bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Yablo Paradox
Authors: Cook Roy T 
Published: September 2014

Abstract
This book examines the Yablo paradox—a paradoxical, infinite sequence of sentences, each of which entails the falsity of all others later than it in the sequence—with special attention paid to the idea that this paradox provides us with an example of a semantic paradox that involves no circularity. The three main chapters of the book focus, respectively, on three questions that can be (and have been) asked about the Yablo construction. First, the Characterization Problem: What patterns of sentential reference (circular or not) generate semantic paradoxes? Addressing this problem requires an interesting and fruitful detour through the theory of directed graphs, allowing us to make connections between philosophical problems and purely mathematical ones. Next is the Circularity Question: Is the Yablo paradox genuinely non-circular? Answering this question is complicated: although the original formulation of the Yablo paradox is circular, it turns out that it is not so in any sense that can bear the blame for the paradox. Further, formulations of the paradox using infinitary conjunction provide genuinely non-circular constructions. Finally, we have the Generalizability Question: Can the Yabloesque pattern be used to generate genuinely non-circular variants of other paradoxes, such as epistemic and set-theoretic paradoxes? Although there are general constructions—unwindings—that transform circular constructions into Yablo-like sequences, it turns out that these sorts of construction are not “well-behaved” when transferred from semantic puzzles to puzzles of other sorts. The text concludes with a short discussion of the connections between the Yablo paradox and the Curry paradox.
Solution of Discrete Navier–Stokes Problems
Authors: Elman Howard C. , Silvester David J. , Wathen Andrew J. 
Published: September 2014

AbstractThis chapter concerns iterative methods for solution of the discrete Navier–Stokes equations. The emphasis is on preconditioning methods tailored to the structure of the linearized differential equations and the impact of boundary conditions on derivation of methods. These ideas are combined with multigrid methods and algorithms for nonlinear iteration.
Circuit QED: superconducting qubits coupled to microwave photons
Authors: Girvin S. M. 
Published: September 2014

AbstractThis chapter introduces the basic concepts of quantum information processing with superconducting quantum circuits. It starts with a demonstration of how,in these electrodynamic systems, both the superconducting gap and the long-range Coulomb interactions contribute to the existence of collective modesthat have extremely low dissipationand that can be quantized. The chapter also gives in-depth coverage of quantum harmonic oscillators in all their glory from various perspectives. Superconducting qubits are then introduced, starting with the fundamental theory of the Josephson effect and moving on to a presentation of the variety of existing superconducting qubits. Particular attention is given to the dispersive readout of qubits through their interaction with a cavity into which flying modes can be scattered. Finally, the opportunities offered for quantum information processing by employing the cavity as a quantum bus are presented.
Quantum optomechanics
Authors: Marquardt F. 
Published: September 2014

Abstract
This chapter provides a general introduction to the basic concepts of quantum optomechanics. It shows how strongly quantum optomechanical systems reduce to a linear interaction between a phonon mode and the mode of the fluctuations of the cavity field. It then presents the effect of light on the response the mechanical system, drawing an analogy with sideband cooling. Homodyne measurement of the position of the mechanical system is described. The chapter ends by explaining how to prepare exotic states of a mechanical oscillator and how the physics of the interaction between light and matter at play in optomechanics may one dayallow investigations of the possible effects of quantum gravity.
Two-electron spin qubits in GaAs: control and dephasing due to nuclear spins
Authors: Yacoby A. , Bluhm H. 
Published: September 2014

Abstract
This chapter presents a review of quantum dots in two-dimensional electron gases. The spin qubits realized in these systems are strongly affected by the surrounding nuclear spins. An elegant demonstration is given that the nuclear spin bath is not as irreversible as one might think. Echo sequences can efficiently undo the dephasing of the qubitbrought about by the motion of nuclear spins.
PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions
Authors: Chen Wei , Zhang Xitong , Brooker Jordan , Lin Hao , Zhang Liqing , Chou Kuo-Chen 
Published: September 2014

Abstract
Summary: The avalanche of genomic sequences generated in the post-genomic age requires efficient computational methods for rapidly and accurately identifying biological features from sequence information. Towards this goal, we developed a freely available and open-source package, called PseKNC-General (the general form of pseudo k-tuple nucleotide composition), that allows for fast and accurate computation of all the widely used nucleotide structural and physicochemical properties of both DNA and RNA sequences. PseKNC-General can generate several modes of pseudo nucleotide compositions, including conventional k-tuple nucleotide compositions, Moreau–Broto autocorrelation coefficient, Moran autocorrelation coefficient, Geary autocorrelation coefficient, Type I PseKNC and Type II PseKNC. In every mode, &gt;100 physicochemical properties are available for choosing. Moreover, it is flexible enough to allow the users to calculate PseKNC with user-defined properties. The package can be run on Linux, Mac and Windows systems and also provides a graphical user interface.
Availability and implementation: The package is freely available at: http://lin.uestc.edu.cn/server/pseknc .
Contact: chenweiimu@gmail.com or lqzhang@vt.edu or kcchou@gordonlifescience.org .
Supplementary information: Supplementary data are available at Bioinformatics online.
Effect of ocean warming and acidification on a plankton community in the NW Mediterranean Sea
Authors: Maugendre L. , Gattuso J.-P. , Louis J. , de Kluijver A. , Marro S. , Soetaert K. , Gazeau F. 
Published: September 2014

AbstractThe effect of ocean warming and acidification was investigated on a natural plankton assemblage from an oligotrophic area, the bay of Villefranche (NW Mediterranean Sea). The assemblage was sampled in March 2012 and exposed to the following four treatments for 12 days: control (∼360 μatm, 14°C), elevated pCO2 (∼610 μatm, 14°C), elevated temperature (∼410 μatm, 17°C), and elevated pCO2 and temperature (∼690 μatm, 17°C). Nutrients were already depleted at the beginning of the experiment and the concentrations of chlorophyll a (chl a), heterotrophic prokaryotes and viruses decreased, under all treatments, throughout the experiment. There were no statistically significant effects of ocean warming and acidification, whether in isolation or combined, on the concentrations of nutrients, particulate organic matter, chl a and most of the photosynthetic pigments. Furthermore, 13C labelling showed that the carbon transfer rates from 13C-sodium bicarbonate into particulate organic carbon were not affected by seawater warming nor acidification. Rates of gross primary production followed the general decreasing trend of chl a concentrations and were significantly higher under elevated temperature, an effect exacerbated when combined to elevated pCO2 level. In contrast to the other algal groups, the picophytoplankton population (cyanobacteria, mostly Synechococcus) increased throughout the experiment and was more abundant in the warmer treatment though to a lesser extent when combined to high pCO2 level. These results suggest that under nutrient-depleted conditions in the Mediterranean Sea, ocean acidification has a very limited impact on the plankton community and that small species will benefit from warming with a potential decrease of the export and energy transfer to higher trophic levels.
Hepatitis C in Sub-Saharan Africa: Urgent Need for Attention
Authors: Layden Jennifer E. , Phillips Richard , Opare-Sem Ohene , Akere Adegboyega , Salako Babatunde L. , Nelson Kenrad , Dugas Lara , Luke Amy , Tayo Bamidele O. , Cooper Richard S. 
Published: September 2014

Abstract
The hepatitis C virus (HCV), which was not recognized as an infectious agent until the 1980s, is responsible for a worldwide epidemic. The World Health Organization estimates global prevalence at 2.8%, with 185 million persons infected. In contrast to hepatitis B, where successful vaccine campaigns have reduced the disease burden, much less progress has been made toward the control of HCV. Phylogenetic studies suggest that HCV originated in Africa and has been endemic in some regions for at least 500–600 years. However, little is known about the epidemiology, transmission, and clinical course of HCV in Africa. With the advent of highly effective anti-HCV agents, there exists great potential to at least curb the global epidemic. For regions such as sub-Saharan Africa, however, this will require a thorough understanding of the regional population-level epidemiology, risk factors, and transmission mechanisms. Only then can effective treatment and prevention strategies be introduced.
Accurate Estimation of Energy Requirements of Young Patients
Authors: Carpenter Andrea , Pencharz Paul , Mouzaki Marialena 
Published: September 2014

ABSTRACTThe provision of optimal nutritional care is based on accurate estimations of patients' resting energy expenditure. The latter can be calculated with the use of predictive equations or measured with indirect calorimetry (IC). Owing to their ease of use, mathematical equations have largely replaced IC in clinical practice. This article examines the limitations and predictive inaccuracy of commonly used equations in pediatrics, which may contribute to the provision of poor nutritional care and directly affect patient outcomes. In addition, the role of IC is discussed and the physiology of nutrient metabolism, in terms of energy expenditure, is reviewed.
miR‐222 Overexpression May Contribute to Liver Fibrosis in Biliary Atresia by Targeting PPP2R2A
Authors: Dong Rui , Zheng Yijie , Chen Gong , Zhao Rui , Zhou Zhijian , Zheng Shan 
Published: September 2014

ABSTRACTObjective:Biliary atresia (BA) is a devastating liver disease in infants. Progressive hepatic fibrosis is often observed in postoperative patients with BA even after a successful Kasai portoenterostomy procedure. MicroRNA‐222 (miRNA) has been linked to the activation of stellate cells and the progression of liver fibrosis.Methods:In this study, the miR‐222 expression profile in BA and infants with anicteric choledochal cyst (CC) was determined. The functional effect of miR‐222 inhibition on the growth of the human hepatic stellate cell line LX‐2 was also evaluated. The downstream signaling pathways and target of miR‐222 were determined by coupling gene expression profiling and pathway analysis and by in silico prediction, respectively. In addition, we demonstrated miR‐222 overexpression in patients with BA compared with choledochal cyst controls.Results:Inhibition of miR‐222 in the LX‐2 cell line significantly decreased cell proliferation. We also identified protein phosphatase 2A subunit B as a target of miR‐222. The downstream signaling pathway, Akt, was also influenced by miR‐222. A consistent reduction of Akt phosphorylation and Ki67 in the LX‐2 line was shown following miR‐222 suppression.Conclusions:Our results show that miR‐222 overexpression is common in BA and contributes to LX‐2 cell proliferation by targeting protein phosphatase 2A subunit B and Akt signaling.
Abdominal Circumference or Gastric Residual Volume as Measure of Feed Intolerance in VLBW Infants
Authors: Kaur Avneet , Kler Neelam , Saluja Satish , Modi Manoj , Soni Arun , Thakur Anup , Garg Pankaj 
Published: September 2014

ABSTRACTBackground:The aim of the study was to compare prefeed abdominal circumference (AC) and gastric residual volume (GRV) as a measure of feed intolerance in very‐low‐birth‐weight infants (VLBW).Methods:Eighty VLBW infants were randomized to 2 groups; feed intolerance was monitored by measuring either GRV group or prefeed AC group. The primary outcome was time to full enteral feeds (180 mL · kg−1 · day−1). Other main outcome measures were feed interruption days, duration of parenteral nutrition, incidence of culture positive sepsis, necrotizing enterocolitis, mortality, and duration of hospital stay.Results:The median (interquartile range) time to achieve full feeds was 10 (9–13) versus 14 (12–17.5) days in AC and GRV groups, respectively (P < 0.001). Infants in AC group had fewer feed interruption days (0 [0–2] vs 2.0 [1, 5], P < 0.001) and shorter duration of parenteral nutrition (P < 0.001). The incidence of culture‐positive sepsis in AC and GRV groups was 17.5% and 30 %, respectively (P = 0.18). Duration of hospital stay and mortality were comparable in both the groups.Conclusions:Prefeed AC as a measure of feed intolerance in VLBW infants may shorten the time taken to achieve full feeds.
Pico Gauges for Minimally Invasive Intracellular Hydrostatic Pressure Measurements
Authors: Knoblauch Jan , Mullendore Daniel L. , Jensen Kaare H. , Knoblauch Michael 
Published: September 2014

AbstractIntracellular pressure has a multitude of functions in cells surrounded by a cell wall or similar matrix in all kingdoms of life. The functions include cell growth, nastic movements, and penetration of tissue by parasites. The precise measurement of intracellular pressure in the majority of cells, however, remains difficult or impossible due to their small size and/or sensitivity to manipulation. Here, we report on a method that allows precise measurements in basically any cell type over all ranges of pressure. It is based on the compression of nanoliter and picoliter volumes of oil entrapped in the tip of microcapillaries, which we call pico gauges. The production of pico gauges can be accomplished with standard laboratory equipment, and measurements are comparably easy to conduct. Example pressure measurements are performed on cells that are difficult or impossible to measure with other methods.
Quantitative gas saturation estimation by frequency‐dependent amplitude‐versus‐offset analysis
Authors: Wu Xiaoyang , Chapman Mark , Li Xiang‐Yang , Boston Patrick 
Published: September 2014

ABSTRACTSeismic amplitudes contain important information that can be related to fluid saturation. The amplitude‐versus‐offset analysis of seismic data based on Gassmann's theory and the approximation of the Zoeppritz equations has played a central role in reservoir characterization. However, this standard technique faces a long‐standing problem: its inability to distinguish between partial gas and “fizz‐water” with little gas saturation. In this paper, we studied seismic dispersion and attenuation in partially saturated poroelastic media by using frequency‐dependent rock physics model, through which the frequency‐dependent amplitude‐versus‐offset response is calculated as a function of porosity and water saturation. We propose a cross‐plotting of two attributes derived from the frequency‐dependent amplitude‐versus‐offset response to differentiate partial gas saturation and “fizz‐water” saturation. One of the attributes is a measure of “low frequency”, or Gassmann, of reflectivity, whereas the other is a measure of the “frequency dependence” of reflectivity. This is in contrast to standard amplitude‐versus‐offset attributes, where there is typically no such separation. A pragmatic frequency‐dependent amplitude‐versus‐offset inversion for rock and fluid properties is also established based on Bayesian theorem. A synthetic study is performed to explore the potential of the method to estimate gas saturation and porosity variations. An advantage of our work is that the method is in principle predictive, opening the way to further testing and calibration with field data. We believe that such work should guide and augment more theoretical studies of frequency‐dependent amplitude‐versus‐offset analysis.
The cumulative effect of trawl fishing on a multispecies fish assemblage in south‐eastern Australia
Authors: Foster Scott D. , Dunstan Piers K. , Althaus Franziska , Williams Alan 
Published: September 2014

Summary

Understanding the effect of anthropogenic pressure on animal assemblages over time is a challenging problem that integrates human activities and community ecology. Our ability to make informed decisions for managing pressures depends on estimating their ecological effects, and a rigorous and objective approach should be used. There are three requirements for this type of approach to be successful: sufficient biological and ecological data, congruent data describing human activity and an appropriate statistical method that can link the ecological information to the pressures.

In this work, we explore the effects of cumulative bottom‐trawl fishing on fish assemblages over a 20‐year period. The analysis captures assemblage responses during the early period of the fishery's development and shows the changes in the abundance of many species as a small and coherent set of ‘archetypical’ responses to cumulative pressure.

The effect of the cumulative pressure is heterogeneous: some archetypical responses show consistent decline with increased fishing effort, some are less sensitive, and some show an increase in abundance.

Some, but not all, archetypical response groups are composed of species with similar ecological and life‐history traits. Most obviously, the archetype showing greatest decline in abundance is made up of species that have the highest mean values of generation time, oldest age at maturity and longest life span.

Applications of the methods include identifying spatially explicit system‐level trade‐offs – between species, species groups (archetypes) and fishery subareas – for ecosystem‐based management.

Synthesis and applications The impact of fishing pressure, accumulated over time, induces heterogeneous patterns of change in fish assemblage composition. The patterns of change are grouped into ‘archetypical response groups’ to provide an interpretable and robust description. The composition of the species groups show that life‐history traits are indicative but do not always provide a complete description of how a species might respond to the pressure.
Causes of and factors associated with stillbirth in low‐ and middle‐income countries: a systematic literature review
Authors: Aminu M , Unkels R , Mdegela M , Utz B , Adaji S , van den Broek N 
Published: September 2014

BackgroundAnnually, 2.6 million stillbirths occur worldwide, 98% in developing countries. It is crucial that we understand causes and contributing factors.MethodsWe conducted a systematic review of studies reporting factors associated with and cause(s) of stillbirth in low‐ and middle‐income countries (2000–13). Narrative synthesis to compare similarities and differences between studies with similar outcome categories.Main resultsA total of 142 studies with 2.1% from low‐income settings were investigated; most report on stillbirths occurring at health facility level. Definition of stillbirth varied; 10.6% of studies (mainly upper middle‐income countries) used a cut‐off point of ≥22 weeks of gestation and 32.4% (mainly lower income countries) used ≥28 weeks of gestation. Factors reported to be associated with stillbirth include poverty and lack of education, maternal age (>35 or <20 years), parity (1, ≥5), lack of antenatal care, prematurity, low birthweight, and previous stillbirth. The most frequently reported cause of stillbirth was maternal factors (8–50%) including syphilis, positive HIV status with low CD4 count, malaria and diabetes. Congenital anomalies are reported to account for 2.1–33.3% of stillbirths, placental causes (7.4–42%), asphyxia and birth trauma (3.1–25%), umbilical problems (2.9–33.3%), and amniotic and uterine factors (6.5–10.7%). Seven different classification systems were identified but applied in only 22% of studies that could have used a classification system. A high percentage of stillbirths remain ‘unclassified’ (3.8–57.4%).ConclusionTo build capacity for perinatal death audit, clear guidelines and a suitable classification system to assign cause of death must be developed. Existing classification systems may need to be adapted. Better data and more data are urgently needed.
Cause of and contributing factors to maternal deaths; a cross‐sectional study using verbal autopsy in four districts in Bangladesh
Authors: Halim A , Utz B , Biswas A , Rahman F , van den Broek N 
Published: September 2014

Verbal autopsy used at community level is an accepted method to identify cause of death and factors contributing to death. Maternal deaths occurring in four districts in Bangladesh over a period of 24 months were identified and community health workers were trained to conduct a verbal autopsy. Of 571 maternal deaths identified almost half (273, 47.8%) occurred at facility level, 97 (17.0%) died en route to a healthcare facility and 201 (35.2%) maternal deaths occurred at home. The majority of maternal deaths occurred in the postpartum period (78.8%) in the first 6 hours after giving birth (41.6% of all postpartum deaths). Women who had accessed care at a healthcare facility were less likely to die in the first 6 hours when compared with women who died at home (relative risk 0.70; 95% confidence interval 0.56–0.88) 70.4% (402) of deaths were classified as direct maternal deaths, 12.4% (71) as indirect and 13.8% (79) as unspecified. The most common cause of death was haemorrhage (38%), followed by eclampsia (20%) and sepsis (8.1%). Almost three out of four women who died had sought care for complications during the index pregnancy. Most mothers who died in Bangladesh had accessed care. It is now crucial that the quality of care received at health facility level is improved. This includes a refocus on strengthening healthcare providers' knowledge and skills to recognise and manage complications and provide emergency obstetric care. The enabling environment must be in place as well as ensuring a fully functional referral pathway between healthcare facilities.
Dietary recommendations for obese pregnant women: current questions and controversies
Authors: Poston Lucilla , Patel Nashita 
Published: September 2014

AbstractWith the increasing prevalence of obesity, maternal obesity is now one of the most common high‐risk obstetric conditions. Obesity and excessive gestational weight gain are important modifiable risk factors for maternal and neonatal morbidity and mortality. Maternal obesity, associated with neonatal adiposity and high birthweight, has been implicated in increased risk of childhood obesity. Considerable effort has been directed towards improving clinical outcomes by lifestyle change in pregnant obese women, but there is at present no evidence‐based intervention of adequate efficacy which can be recommended. The focus has been on preventing excessive weight gain, but studies have lacked the power to address effects on clinical outcomes; therefore preventing clinical practice translation. Adequately powered intervention studies devised to reduce neonatal adiposity by improvement of maternal glucose homeostasis, are needed to inform the optimal dietary and/or physical activity regimen.