatively large Ne estimates of 3,535 and 2,823 for the northern and southern regions, respectively, although a large variance in reproductive success is likely responsible for a low Ne/N ratio. The observed genetic divergence suggests that it would be advantageous to manage the two regions separately to maintain productivity and evolutionary potential for Eulachon. Mixed‐stock analysis (MSA) of simulated and known‐origin mixtures supports the feasibility of regional stock separation. The northern and southern regions had MSA accuracies that were near or greater than 90% when fish from a single region comprised the mixtures. Further population structure may be present within regions, but additional analyses of collections across sampling years are necessary to clarify the microevolutionary processes.
The romance of wonder in organization studies
Authors: Sandelands Lloyd E. , Carlsen Arne
Published: June 2013

Wonder is the romance of all human study – a two-in-oneness of beautiful mystery and a rational inquiring mind. To wonder is to be open to mysteries beyond the known; it is to engage the largest questions of life; and above all, it is to come into being as a human person by reaching to the humanity of all peoples that resides in the transcendent. In this essay, we describe the wonder of organizational studies as literally a romance; a marriage of distinctive forms of human reasoning that, while they may show up in one and the same person, are essentially male and female. We look for wonder in a collection of stories about qualitative research in organizations in which organizational scholars at their best unite male and female aspects of human reasoning in wonder. In their stories, we find the soulful mystery and romance that delights and enchants the study of persons and organizations.
Spirituality and the work–home interface: a demands–resources perspective
Authors: Dust Scott B. , Greenhaus Jeffrey H.
Published: June 2013

Literature reviews of spirituality in the workplace expose the breadth of the phenomenon but also reveal the need to connect this literature with other research areas within management. In particular, the work–home (WH) interface is commonly viewed as having significant overlap
with spirituality, yet the connections between spirituality and the WH interface have received limited attention. Therefore, we offer a theoretical framework to encourage and guide research linking these two important areas. Empirical studies suggest that spirituality is associated with such
personal characteristics as hope, optimism, and sanctification as well as with such relational characteristics as forgiveness, gratitude, and interconnectedness. We illustrate how these personal and relational spiritual characteristics can determine whether individuals’ work and home
roles interfere with one another or whether they strengthen or enrich one another. We also propose a number of areas for future research.
The question of theoretical foundations for the spirituality at work movement
Authors: Hudson Richard
Published: June 2013

Over ten years ago, Benefiel called for the creation of a philosophical foundation for the spirituality at work movement, which she believed to be at risk because of the lack of theory and disagreement about key terms. This paper examines problems involved in setting up such a foundation.
Hypergeometric functions over 𝔽_{𝕢} and traces of Frobenius for elliptic curves
Authors: Barman Rupam , Kalita Gautam
Published: June 2013

We present explicit relations between the traces of Frobenius endomorphisms of certain families of elliptic curves and special values of

2

F
1

{_{2}}F_1

-hypergeometric functions over

F

q

\mathbb {F}_q

for

q
≡
1
(
mod
 
6
)

q \equiv 1 ( \text {mod}~6)

and

q
≡
1
(
mod
 
4
)

q \equiv 1 ( \text {mod}~4)

.
Household‐Level Welfare Effects of Organic Milk Introduction
Authors: Choi Hee-Jung , Wohlgenant Michael K. , Zheng Xiaoyong
Published: June 2013

Using household scanner data and a discrete choice modeling approach, we estimate demand for milk products at the micro‐level and compute the distribution of welfare effects from introducing organic milk across households with different characteristics within the partial equilibrium framework. The price effects of introducing organic milk are larger for low‐income households than for high‐income households, and the differences in the variety effects of introducing organic milk to groups with various levels of education are larger than the differences in the variety effects among groups with different income levels. Policy implications of these findings are discussed.
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
Authors: Koslicki David , Foucart Simon , Rosen Gail
Published: June 2013

Motivation: Many metagenomic studies compare hundreds to thousands of environmental and health-related samples by extracting and sequencing their 16S rRNA amplicons and measuring their similarity using beta-diversity metrics. However, one of the first steps—to classify the operational taxonomic units within the sample—can be a computationally time-consuming task because most methods rely on computing the taxonomic assignment of each individual read out of tens to hundreds of thousands of reads.

Results: We introduce Quikr: a QUadratic, K-mer–based, Iterative, Reconstruction method, which computes a vector of taxonomic assignments and their proportions in the sample using an optimization technique motivated from the mathematical theory of compressive sensing. On both simulated and actual biological data, we demonstrate that Quikr typically has less error and is typically orders of magnitude faster than the most commonly used taxonomic assignment technique (the Ribosomal Database Project’s Naïve Bayesian Classifier). Furthermore, the technique is shown to be unaffected by the presence of chimeras, thereby allowing for the circumvention of the time-intensive step of chimera filtering.

Availability: The Quikr computational package (in MATLAB, Octave, Python and C) for the Linux and Mac platforms is available at http://sourceforge.net/projects/quikr/.

Contact:  koslicki.1@mbi.osu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data
Authors: Woo Sangsoon , Zhang Xuekui , Sauteraud Renan , Robert François , Gottardo Raphael
Published: June 2013

Summary: MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase– or sonicated– ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance with nucleR and ChIPseqR.

Availability: PING 2.0 is available from the Bioconductor website at http://bioconductor.org. It can run on Linux, Mac and Windows.

Contact:  rgottard@fhcrc.org

Supplementary Information:  Supplementary material is available at Bioinformatics online.
Harnessing virtual machines to simplify next-generation DNA sequencing analysis
Authors: Nocq Julie , Celton Magalie , Gendron Patrick , Lemieux Sebastien , Wilhelm Brian T.
Published: June 2013

Motivation: The growth of next-generation sequencing (NGS) has not only dramatically accelerated the pace of research in the field of genomics, but it has also opened the door to personalized medicine and diagnostics. The resulting flood of data has led to the rapid development of large numbers of bioinformatic tools for data analysis, creating a challenging situation for researchers when choosing and configuring a variety of software for their analysis, and for other researchers trying to replicate their analysis. As NGS technology continues to expand from the research environment into clinical laboratories, the challenges associated with data analysis have the potential to slow the adoption of this technology.

Results: Here we discuss the potential of virtual machines (VMs) to be used as a method for sharing entire installations of NGS software (bioinformatic ‘pipelines’). VMs are created by programs designed to allow multiple operating systems to co-exist on a single physical machine, and they can be made following the object-oriented paradigm of encapsulating data and methods together. This allows NGS data to be distributed within a VM, along with the pre-configured software for its analysis. Although VMs have historically suffered from poor performance relative to native operating systems, we present benchmarking results demonstrating that this reduced performance can now be minimized. We further discuss the many potential benefits of VMs as a solution for NGS analysis and describe several published examples. Lastly, we consider the benefits of VMs in facilitating the introduction of NGS technology into the clinical environment.

Contact:  brian.wilhelm@umontreal.ca
Serum aldosterone is associated with mortality and re‐hospitalization in patients with reduced ejection fraction hospitalized for acute heart failure: analysis from the EVEREST trial
Authors: Girerd Nicolas , Pang Peter S. , Swedberg Karl , Fought Angela , Kwasny Mary J. , Subacius Haris , Konstam Marvin A. , Maggioni Aldo , Gheorghiade Mihai , Zannad Faiez ,   for the EVEREST investigators
Published: June 2013

Aims

Post‐discharge morbidity and mortality for acute heart failure (AHF) patients remains high. Although the adverse effects of neurohormonal activation are well known in chronic HF, the prognostic significance of serum aldosterone in patients hospitalized for AHF has not been well studied.

Methods and results

A secondary analysis was carried out of the placebo arm (n = 1850) from the EVEREST trial which had aldosterone measured at baseline. All patients were hospitalized for worsening HF and had an LVEF <40%. The median follow‐up was 9.9 months. The association between serum aldosterone levels at baseline and the independently adjudicated outcomes [all‐cause mortality (ACM) and the combined outcome of cardiovascular mortality (CVM) and HF re‐hospitalization] were explored with multivariable Cox models. Median aldosterone levels increased during the hospital stay from 11 ng/dL at baseline to 15 ng/dL at discharge (P < 0.001) and remained increased after discharge (16 ng/dL at 24 weeks, P < 0.001). After adjusting for potential confounders, higher baseline aldosterone levels were associated with an increased risk for ACM and CVM or HF re‐hospitalization [hazard ratio (HR) 1.49, 95% confidence intrerval (CI) 1.11–1.99; and HR 1.40, 95% CI 1.11–1.78, respectively, in the highest quartile when compared with the lowest].

Conclusion

In patients with LVEF <40% hospitalized for AHF and receiving standard therapy, serum aldosterone levels correlated with worse post‐discharge outcomes. Aldosterone levels increase during AHF hospitalization and remain increased long after discharge. These results suggest that further modulation of the renin–angiotensin–aldosterone system in patients admitted with worsening HF might favourably improve post‐discharge outcomes.
Discrimination of western Baltic spring-spawning and central Baltic herring (Clupea harengus L.) based on growth vs. natural tag information
Authors: Gröhsler Tomas , Oeberst Rainer , Schaber Matthias , Larson Niklas , Kornilovs Georgs
Published: June 2013

Gröhsler, T., Oeberst, R., Schaber, M., Larson, N., and Kornilovs, G. 2013. Discrimination of western Baltic spring-spawning and central Baltic herring (Clupea harengus L.) based on growth vs. natural tag information. – ICES Journal of Marine Science, 70: 1108–1117. In the Baltic Sea, several stocks of herring (Clupea harengus L.) are surveyed and managed separately. For assessment purposes, a spatial stock separation based on ICES subdivisions is implemented. However, especially in the western Baltic, the distribution areas of two stocks, the western Baltic spring-spawning herring and the central Baltic herring, overlap. Results of regularly conducted surveys for assessment purposes indicated variable degrees of mixing of both stocks in the survey area, based on conspicuous differences in weights/lengths within certain age groups, especially in an area known for overlapping distribution of both stocks. At present, varying fractions of the central Baltic herring stock have not been taken into account during regular surveys conducted in the western Baltic, leading to possible undetected biases in assessment indices derived from these surveys. Additionally, methods otherwise applied for stock separation of Baltic herring so far are based on parameters that cannot readily be derived during regular surveys. In this paper, we present a simple and quick method to reliably allocate herring to either stock based on a separation function derived from survey-based length-at-age data, thus facilitating a more precise estimate of biomass and abundance indices from regular surveys and commercial fisheries.
Ecosystem-based management objectives for the North Sea: riding the forage fish rollercoaster
Authors: Dickey-Collas M. , Engelhard G. H. , Rindorf A. , Raab K. , Smout S. , Aarts G. , van Deurs M. , Brunel T. , Hoff A. , Lauerburg R. A. M. , Garthe S. , Haste Andersen K. , Scott F. , van Kooten T. , Beare D. , Peck M. A.
Published: June 2013

Dickey-Collas, M., Engelhard, G. H., Rindorf, A., Raab, K., Smout, S., Aarts, G., van Deurs, M., Brunel, T., Hoff, A., Lauerburg R. A. M., Garthe, S., Haste Andersen, K., Scott, F., van Kooten, T., Beare, D., and Peck, M. A. Ecosystem-based management objectives for the North Sea: riding the forage fish rollercoaster. – ICES Journal of Marine Science, 71: . The North Sea provides a useful model for considering forage fish (FF) within ecosystem-based management as it has a complex assemblage of FF species. This paper is designed to encourage further debate and dialogue between stakeholders about management objectives. Changing the management of fisheries on FF will have economic consequences for all fleets in the North Sea. The predators that are vulnerable to the depletion of FF are Sandwich terns, great skua and common guillemots, and to a lesser extent, marine mammals. Comparative evaluations of management strategies are required to consider whether maintaining the reserves of prey biomass or a more integral approach of monitoring mortality rates across the trophic system is more robust under the ecosystem approach. In terms of trophic energy transfer, stability, and resilience of the ecosystem, FF should be considered as both a sized-based pool of biomass and as species components of the system by managers and modellers. Policy developers should not consider the knowledge base robust enough to embark on major projects of ecosystem engineering. Management plans appear able to maintain sustainable exploitation in the short term. Changes in the productivity of FF populations are inevitable so management should remain responsive and adaptive.
Recurrence of Prolapse After Transvaginal Mesh Excision
Authors: George Amy , Mattingly Marlena , Woodman Patrick , Hale Douglass
Published: June 2013

Objective

Recurrence of pelvic organ prolapse (POP) is a potential complication after mesh removal. We evaluated anatomical and functional outcomes preoperatively and postoperatively in patients undergoing mesh excision.

Materials and Methods

We conducted a retrospective cohort analysis of consecutive patients who underwent mesh excision from years 2005 to 2009. Anatomical outcomes were evaluated using the POP quantification (POP-Q) system. Recurrence of prolapse was defined as stage II or higher-stage prolapse on the POP-Q system, reoperation for prolapse, or postoperative use of a pessary for prolapse reduction. Functional outcomes were assessed using the pelvic floor distress inventory and pelvic floor impact questionnaire scores.

Results

Data were analyzed from 71 patients who underwent either partial or complete mesh excision. Most (44/70 [63%]) of the patients underwent partial mesh excision, and 26 patients (37%) underwent total mesh removal. Nineteen patients (26.7%) had preoperative prolapse and 27 (38.0%) of the 71 patients underwent concomitant native tissue prolapse repair. Overall change in POP-Q stage in women who underwent partial removal (median, 0 [−1 to 2]) was less advanced than in women with total excision. (median, −1 [−3 to 0]; P = 0.006) at 1 year postoperatively. Four patients prolapsed to the hymen, with all patients having defects in the anterior compartment. No patients required a second surgery, and one patient was treated with a pessary.

Total pelvic floor distress inventory and pelvic floor impact questionnaire scores before mesh excision were significantly improved 6 months after mesh removal (P < 0.05). Dyspareunia improved significantly after mesh excision (P = 0.034).

Conclusion

In our patient population, total and partial mesh excision is associated with re-treatment of POP in 1.4% of the patients. Patient functional outcomes significantly improved after mesh removal.
Perceptions and Practice Patterns of General Gynecologists Regarding Urogynecology and Pelvic Reconstructive Surgery
Authors: Yune Junchan Joshua , Siddighi Sam
Published: June 2013

Objectives

The purpose of this study was to describe the current practice patterns of general gynecologists regarding management of various urogynecologic conditions.

Methods

A 15-item Web-based survey was sent to obstetrician and gynecologists in 2011. Subjects who chose to participate answered questions about their comfort level with management of various urogynecologic conditions, their perceptions of the need for a pelvic reconstructive surgeon in their community, and when they feel it is appropriate to refer to a specialist.

Results

Two hundred ninety-four obstetrics/gynecology generalists responded to the survey with overall 33% response rate. There was a wide range of comfort level depending on the complexity of the condition. Most of the subjects felt comfortable in the management of stress and urge incontinence, cystocele, rectocele, and uterine prolapse. On the other hand, most of the subjects were uncomfortable with management of intrinsic sphincter deficiency, fecal incontinence, recurrent incontinence after failed surgery, and complications of vaginal mesh surgery. In addition, there was wide variation in types of surgical options offered by different practitioners. When we compared the results by age, younger gynecologists have a smaller repertoire of procedures they offer for treatment of urogynecologic conditions. Burch colposuspension, uterosacral ligament suspension, and colpocleisis were performed more often by older surgeons than younger surgeons. On the other hand, cystoscopy was performed more commonly by the younger group.

Conclusions

Among general gynecologists, there is a wide range in both comfort level for management of different urogynecologic conditions and types of urogynecologic services performed.
Pathologic Evaluation of Explanted Vaginal Mesh
Authors: Smith Tovia M. , Smith Steven C. , DeLancey John O. , Fenner Dee E. , Schimpf Megan O. , Roh Michael H. , Morgan Daniel M.
Published: June 2013

Objectives

In light of vaginal mesh safety concerns, we reviewed our institutional experience with analytic processes and pathologic findings of explanted vaginal mesh to identify problems and opportunities to facilitate improved documentation and research.

Methods

We reviewed gross and microscopic pathology reports and archival slides of explanted mesh specimens from January 2010 through February 2012. Specimen requisition clinical history, number of mesh specimens per case, and type of examination (gross or histologic) were abstracted from pathology records using the initial search word “mesh”.

Results

One hundred two cases were reviewed. Explanted mesh specimens included tissue in 97%. Forty-eight percent of these cases were submitted for histopathologic evaluation (as opposed to gross examination only). Specimen requisitions listed clinical history as pain (28.4%), vaginal mesh erosion (24.5%), erosion (17.6%), urinary retention (5.9%), and infection (2.9%). When no history was provided (24.5%), the case was more frequently submitted for histologic examination (74% vs 41%, P = 0.05). In all but 2 cases, the mesh material was polypropylene; no requisition mentioned this information. Gross descriptions of mesh varied significantly; in 18% of the cases, mesh was inaccurately described as “metallic”. No cases of neoplasm were diagnosed histologically; all tissue diagnoses described benign reactive processes.

Conclusions

Our experience suggests that either gross or histopathologic examination is appropriate for mesh explants. Documentation of clinical history, mesh product, and material was frequently incomplete and associated with increased submission of tissue for histologic examination and inaccurate gross impression of material type. We recommend improved documentation to aid pathologic examination and enable future pathophysiologic study of mesh complications.
Rapid detection of Clostridium difficile toxins from stool samples using real-time multiplex PCR
Authors: Pallis Ann , Jazayeri Jalal , Ward Peter , Dimovski Karolina , Svobodova Suzanne
Published: June 2013

In this study, a total of 650 stool samples were tested to show that our method is capable of detecting four Clostridium difficile genes; tcdA, tcdB, encoding toxin A (TcdA) and toxin B (TcdB), and the binary toxin C. difficile transferase genes (cdtA and/or cdtB) encoding CDT toxin. Besides detecting the targeted C. difficile genes, our method can be used to detect the presence of any inhibitory components in the PCR. This assay, combined with a selective culture medium, such as the chromID™ C. difficile, can be applied directly for screening C. difficile-associated disease. The PCR-based assay developed here is rapid (4 h per 21 stool samples) and accurate in diagnosing C. difficile infection, 100 % assay sensitivity and negative predictive value (NPV) were obtained. However, the assay specificity of 99.1 % and positive predictive value (PPV) of 94.9 % were slightly lower than the optimal value of 100 %. The assay protocol outlined here can be used as a rapid screening tool to assist infection control units and in managing infected patients by reducing the number of patients requiring isolation and extended hospitalization. Rapid detection can prevent unnecessary antibiotic therapy and potentially reduce the spread of infection by emerging hypervirulent C. difficile strains.
DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast
Authors: Graber Joel H. , Nazeer Fathima I. , Yeh Pei-chun , Kuehner Jason N. , Borikar Sneha , Hoskinson Derick , Moore Claire L.
Published: June 2013

Systemic response to DNA damage and other stresses is a complex process that includes changes in the regulation and activity of nearly all stages of gene expression. One gene regulatory mechanism used by eukaryotes is selection among alternative transcript isoforms that differ in polyadenylation [poly(A)] sites, resulting in changes either to the coding sequence or to portions of the 3′ UTR that govern translation, stability, and localization. To determine the extent to which this means of regulation is used in response to DNA damage, we conducted a global analysis of poly(A) site usage in Saccharomyces cerevisiae after exposure to the UV mimetic, 4-nitroquinoline 1-oxide (4NQO). Two thousand thirty-one genes were found to have significant variation in poly(A) site distributions following 4NQO treatment, with a strong bias toward loss of short transcripts, including many with poly(A) sites located within the protein coding sequence (CDS). We further explored one possible mechanism that could contribute to the widespread differences in mRNA isoforms. The change in poly(A) site profile was associated with an inhibition of cleavage and polyadenylation in cell extract and a decrease in the levels of several key subunits in the mRNA 3′-end processing complex. Sequence analysis identified differences in the cis-acting elements that flank putatively suppressed and enhanced poly(A) sites, suggesting a mechanism that could discriminate between variable and constitutive poly(A) sites. Our analysis indicates that variation in mRNA length is an important part of the regulatory response to DNA damage.
Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma
Authors: Kan Zhengyan , Zheng Hancheng , Liu Xiao , Li Shuyu , Barber Thomas D. , Gong Zhuolin , Gao Huan , Hao Ke , Willard Melinda D. , Xu Jiangchun , Hauptschein Robert , Rejto Paul A. , Fernandez Julio , Wang Guan , Zhang Qinghui , Wang Bo , Chen Ronghua , Wang Jian , Lee Nikki P. , Zhou Wei , Lin Zhao , Peng Zhiyu , Yi Kang , Chen Shengpei , Li Lin , Fan Xiaomei , Yang Jie , Ye Rui , Ju Jia , Wang Kai , Estrella Heather , Deng Shibing , Wei Ping , Qiu Ming , Wulur Isabella H. , Liu Jiangang , Ehsani Mariam E. , Zhang Chunsheng , Loboda Andrey , Sung Wing Kin , Aggarwal Amit , Poon Ronnie T. , Fan Sheung Tat , Wang Jun , Hardwick James , Reinhard Christoph , Dai Hongyue , Li Yingrui , Luk John M. , Mao Mao
Published: June 2013

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole-genome sequencing (WGS) study of 88 matched HCC tumor/normal pairs, 81 of which are Hepatitis B virus (HBV) positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find beta-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumor suppressor (35.2%). The Wnt/beta-catenin and JAK/STAT pathways, altered in 62.5% and 45.5% of cases, respectively, are likely to act as two major oncogenic drivers in HCC. This study also identifies several prevalent and potentially actionable mutations, including activating mutations of Janus kinase 1 (JAK1), in 9.1% of patients and provides a path toward therapeutic intervention of the disease.
Relationship between performance and microvoids of aramid fibers revealed by two-dimensional small-angle X-ray scattering
Authors: Zhu Caizhen , Liu Xiaofang , Guo Jing , Zhao Ning , Li Changsheng , Wang Jie , Liu Jianhong , Xu Jian
Published: June 2013

Although the crystal structure in aramid fibers and the relationship between the size and orientation of crystallites and the performance of a material have been explored in detail, the effect of microvoids in an aramid fiber on its performance is still not clear. However, it is known that the mechanical properties depend strongly on the fiber morphology. In the present research, two-dimensional small-angle X-ray scattering is applied to characterize the microvoids in aramid fibers. Pauw's two-dimensional full pattern fitting method and scattering model have been enhanced by introducing orientation parameters, such as zenith angle distribution and azimuthal angle distribution, and instrumental parameters like point spread function and beam profile function. A series of aramid fibers with different strengths were studied using the new two-dimensional full pattern fitting method to extract the microvoid parameters from the scattering patterns. The results show that the microvoids in the aramid fiber affect the fiber strength directly. The greater the number of spherical microvoids and the larger the ellipsoidal microvoids, the weaker the aramid fiber.
Safety interlock and vent system to alleviate potentially dangerous ice blockage of top-loading cryostat sample sticks
Authors: Pangelis S. , Olsen S. R. , Scherschligt J. , Leão J. B. , Pullen S. A. , Dender D. , Hester J. R. , Imperia P.
Published: June 2013

A combined solution is presented for minimizing the safety hazards associated with closed cycle cryostats described by Swainson & Cranswick [J. Appl. Cryst.(2010),43, 206–210]. The initial solution is to install a vent tube with one open end deep inside the sample space and a pressure relief valve at the top. This solution works for either a cryogen or a cryogen-free (closed cycle) system. The second approach, which can be combined with the first and is applicable to cryogen-free cryostats, involves electrically interlocking the closed cycle refrigerator compressor to the sample space, so that the system cannot be cooled in the presence of a leak path to air.
Representative reduction of crystallographic orientation data
Authors: Jöchen Katja , Böhlke Thomas
Published: June 2013

Experimental techniques [e.g.electron backscatter diffraction (EBSD)] yield detailed crystallographic information on the grain scale. In both two- and three-dimensional applications of EBSD, large data sets in the range of 105–109single-crystal orientations are obtained. With regard to the precise but efficient micromechanical computation of the polycrystalline material response, small representative sets of crystallographic orientation data are required. This paper describes two methods to systematically reduce experimentally measured orientation data. Inspired by the work of Gao, Przybyla & Adams [Metall. Mater. Trans. A(2006),37, 2379–2387], who used a tessellation of the orientation space in order to compute correlation functions, one method in this work uses a similar procedure to partition the orientation space into boxes, but with the aim of extracting the mean orientation of the data points of each box. The second method to reduce crystallographic texture data is based on a clustering technique. It is shown that, in terms of representativity of the reduced data, both methods deliver equally good results. While the clustering technique is computationally more costly, it works particularly well when the measured data set shows pronounced clusters in the orientation space. The quality of the results and the performance of the tessellation method are independent of the examined data set.
Pair distribution function analysis of X-ray diffraction from amorphous spheres in an asymmetric transmission geometry: application to a Zr58.5Cu15.6Ni12.8Al10.3Nb2.8glass
Authors: Bendert J. C. , Mauro N. A. , Kelton K. F.
Published: June 2013

A method for the calculation of the pair distribution and structure functions from X-ray intensity data obtained with an area detector for an off-center incident X-ray beam on an amorphous sphere is presented. Error propagation for converting from the structure function to the pair distribution function is also described, including a summation series approach to treat the error from a high-qtruncation. A Zr58.5Cu15.6Ni12.8Al10.3Nb2.8glass (Vitreloy 106a) is used to demonstrate the techniques. In particular, the semi-analytical corrections presented to calculate the effects of secondary scatter within and asymmetric transmission through a spherical sample are verified.