bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements
Authors: Stedtfeld Robert D , Guo Xueping , Stedtfeld Tiffany M , Sheng Hongjie , Williams Maggie R , Hauschild Kristin , Gunturu Santosh , Tift Leo , Wang Fang , Howe Adina , Chai Benli , Yin Daqiang , Cole James R , Tiedje James M , Hashsham Syed A 
Published: July 2018

ABSTRACTThe high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.
Maternal reproductive history: trends and inequalities in four population-based birth cohorts in Pelotas, Brazil, 1982–2015
Authors: Matijasevich Alicia , Victora Cesar G , Silveira Mariangela F , Wehrmeister Fernando C , Horta Bernardo L , Barros Fernando C ,   Pelotas Cohorts Study Group, Menezes Ana M B , Barros Aluisio J D , Bertoldi Andrea Dâmaso , Bassani Diego G , Gonçalves Helen , Santos Iná S , Murray Joseph , Tovo-Rodrigues Luciana , Assunção Maria Cecilia F , Domingues Marlos Rodrigues , Hallal Pedro R C 
Published: July 2018

Abstract

Background
Brazil experienced important progress in maternal and child health in recent decades. We aimed at describing secular trends as well as socioeconomic and ethnic inequalities in reproductive history indicators (birth spacing, previous adverse perinatal outcome, parity and multiple births) over a 33-year span.

Methods
Four population-based birth cohort studies included all hospital births in 1982, 1993, 2004 and 2015 in Pelotas, Southern Brazil. Information on reproductive history was collected through interviews. Indicators were stratified by family income quintiles and skin colour. Absolute and relative measures of inequality were calculated.

Results
From 1982 to 2015, the proportion of primiparae increased from 39.2% to 49.6%, and median birth interval increased by 23.2 months. Poor women were more likely to report short intervals and higher parity, although reductions were observed in all income and ethnic groups. History of previous low birthweight was inversely related to income and increased by 7.7% points (pp) over time—more rapidly in the richest (12.1 pp) than in the poorest quintile (0.4 pp). Multiple births increased from 1.7% to 2.7%, with the highest increase observed among the richest quintile and for white women (220% and 70% increase, respectively). Absolute and relative income and ethnic-related inequalities for short birth intervals increased, whereas inequalities for previous low birthweight decreased over time.

Conclusions
In this 33-year period there were increases in birth intervals, multiple births and reports of previous low-birthweight infants. These trends may be explained by increased family planning coverage, assisted reproduction and a rise in preterm births, respectively. Our results show that socioeconomic and ethnic inequalities in health are dynamic and vary over time, within the same location.
Nef Line Bundles on Calabi–Yau Threefolds, I
Authors: Lazić Vladimir , Oguiso Keiji , Peternell Thomas 
Published: July 2018

Abstract
We prove that a nef line bundle ${\mathcal{L}}$ with $c_1({\mathcal{L}})^2 \ne 0$ on a Calabi–Yau threefold $X$ with Picard number $2$ and with $c_3(X) \ne 0$ is semiample, that is, some multiple of $\mathcal L$ is generated by global sections.
Congress of Neurological Surgeons Systematic Review and Evidence-Based Guidelines on the Evaluation and Treatment of Patients With Thoracolumbar Spine Trauma: Classification of Injury
Authors: Dailey Andrew T , Arnold Paul M , Anderson Paul A , Chi John H , Dhall Sanjay S , Eichholz Kurt M , Harrop James S , Hoh Daniel J , Qureshi Sheeraz , Rabb Craig H , Raksin P B , Kaiser Michael G , O’Toole John E 
Published: July 2018

Abstract

QUESTION 1
Are there classification systems for fractures of the thoracolumbar spine that have been shown to be internally valid and reliable (ie, do these instruments provide consistent information between different care providers)?

RECOMMENDATION 1
A classification scheme that uses readily available clinical data (eg, computed tomography scans with or without magnetic resonance imaging) to convey injury morphology, such as Thoracolumbar Injury Classification and Severity Scale or the AO Spine Thoracolumbar Spine Injury Classification System, should be used to improve characterization of traumatic thoracolumbar injuries and communication among treating physicians.
Strength of Recommendation: Grade B

QUESTION 2
In treating patients with thoracolumbar fractures, does employing a formally tested classification system for treatment decision-making affect clinical outcomes?

RECOMMENDATION 2
There is insufficient evidence to recommend a universal classification system or severity score that will readily guide treatment of all injury types and thereby affect outcomes.
Strength of Recommendation: Grade Insufficient
The full version of the guideline can be reviewed at: https://www.cns.org/guideline-chapters/congress-neurological-surgeons-systematic-review-evidence-based-guidelines/chapter_2.
Is Length of Stay Influenced by the Weekday On Which Lumbar Surgery is Performed?
Authors: Sivaganesan Ahilan , Devin Clinton J , Khan Inamullah , Kerezoudis Panagiotis , Nian Hui , Harrell Frank E , Bydon Mohamad , Asher Anthony L 
Published: July 2018

Abstract

BACKGROUND
Reducing length of stay (LOS) in a safe manner has the potential to save significant costs for the care of patients undergoing elective lumbar spine surgery. Due to the relative absence on weekends of staff required for discharging patients to rehabilitation or nursing facilities, we hypothesize that patients undergoing lumbar surgery later in the week have a longer LOS than their counterparts.

OBJECTIVE
To analyze the effect of day of the week for lumbar surgery on LOS.

METHODS
Patients undergoing surgery for lumbar degenerative disease were prospectively enrolled in the multicenter quality and outcomes database registry. A multivariable proportional odds regression model was built with LOS as the outcome of interest and patient and surgical variables as covariates.

RESULTS
A total of 11 897 patients were analyzed. Among those discharged home, the regression analysis demonstrated significantly higher odds of longer LOS for patients undergoing surgery on Friday as compared to Monday (P < .001). Among those discharged to a facility, there were significantly higher odds of longer LOS for patients undergoing surgery on Wednesday (P < .001), Thursday (P < .001), and Friday (P = .002) as compared to Monday.

CONCLUSION
The findings of this study suggest that lumbar patients undergoing fusions and those discharged to a facility have longer LOS when surgery is later in the week. Scheduling these patients for surgery earlier in the week and ensuring adequate resources for patient disposition on weekends may lead to LOS reduction and cost savings for hospitals, payers, and patients alike.
Relationships of Long-Term Smoking and Moist Snuff Consumption With a DNA Methylation Age Relevant Smoking Index: An Analysis in Buccal Cells
Authors: Nwanaji-Enwerem Jamaji C , Cardenas Andres , Chai Peter R , Weisskopf Marc G , Baccarelli Andrea A , Boyer Edward W 
Published: July 2018

Abstract

Introduction
Currently, there is no widely accepted, non-self-report measure that simultaneously reflects smoking behaviors and is molecularly informative of general disease processes. Recently, researchers developed a smoking index (SI) using nucleated blood cells and a multi-tissue DNA methylation–based predictor of chronological age and disease (DNA methylation age [DNAm-age]). To better understand the utility of this novel SI in readily accessible cell types, we used buccal cell DNA methylation to examine SI relationships with long-term tobacco smoking and moist snuff consumption.

Methods
We used a publicly available dataset composed of buccal cell DNA methylation values from 120 middle-aged men (40 long-term smokers, 40 moist snuff consumers, and 40 nonsmokers). DNAm-age (353-CpGs) and SI (66-CpGs) were calculated using CpG sites measured using the Illumina HumanMethylation450 BeadChip. We estimated associations of tobacco consumption habits with both SI and DNAm-age using linear regression models adjusted for chronological age, race, and methylation technical covariates.

Results
In fully adjusted models with nonsmokers as the reference, smoking (β = 1.08, 95% CI = 0.82 to 1.33, p &lt; .0001) but not snuff consumption (β = .06, 95% CI = −0.19 to 0.32, p = .63) was significantly associated with SI. SI was an excellent predictor of smoking versus nonsmoking (area under the curve = 0.92, 95% CI = 0.85 to 0.98). Four DNAm-age CpGs were differentially methylated between smokers and nonsmokers including cg14992253 [EIF3I], which has been previously shown to be differentially methylated with exposure to long-term fine-particle air pollution (PM2.5).

Conclusions
The 66-CpG SI appears to be a useful tool for measuring smoking-specific behaviors in buccal cells. Still, further research is needed to broadly confirm our findings and SI relationships with DNAm-age.

Implications
Our findings demonstrate that this 66-CpG blood-derived SI can reflect long-term tobacco smoking, but not long-term snuff consumption, in buccal cells. This evidence will be useful as the field works to identify an accurate non-self-report smoking biomarker that can be measured in an easily accessible tissue. Future research efforts should focus on (1) optimizing the relationship of the SI with DNAm-age so that the metric can maximize its utility as a tool for understanding general disease processes, and (2) determining normal values for the SI CpGs so that the measure is not as study sample specific.
Zapatistas between Sliding Doors of Opportunity
Authors: Inclán María 
Published: July 2018

AbstractThis chapter summarizes the main arguments of the book and offers an explanation of why a seemingly successful insurgent social movement might be able to mobilize sympathy and support for its agenda but fail to force state authorities to address its demands. The conclusion is that despite relative failures, through protest mobilization and the support of solidaristic social movement organizations, insurgent social movements like the Zapatista movement may be able to survive as salient actors within a new democratic regime and as iconic figures among other social movements around the world. This chapter also compares the fate of the Zapatista movement to the outcomes of other social, indigenous, and guerrilla movements within different transitional conditions and offer some expectations for the future of Mexico’s democracy.
All This Have I Proved by Wisdom
Authors: Larsen Timothy 
Published: July 2018

Abstract
This chapter covers the two books that made Mill’s wider reputation as an intellectual: A System of Logic (1843) and Principles of Political Economy (1848). It explores what they reveal about how Mill’s mind worked, as well as the ways that they shed a sidelight on his views on religion. A System of Logic, in particular, is surprisingly permeated with religious themes. Not even counting pronouns, Mill refers to God directly in this textbook on logic, ratiocinative and inductive, over eighty times. Attention is paid to religious reactions to these works—as well as to Mill’s reactions to these reactions. Through these two highly successful, major works, Mill first gained a place that he would never lose as an eminent Victorian.
By Their Fruits Ye Shall Know Them
Authors: Larsen Timothy 
Published: July 2018

Abstract
This chapter focuses on Mill as political and social activist, including his parliamentary career as MP for Westminster. ‘By their fruits ye shall know them’ was the scriptural text he offered to defend his conviction that the parliamentary candidacy of the atheist Charles Bradlaugh should be supported because he was a productive worker on behalf of much-needed, practical reforms. The moralistic, passionate Mill who agitated against slavery, the Confederacy during the American Civil War, and Governor Eyre is on display. Not least, this chapter explores The Subjection of Women (1869) and Mill’s courageous, pioneering advocacy for women’s rights and gender equality.
Complex Systems as Multilayer Networks
Authors: Bianconi Ginestra 
Published: July 2018

Abstract
Chapter 1 constitutes Part I of the book: ‘Single and Multilayer Networks’. This chapter introduces multilayer networks as an important new development of Network Science that allows a more comprehensive understanding of Complex Systems. It identifies the main motivations driving the research activity in this field of multilayer networks and emphasizes the benefits of taking a multilayer network perpective to characterize network data. The main advantages of a multilayer network approach with respect to the more traditional single layer characterization of complex networks are broadly discussed, focusing on the information gain resulting from the analysis of multilayer networks, the non-reducibility of a multilayer network to a large single network and the rich interplay between structure and function in multilayer networks.
Multilayer Network Models
Authors: Bianconi Ginestra 
Published: July 2018

AbstractThis chapter presents the existing modelling frameworks for multiplex and multilayer networks. Multiplex network models are divided into growing multiplex network models and null models of multiplex networks. Growing multiplex networks are here shown to explain the main dynamical rules responsible to the emergent properties of multiplex networks, including the scale-free degree distribution, interlayer degree correlations and multilayer communities. Null models of multiplex networks are described in the context of maximum-entropy multiplex network ensembles. Randomization algorithms to test the relevant of network properties against null models are here described. Moreover, Multi-slice temporal networks Models capturing main properties of real temporal network data are presented. Finally, null models of general multilayer networks and networks of networks are characterized.
Epidemic Spreading
Authors: Bianconi Ginestra 
Published: July 2018

Abstract
Epidemic processes are relevant to studying the propagation of infectious diseases, but their current use extends also to the study of propagation of ideas in the society or memes and news in online social media. In most of the relevant applications epidemic spreading does not actually take place on a single network but propagates in a multilayer network where different types of interaction play different roles. This chapter provides a comprehensive view of the effect that multilayer network structures have on epidemic processes. The Susceptible–Infected–Susceptible (SIS) Model and the Susceptible–Infected–Removed (SIR) Model are characterized on multilayer networks. Additionally, it is shown that the multilayer networks framework can also allow us to study interacting Awareness and epidemic spreading, competing networks and epidemics in temporal networks.
Synchronization, Non-linear Dynamics and Control
Authors: Bianconi Ginestra 
Published: July 2018

Abstract
This chapter is entirely devoted to characterizing non-linear dynamics on multilayer networks. Special attention is given to recent results on the stability of synchronization that extend the Master Stability Function approach to the multilayer networks scenario. Discontinous synchronization transitions on multiplex networks recently reported in the literature are also discussed, and their application discussed in the context of brain networks. This chapter also presents an overview of the major results regarding pattern formation in multilayer networks, and the proposed characterization of multivariate time series using multiplex visibility graphs. Finally, the chapter discusses several approaches for multiplex network control where the dynamical state of a multiplex network needs to be controlled by eternal signals placed on replica nodes satisfying some structural constraints.
‘A Double Delight’
Authors: Newton Hannah 
Published: July 2018

Abstract
Recovery from disease was an event of profound religious significance in early modern England, because it was thought to be ordained by God. This chapter investigates the perceived impact of bodily recovery on spiritual well-being, and asks how patients and their loved ones reacted to the belief that ultimately it was the Lord who had raised them from the sickbed. It shows that across the Protestant spectrum, experiences of recovery were shaped by what can be called the ‘art of recovery’, a set of moral duties and devotional practices derived from Scripture, which were supposed to be performed in the wake of illness. These included resisting sin, cultivating ‘holy affections’, and joining together in collective praise. When patients succeeded in these duties, the joy of recovery was greatly multiplied, since it signified that their souls as well as their bodies were better; but when they failed, the happiness was undermined.
Waddington’s Processual Epigenetics and the Debate over Cryptic Variability
Authors: Fabris Flavia 
Published: July 2018

Abstract
This chapter reappraises Waddington’s processual theory of epigenetics and examines its implications for contemporary evolutionary biology. It focuses in particular on the ontological difference between two conflicting assumptions that have been conflated in the recent debate over the nature of cryptic variability: a substance view that is consistent with the modern synthesis and construes variability as a preexisting pool of random genetic variation; and a processual view, which derives from Waddington’s conception of developmental canalization and understands variability as an epigenetic process. The chapter also discusses how these opposing interpretations fare in their capacity to explain the genetic assimilation of acquired characters.
The Effect of Vacuum-Assisted Closure Therapy on Methicillin-Resistant Staphylococcus aureus Wound Biofilms
Authors: Ćirković Ivana , Jocić Dario , Božić Dragana D. , Djukić Slobodanka , Konstantinović Neda , Radak Djordje 
Published: July 2018

ABSTRACT
Biofilm-associated wound infections are a major global health issue, and methicillin-resistant Staphylococcus aureus (MRSA) is among the greatest therapeutic challenges. Vacuum-assisted closure (VAC) therapy is now being revisited as an alternative treatment for both acute and chronic wounds. However, data supporting the concept of its antibiofilm effect remain limited. Using quantitative biofilm-forming assay and a range of genotypic methods (spa, SCCmec, and agr typing), study authors showed that VAC therapy can significantly prevent biofilm formation (P < .01) of a range of MRSA wound isolates differing widely in their biofilm-forming abilities and genetic background. The best effect was presented on CC5-MRSA-SCCmecI-agrII, a dominant MRSA clone among wound isolates worldwide. An assessment of effects of different protocols on dressing changes (1 or 2 times per week) demonstrated significantly greater antibiofilm activity (P < .05) of 3-day dressing changes. These findings support the use of VAC therapy as a topical antibiofilm treatment for the effective management of wound healing.
Mind & body practices in the treatment of adolescent anxiety
Authors: Fulweiler Bernadette , John Rita Marie 
Published: July 2018

Abstract:
Although anxiety is the most common mental health condition among adolescents in the United States, the current standards of practice for treatment are expensive, may be difficult to obtain, and potentially harmful. Although mind and body practices show great promise in the treatment of adolescent anxiety, financial constraints, lack of education, and structural barriers can hinder the integration of these practices into primary care.
Recognizing and treating Lyme disease
Authors: Saccomano Scott J. , Hrelic Debra A. 
Published: July 2018

Abstract:
Lyme disease is the most commonly reported vector-borne disease in the United States. After initial antibiotic treatment for patients with Lyme disease, ongoing symptoms that may persist have considerable long-term impact on healthcare costs. Posttreatment Lyme disease syndrome is characterized by a host of chronic symptoms that can leave patients physically and mentally disabled.
Resting-state Dynamics as a Cortical Signature of Anesthesia in Monkeys
Authors: Uhrig Lynn , Sitt Jacobo D. , Jacob Amaury , Tasserie Jordy , Barttfeld Pablo , Dupont Morgan , Dehaene Stanislas , Jarraya Bechir 
Published: July 2018

Abstract

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New

Background
The mechanism by which anesthetics induce a loss of consciousness remains a puzzling problem. We hypothesized that a cortical signature of anesthesia could be found in an increase in similarity between the matrix of resting-state functional correlations and the anatomical connectivity matrix of the brain, resulting in an increased function-structure similarity.

Methods
We acquired resting-state functional magnetic resonance images in macaque monkeys during wakefulness (n = 3) or anesthesia with propofol (n = 3), ketamine (n = 3), or sevoflurane (n = 3). We used the k-means algorithm to cluster dynamic resting-state data into independent functional brain states. For each condition, we performed a regression analysis to quantify function-structure similarity and the repertoire of functional brain states.

Results
Seven functional brain states were clustered and ranked according to their similarity to structural connectivity, with higher ranks corresponding to higher function-structure similarity and lower ranks corresponding to lower correlation between brain function and brain anatomy. Anesthesia shifted the brain state composition from a low rank (rounded rank [mean ± SD]) in the awake condition (awake rank = 4 [3.58 ± 1.03]) to high ranks in the different anesthetic conditions (ketamine rank = 6 [6.10 ± 0.32]; moderate propofol rank = 6 [6.15 ± 0.76]; deep propofol rank = 6 [6.16 ± 0.46]; moderate sevoflurane rank = 5 [5.10 ± 0.81]; deep sevoflurane rank = 6 [5.81 ± 1.11]; P < 0.0001).

Conclusions
Whatever the molecular mechanism, anesthesia led to a massive reconfiguration of the repertoire of functional brain states that became predominantly shaped by brain anatomy (high function-structure similarity), giving rise to a well-defined cortical signature of anesthesia-induced loss of consciousness.