bluuebunny/crossref_metadata_2025_split huggingface dataset:
How I Met Your Mother and other Lucky Accidents
Authors: Jaffe Audrey 
Published: April 2016

Abstract
This chapter is divided into discussions of Dickens’s Oliver Twist and Hardy’s The Mayor of Casterbridge. For both novels it considers the framing of class identity and realist uniqueness as simultaneously grounded in the real and as products of fantasy, especially in the mapping of class onto family articulated by Freud’s idea of the family romance. Both novels use the fantasmatic device of coincidence to shore up the reality of familial connections. The chapter also discusses the structuring of realist character in the blankness and fungibility of Dickens’s Oliver and Hardy’s Elizabeth-Jane, as well as the idea of secondariness in the latter, continuing a discussion of the tension between realist subjectivity and uniqueness, on the one hand, and a sensational emphasis on position on the other that began in chapter 1 and continues throughout the book.
The Facts in Logical Space
Authors: Turner Jason 
Published: April 2016

AbstractThis book develops and defends in detail a factalist ontological picture, according to which reality’s ultimate constituents are structureless atomic facts. The existence (or appearances as) of non-facts are ultimately grounded in a system of quasi-geometric relations that the facts participate in. Axioms for this quasi-geometric system are given, and a representation theorem is proven. It establishes that if the facts satisfy the axioms, then they have a unique (up to isomorphism) ‘object-and-property’ representation: each fact can be thought of as though it were made up of individuals and properties (or relations), even though it is not. The metaphysical picture also makes room for an attractive combinatorial modal theory, according to which possibilities are simply collections of (possible) facts.
Effect of Cuff Design on Auscultatory and Oscillometric Blood Pressure Measurements
Authors: Ringrose Jennifer S. , McLean Donna , Ao Peter , Yousefi Farahnaz , Sankaralingam Sowndramalingam , Millay Jack , Padwal Raj 
Published: April 2016

Abstract

BACKGROUND
Two-piece blood pressure (BP) cuffs are the historical cuff standard. Use of 1-piece cuffs is increasing. Substituting 1-piece for 2-piece cuffs has an unknown effect on measurement accuracy. We compared these cuff types in a 2-phase study using auscultatory and oscillometric techniques.

METHODS
Consenting subjects (aged ≥18 years) with BP levels between 80 and 220mm Hg/50 and 120mm Hg and arm circumferences between 25 and 43cm were studied using the International Standards Organization (ISO) 2013 protocol (modified). A Baum 2-piece cuff was used as the reference standard. A 1-piece Welch Allyn cuff was the comparator. In phase 1 (2-observer auscultation with a mercury sphygmomanometer), 88 subjects were required to obtain 255 paired BP determinations. In phase 2 (oscillometric measurement with a Spacelabs 90207 device), 85 subjects were studied. Each phase was analyzed separately using paired t -tests.

RESULTS
Phase 1 mean age was 54.2±20.5 years, mean arm circumference was 29.9±3.7cm, 60% were female, and 32% had hypertension. One-piece cuff mean BPs were lower than the 2-piece cuff means (115.5±15.5/66.4±9.3 vs. 117.8±15.2/67.9±9.2; difference of −2.4±3.6/−1.5±2.4; P values &lt;0.0001 for systolic and diastolic comparisons). Phase 2 mean age was 52.8±20.8 years, mean arm circumference was 29.4±3.9cm, 67% were female, and 38% had hypertension. Mean BPs were lower for the 1-piece compared to the 2-piece cuff (116.5±12.8/67.1±8.1 vs. 120.8±13.5/70.4±8.5; difference of −4.4±3.6/−3.3±2.7; P values &lt;0.0001 for both).

CONCLUSIONS
Mean BP is lower with 1-piece cuffs vs. 2-piece cuffs. Differences are greater with oscillometry. When performing validation studies and measurements for clinical purposes, cuff type should be taken into account.
Importance of Calibration Method in Central Blood Pressure for Cardiac Structural Abnormalities
Authors: Negishi Kazuaki , Yang Hong , Wang Ying , Nolan Mark T. , Negishi Tomoko , Pathan Faraz , Marwick Thomas H. , Sharman James E. 
Published: April 2016

Abstract

BACKGROUND
Central blood pressure (CBP) independently predicts cardiovascular risk, but calibration methods may affect accuracy of central systolic blood pressure (CSBP). Standard central systolic blood pressure (Stan-CSBP) from peripheral waveforms is usually derived with calibration using brachial SBP and diastolic BP (DBP). However, calibration using oscillometric mean arterial pressure (MAP) and DBP (MAP-CSBP) is purported to provide more accurate representation of true invasive CSBP. This study sought to determine which derived CSBP could more accurately discriminate cardiac structural abnormalities.

METHODS
A total of 349 community-based patients with risk factors (71±5years, 161 males) had CSBP measured by brachial oscillometry (Mobil-O-Graph, IEM GmbH, Stolberg, Germany) using 2 calibration methods: MAP-CSBP and Stan-CSBP. Left ventricular hypertrophy (LVH) and left atrial dilatation (LAD) were measured based on standard guidelines.

RESULTS
MAP-CSBP was higher than Stan-CSBP (149±20 vs. 128±15mm Hg, P &lt; 0.0001). Although they were modestly correlated (rho = 0.74, P &lt; 0.001), the Bland–Altman plot demonstrated a large bias (21mm Hg) and limits of agreement (24mm Hg). In receiver operating characteristic (ROC) curve analyses, MAP-CSBP significantly better discriminated LVH compared with Stan-CSBP (area under the curve (AUC) 0.66 vs. 0.59, P = 0.0063) and brachial SBP (0.62, P = 0.027). Continuous net reclassification improvement (NRI) ( P &lt; 0.001) and integrated discrimination improvement (IDI) ( P &lt; 0.001) corroborated superior discrimination of LVH by MAP-CSBP. Similarly, MAP-CSBP better distinguished LAD than Stan-CSBP (AUC 0.63 vs. 0.56, P = 0.005) and conventional brachial SBP (0.58, P = 0.006), whereas Stan-CSBP provided no better discrimination than conventional brachial BP ( P = 0.09).

CONCLUSIONS
CSBP is calibration dependent and when oscillometric MAP and DBP are used, the derived CSBP is a better discriminator for cardiac structural abnormalities.
An extreme paucity of second population AGB stars in the ‘normal’ globular cluster M4
Authors: MacLean B. T. , Campbell S. W. , De Silva G. M. , Lattanzio J. , D'Orazi V. , Simpson J. D. , Momany Y. 
Published: April 2016

Abstract
Galactic globular clusters (GCs) are now known to harbour multiple stellar populations, which are chemically distinct in many light element abundances. It is becoming increasingly clear that asymptotic giant branch (AGB) stars in GCs show different abundance distributions in light elements compared to those in the red giant branch (RGB) and other phases, skewing towards more primordial, field-star-like abundances, which we refer to as subpopulation one (SP1). As part of a larger programme targeting giants in GCs, we obtained high-resolution spectra for a sample of 106 RGB and 15 AGB stars in Messier 4 (NGC 6121) using the 2dF+HERMES facility on the Anglo–Australian Telescope. In this Letter, we report an extreme paucity of AGB stars with [Na/O] &gt;−0.17 in M4, which contrasts with the RGB that has abundances up to [Na/O] =0.55. The AGB abundance distribution is consistent with all AGB stars being from SP1. This result appears to imply that all subpopulation two stars (SP2; Na-rich, O-poor) avoid the AGB phase. This is an unexpected result given M4's horizontal branch morphology – it does not have an extended blue horizontal branch. This is the first abundance study to be performed utilizing the HERMES spectrograph.
PECULIARITIES OF VITRECTOMY AND MORPHOLOGIC CHANGES IN THE EPIRETINAL MEMBRANE AFTER INTRAVITREAL AFLIBERCEPT IN PATIENTS WITH SEVERE PROLIFERATIVE DIABETIC RETINOPATHY
Authors: Umanets Nikolai , Korol Andrii , Vit Valerii , Zavodnaya Vera , Pasyechnikova Natalya 
Published: April 2016

Purpose:
To examine the peculiarities of vitrectomy and morphologic changes in the epiretinal membrane after intravitreal aflibercept in patients with proliferative diabetic retinopathy.

Methods:
Prospective study of 21 consecutive cases with proliferative diabetic retinopathy complicated by vascularized epiretinal membrane forming tractional retinal detachment that underwent pars plana vitrectomy 4 days after intravitreal injection of aflibercept. After removal, the epiretinal membranes were taken for histologic examination using light microscopy. Obliteration of neovascularization of epiretinal membranes, the lack of bleeding in the intraoperative and early postoperative periods, retinal attachment, and improvement of visual acuity were taken for the criteria of treatment effectiveness.

Results:
On the fourth day after intravitreal injection, newly formed vessels of epiretinal membranes were completely obliterated. There was no bleeding during segmentation and delamination of epiretinal membranes during vitrectomy. In the early postoperative period, bleeding complications were not noted. A microscopic examination of epiretinal membranes showed single-thin-walled capillary vessels lined with endothelial cells, the lumen of which does not contain blood cells. Capillaries are submerged in the connective tissue of different degrees of maturity.

Conclusion:
Intravitreal aflibercept resulted in the obliteration of neovascularization of epiretinal membranes, thus avoiding intraoperative and postoperative bleeding during vitrectomy. The improvement in visual acuity was noted in all cases. Histologic examination of epiretinal membranes determined single-thin-walled capillary vessels lined with endothelial cells without blood cells.
A statistical guide to the design of deep mutational scanning experiments
Authors: Matuszewski Sebastian , Hildebrandt Marcel E. , Ghenu Ana-Hermina , Jensen Jeffrey D. , Bank Claudia 
Published: April 2016

AbstractThe characterization of the distribution of mutational effects is a key goal in evolutionary biology. Recently developed deep-sequencing approaches allow for accurate and simultaneous estimation of the fitness effects of hundreds of engineered mutations by monitoring their relative abundance across time points in a single bulk competition. Naturally, the achievable resolution of the estimated fitness effects depends on the specific experimental setup, the organism and type of mutations studied, and the sequencing technology utilized, among other factors. By means of analytical approximations and simulations, we provide guidelines for optimizing time-sampled deep-sequencing bulk competition experiments, focusing on the number of mutants, the sequencing depth, and the number of sampled time points. Our analytical results show that sampling more time points together with extending the duration of the experiment improves the achievable precision disproportionately as compared with increasing the sequencing depth, or reducing the number of competing mutants. Even if the duration of the experiment is fixed, sampling more time points and clustering these at the beginning and the end of the experiment increases experimental power, and allows for efficient and precise assessment of the entire range of selection coefficients. Finally, we provide a formula for calculating the 95%-confidence interval for the measurement error estimate, which we implement as an interactive web tool. This allows for quantification of the maximum expecteda prioriprecision of the experimental setup, as well as for a statistical threshold for determining deviations from neutrality for specific selection coefficient estimates.
An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy
Authors: Bank Claudia , Renzette Nicholas , Liu Ping , Matuszewski Sebastian , Shim Hyunjin , Foll Matthieu , Bolon Daniel N. A. , Zeldovich Konstantin B. , Kowalik Timothy F. , Finberg Robert W. , Wang Jennifer P. , Jensen Jeffrey D. 
Published: April 2016

ABSTRACTThe rapid evolution of drug resistance remains a critical public health concern. The treatment of influenza A virus (IAV) has proven particularly challenging, due to the ability of the virus to develop resistance against current antivirals and vaccines. Here we evaluate a novel antiviral drug therapy, favipiravir, for which the mechanism of action in IAV involves an interaction with the viral RNA-dependent RNA polymerase resulting in an effective increase in the viral mutation rate. We utilized an experimental evolution framework, combined with novel population genetic method development for inference from time-sampled data, in order to evaluate the effectiveness of favipiravir against IAV. Evaluating whole genome polymorphism data across fifteen time points under multiple drug concentrations and in controls, we present the first evidence for the ability of viral populations to effectively adapt to low concentrations of favipiravir. In contrast, under high concentrations, we observe population extinction, indicative of mutational meltdown. We discuss the observed dynamics with respect to the evolutionary forces at play and emphasize the utility of evolutionary theory to inform drug development.
Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data
Authors: Carissimo Guillaume , van den Beek Marius , Pegoraro Juliana , Vernick Kenneth D , Antoniewski Christophe 
Published: April 2016

AbstractWe present user-friendly and adaptable software to provide biologists, clinical researchers and possibly diagnostic clinicians with the ability to robustly detect and reconstruct viral genomes from complex deep sequence datasets. A set of modular bioinformatic tools and workflows was implemented as the Metavisitor package in the Galaxy framework. Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules. Metavisitor can be used on our Mississippi server, or can be installed on any Galaxy server instance and a pre-configured Metavisitor server image is provided. Metavisitor works with DNA, RNA or small RNA sequencing data over a range of read lengths and can use a combination of de novo and guided approaches to assemble genomes from sequencing reads. We show that the software has the potential for quick diagnosis as well as discovery of viruses from a vast array of organisms. Importantly, we provide here executable Metavisitor use cases, which increase the accessibility and transparency of the software, ultimately enabling biologists or clinicians to focus on biological or medical questions.
Analysis of Shared Heritability in Common Disorders of the Brain
Authors: Anttila V , Bulik-Sullivan B , Finucane H , Walters R , Bras J , Duncan L , Escott-Price V , Falcone G , Gormley P , Malik R , Patsopoulos N , Ripke S , Wei Z , Yu D , Lee PH , Turley P ,   IGAP consortium,   IHGC consortium,   ILAE Consortium on Complex Epilepsies,   IMSGC consortium,   IPDGC consortium,   METASTROKE and Intracerebral Hemorrhage Studies of the International Stroke Genetics Consortium,   Attention-Deficit Hyperactivity Disorder Working Group of the Psychiatric Genomics Consortium,   Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium,   Bipolar Disorders Working Group of the Psychiatric Genomics Consortium,   Eating Disorders Working Group of the Psychiatric Genomics Consortium,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium,   Tourette Syndrome and Obsessive Compulsive Disorder Working Group of the Psychiatric Genomics Consortium,   Schizophrenia Working Group of the Psychiatric Genomics Consortium, Breen G , Churchhouse C , Bulik C , Daly M , Dichgans M , Faraone SV , Guerreiro R , Holmans P , Kendler K , Koeleman B , Mathews CA , Price AL , Scharf JM , Sklar P , Williams J , Wood N , Cotsapas C , Palotie A , Smoller JW , Sullivan P , Rosand J , Corvin A , Neale BM ,   on behalf of the Brainstorm consortium
Published: April 2016

AbstractDisorders of the brain exhibit considerable epidemiological comorbidity and frequently share symptoms, provoking debate about the extent of their etiologic overlap. We quantified the genetic sharing of 25 brain disorders based on summary statistics from genome-wide association studies of 215,683 patients and 657,164 controls, and their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders show substantial sharing of common variant risk, while neurological disorders appear more distinct from one another. We observe limited evidence of sharing between neurological and psychiatric disorders, but do identify robust sharing between disorders and several cognitive measures, as well as disorders and personality types. We also performed extensive simulations to explore how power, diagnostic misclassification and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a source of risk for brain disorders and the value of heritability-based methods in understanding their etiology.
Cortical rhythms are modulated by respiration
Authors: Heck Detlef H. , McAfee Samuel S. , Liu Yu , Babajani-Feremi Abbas , Rezaie Roozbeh , Freeman Walter J. , Wheless James W. , Papanicolaou Andrew C. , Ruszinkó Miklós , Kozma Robert 
Published: April 2016

SummaryThe brain generates oscillatory neuronal activity at a broad range of frequencies and the presence and amplitude of certain oscillations at specific times and in specific brain regions are highly correlated with states of arousal, sleep, and with a wide range of cognitive processes. The neuronal mechanisms underlying the generation of brain rhythms are poorly understood, particularly for low-frequency oscillations. We recently reported that respiration-locked olfactory bulb activity causes delta band (0.5-4 Hz) oscillatory neuronal activity in the whisker sensory (barrel) cortex in mice. Furthermore, gamma oscillations (30 – 100Hz), which are widely implicated in cognitive processing, were power-modulated in synchrony with the respiratory rhythm. These findings link afferent sensory activity caused by respiration directly to cortical rhythms associated with cognitive functions. Here we review the related literature and present new evidence to propose that respiration has a direct influence on oscillatory cortical activity, including gamma oscillations, and on transitions between synchronous and asynchronous cortical network states (marked by phase transitions). Oscillatory cortical activity, as well as phase transitions, has been implicated in cognitive functions, potentially linking respiratory phase to cognitive processing. We further argue that respiratory influence on cortical activity is present in most, and possibly in all areas of the neocortex in mice and humans. We furthermore suggest that respiration had a role in modulating cortical rhythms from early mammalian evolution. Early mammals relied strongly on their olfactory sense and had proportionately large olfactory bulbs. We propose that to this day the respiratory rhythm remains an integral element of dynamic cortical activity in mammals. We argue that breathing modulates all cortical functions, including cognitive and emotional processes, which could elucidate the well-documented but largely unexplained effects of respiratory exercises on mood and cognitive function.
Network-based Computational Drug Combination Prediction
Authors: Li Fuhai , Lei Huang , Sheng Jianting , Wong Stephen 
Published: April 2016

AbstractCancers are complex diseases that are regulated by multiple signaling pathways. Patients often acquire resistance to single drug treatment. Use of drug combinations that target multiple parallel pathways is a promising strategy to reduce the drug resistance. Pharmacogenomics big data are being generated to uncover complex signaling mechanisms of cancers and correlate cancer-specific signaling with diverse drug responses. Thus, converting pharmacogenomics big data into knowledge can help the discovery of synergistic drug combination. However, it is challenging and remains an open problem due to the enormous number of combination possibilities and noise of genomics data.
Alternative Growth Behavior ofMycobacterium AviumSubspecies and Staphylococci with Implications for Clinical Microbiology and Blood Culture
Authors: Zhang Peilin , Minardi Lawrence M. , Kuenstner J. Todd , Zekan Steve M. 
Published: April 2016

AbstractRapid culture ofMycobacteriumavium subspecies paratuberculosis (MAP) from patients remains a challenge. During the process of developing a rapid culture method for MAP, we found that there is an alternative growth behavior present in MAP, MAH (Mycobacterium aviumsubspecies hominissuis) and other bacteria such asStaphylococcus aureus, andStaphylococcus pseudintermedius. The bacterial DNA, RNA and proteins are present in the supernatants of the liquid culture media after routine microcentrifugation. When cultured in the solid media plate, there are a limited number of colonies developed for MAP and MAH disproportionate to the growth. We believe there is an alternative growth behavior for MAP, MAH and other bacteria similar to “phenoptosis”. Based on the alternative bacterial growth behavior, we tested 62 blood culture specimens that have been reported negative by routine automated blood culture method after 5 days of incubation. We used alternative culture media and molecular diagnostic techniques to test these negative culture bottles, and we found a large percentage of bacterial growth by alternative culture media (32%) and by molecular PCR amplification using 16s rDNA primer set and DNA sequencing (69%). The sensitivity of detection by the molecular PCR/sequencing method is significantly higher than by routine automated blood culture. Given the challenge of early diagnosis of sepsis in the hospital setting, it is necessary to develop more sensitive and faster diagnostic tools to guide clinical practice and improve the outcome of sepsis management.
Eukaryotic Association Module in Phage WO Genomes fromWolbachia
Authors: Bordenstein Sarah R. , Bordenstein Seth R. 
Published: April 2016

AbstractViruses are trifurcated into eukaryotic, archaeal and bacterial categories. This domain-specific ecology underscores why eukaryotic viruses typically co-opt eukaryotic genes and bacteriophages commonly harbor bacterial genes. However, the presence of bacteriophages in obligate intracellular bacteria of eukaryotes may promote DNA transfers between eukaryotes and bacteriophages. Here we report the metagenomic analysis of purified bacteriophage WO particles ofWolbachiaand uncover a eukaryotic association module. It encodes domains, such as the black widow latrotoxin C-terminal domain, that are uninterrupted in bacteriophage genomes, enriched with eukaryotic protease cleavage sites, and combined with additional domains to forge one of the largest bacteriophage genes to date (14,256 bp). These domains have never before been reported in packaged bacteriophages, to our knowledge, and their phylogeny, distribution and sequence diversity imply lateral transfers between animal and bacteriophage genomes. Finally, the WO genome sequences and identification of attachment sites will potentially advance genetic manipulation ofWolbachia.