bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fieldwork in the Era of Social Media: Opportunities and Challenges
Authors: Côté Isabelle 
Published: June 2013

AbstractSocial networking sites have recently garnered academic attention for their role in fostering democracy and openness in both developed and developing regions. Unfortunately, in political science, this newfound interest has not yet translated into a greater interest in social media as a methodological tool for researchers conducting fieldwork. How has the era of social media influenced the way political scientists conduct their fieldwork? How can researchers make the most of the opportunities offered by social networking sites while abiding by the strict standards of their ethics board? This article highlights the potential in social networking sites for recruiting participants and gathering data and looks at the impact sites such as Facebook have had on building and maintaining trust with research participants. In contrast, it explores how social media may compromise one's ability to uphold the “do no harm” principle guiding all academic research by jeopardizing participants' confidentiality and anonymity, a risk deemed especially high for vulnerable populations or sensitive regions. Insight gleaned from the researcher's own fieldwork in two minority provinces of Indonesia in 2010–2011 is used as a case in point.
How Social Science Research Can Improve Teaching
Authors: King Gary , Sen Maya 
Published: June 2013

AbstractWe marshal discoveries about human behavior and learning from social science research and show how these can be used to improve teaching and learning. The discoveries are easily stated as three social science generalizations: (1) social connections motivate, (2) teaching teaches the teacher, and (3) instant feedback improves learning. We show how to apply these generalizations via innovations in modern information technology inside, outside, and across university classrooms. We also give concrete examples of these ideas from innovations we have experimented with in our own teaching.
The Anatomy of a Regicide Attempt: Shāhrukh, the Ḥurūfīs, and the Timurid Intellectuals in 830/1426–27
Authors: BİNBAŞ İLKER EVRİM 
Published: June 2013

AbstractThis article provides a contextual analysis of the assassination attempt on the Timurid ruler Shāhrukh's life on 21 February 1427 in Herat. According to the contemporary Timurid chroniclers, Aḥmad-i Lur, a Ḥurūfī by profession, tried to kill Shāhrukh. Having survived the attack with light injuries, Shāhrukh reacted harshly and executed many of those who were accused of conspiring against him. During the interrogations, many other intellectuals who professed as a method of inquiry the‘ilm-i ḥurūf(the science of letters) were also accused of participating in the conspiracy. In this article, I treat the assassination attempt as a moment of crisis in Timurid politics, study it in relation to the transformation of the intellectual landscape towards the mid-fifteenth century, and provide an in-depth textual and contextual analysis of the historiographical sources as well as the writings of those intellectuals who left a first-hand testimony of the subsequent interrogations. After a close scrutiny of the available evidence, I demonstrate that the interrogations of those intellectuals who practiced the science of letters predated the assassination attempt, and I argue that the assassination attempt was just an episode, albeit an important one, in Shāhrukh's attempts to control and regulate the emerging public sphere in Iran and Central Asia.
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&gt;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.
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

AbstractEstimation 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.
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)

.
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
Authors: Koslicki David , Foucart Simon , Rosen Gail 
Published: June 2013

Abstract
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

Abstract
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

Abstract
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

AimsPost‐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 resultsA 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].ConclusionIn 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

Abstract
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

AbstractDickey-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.