bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk Factors for Longer Hospital Stay Following the Fontan Operation
Authors: Sasaki Jun , Dykes John C. , Sosa Lisa J. , Salvaggio Jane L. , Tablante Milagros D. , Ojito Jorge , Khan Danyal M. , Hannan Robert L. , Rossi Anthony F. , Burke Redmond P. , Wernovsky Gil 
Published: February 2016

Objectives:
Children with functional single ventricle undergoing the Fontan operation consume considerable resources. The purpose of this study is to evaluate pre- and intraoperative risk factors for longer hospital stay and to describe the perioperative course at a single institution over a 15-year period.

Design:
Retrospective cohort study.

Setting:
A single pediatric cardiac ICU.

Patients:
All consecutive patients undergoing a first-time Fontan operation from 2000 to 2014.

Interventions:
None.

Measurements and Main Results:
Prolonged length of stay was defined as hospital stay greater than 75 percentile at our institution after surgery. Of 218 patients who met inclusion criteria, median length of stay was 10 days (interquartile range, 8–14 d); prolonged length of stay was defined greater than or equal to 15 days. Independent pre- and intraoperative risk factors for prolonged length of stay included higher hemoglobin (odds ratio, 1.29; p = 0.003), higher mean pulmonary artery pressure (odds ratio, 1.14; p = 0.037), and lower aortic saturation (odds ratio, 0.92; p = 0.008) in the entire group. When patients with hepatic vein inclusion (following previous Kawashima) were excluded, higher hemoglobin (odds ratio, 1.24; p = 0.027), lower aortic saturation (odds ratio, 0.92; p = 0.017), and placement of a fenestration (odds ratio, 2.438; p = 0.021) were associated with prolonged length of stay. Fifty-eight patients (26.6%) had major complications defined by Pediatric Cardiac Critical Care Consortium. Placement of a fenestration (odds ratio, 2.297; p = 0.014) and longer aortic cross-clamp time (odds ratio, 1.015; p = 0.003) were independently associated with Pediatric Cardiac Critical Care Consortium major complications.

Conclusions:
In this series, 75% of patients had a postoperative length of stay less than or equal to 2 weeks. Preoperative factors suggesting worse hypoxemia/decreased pulmonary blood flow (higher hemoglobin and lower oxygen saturation) and increased pulmonary artery pressure were associated with prolonged length of stay. These findings may help risk stratify this complex patient population, provide more accurate family counseling, and provide preliminary data for changes in preoperative timing of the Fontan and/or changes to postoperative management strategies for those at high risk for increased ICU morbidity.
VcfR: a package to manipulate and visualize VCF format data in R
Authors: Knaus Brian J. , Grünwald Niklaus J. 
Published: February 2016

AbstractSoftware to call single nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice. This has created a need for tools to work with VCF files. While an increasing number of software exists to read VCF data, many only extract the genotypes without including the data associated with each genotype that describes its quality. We created the R package vcfR to address this issue. We developed a VCF file exploration tool implemented in the R language because R provides an interactive experience and an environment that is commonly used for genetic data analysis. Functions to read and write VCF files into R as well as functions to extract portions of the data and to plot summary statistics of the data are implemented. VcfR further provides the ability to visualize how various parameterizations of the data affect the results. Additional tools are included to integrate sequence (FASTA) and annotation data (GFF) for visualization of genomic regions such as chromosomes. Conversion functions translate data from the vcfR data structure to formats used by other R genetics packages. Computationally intensive functions are implemented in C++ to improve performance. Use of these tools is intended to facilitate VCF data exploration, including intuitive methods for data quality control and easy export to other R packages for further analysis. VcfR thus provides essential, novel tools currently not available in R.
Learning In Spike Trains: Estimating Within-Session Changes In Firing Rate Using Weighted Interpolation
Authors: Jensen Greg , Muñoz Fabian , Ferrera Vincent P. 
Published: February 2016

AbstractThe electrophysiological study of learning is hampered by modern procedures for estimating firing rates: Such procedures usually require large datasets, and also require that included trials be functionally identical. Unless a method can track the real-time dynamics of how firing rates evolve, learning can only be examined in the past tense. We propose a quantitative procedure, called ARRIS, that can uncover trial-by-trial firing dynamics. ARRIS provides reliable estimates of firing rates based on small samples using the reversible-jump Markov chain Monte Carlo algorithm. Using weighted interpolation, ARRIS can also provide estimates that evolve over time. As a result, both real-time estimates of changing activity, and of task-dependent tuning, can be obtained during the initial stages of learning.
The architecture of the human RNA-binding protein regulatory network
Authors: Quattrone Alessandro , Dassi Erik 
Published: February 2016

AbstractRNA-binding proteins (RBPs) are key players of post-transcriptional regulation of gene expression. These proteins influence both cellular physiology and pathology by regulating processes ranging from splicing and polyadenylation to mRNA localization, stability, and translation. To fine-tune the outcome of their regulatory action, RBPs rely on an intricate web of competitive and cooperative interactions. Several studies have described individual interactions of RBPs with RBP mRNAs, suggestive of a RBP-RBP regulatory structure. Here we present the first systematic investigation of this structure, based on a network including almost fifty thousand experimentally determined interactions between RBPs and bound RBP mRNAs.Our analysis identified two features defining the structure of the RBP-RBP regulatory network. What we call “RBP clusters” are groups of densely interconnected RBPs which co-regulate their targets, suggesting a tight control of cooperative and competitive behaviors. “RBP chains”, instead, are hierarchical structures driven by evolutionarily ancient RBPs, which connect the RBP clusters and could in this way provide the flexibility to coordinate the tuning of a broad set of biological processes.The combination of these two features suggests that RBP chains may use the modulation of their RBP targets to coordinately control the different cell programs controlled by the RBP clusters. Under thisisland-hoppingmodel, the regulatory signal flowing through the chains hops from one RBP cluster to another, implementing elaborate regulatory plans to impact cellular phenotypes. This work thus establishes RBP-RBP interactions as a backbone driving post-transcriptional regulation of gene expression to allow the fine-grained control of RBPs and their targets.
The Genetic Architecture of Quantitative Traits Cannot Be Inferred From Variance Component Analysis
Authors: Huang Wen , Mackay Trudy F.C. 
Published: February 2016

AbstractClassical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals. The genetic variance components are defined in terms of genotypic values reflecting underlying genetic architecture (additive, dominance and epistatic genotypic effects) and allele frequencies. However, the dependency of the definition of genetic variance components on the underlying genetic models is not often appreciated. Here, we show how the partitioning of additive and non-additive genetic variation is affected by the genetic models and parameterization of allelic effects. We show that arbitrarily defined variance components often capture a substantial fraction of total genetic variation regardless of the underlying genetic architecture in simulated and real data. Therefore, variance component analysis cannot be used to infer genetic architecture of quantitative traits. The genetic basis of quantitative trait variation in a natural population can only be defined empirically using high resolution mapping methods followed by detailed characterization of QTL effects.
Copy number variants in the sheep genome detected using multiple approaches
Authors: Jenkins Gemma M , Goddard Michael E , Black Michael A , Brauning Rudiger , Auvray Benoit , Dodds Ken G , Kijas James W , Cockett Noelle , McEwan John C 
Published: February 2016

Background.Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a study of CNV in sheep, using multiple methods to identify and characterise copy number changes. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data then analysed via multiple approaches to identify and verify CNVs.Results.In total, 3,488 autosomal CNV regions (CNVRs) were identified in this study, which substantially builds on an initial survey of the sheep genome that identified 135 CNVRs. The average length of the identified CNVRs was 19kb (range of 1kb to 3.6Mb), with shorter CNVRs being more frequent than longer CNVRs. The total length of all CNVRs was 67.6Mbps, which equates to 2.7% of the sheep autosomes. For individuals this value ranged from 0.24 to 0.55%, and the majority of CNVRs were identified in single animals. Rather than being uniformly distributed throughout the genome, CNVRs tended to be clustered. Application of three independent approaches for CNVR detection facilitated a comparison of validation rates. CNVs identified on the Roche-NimbleGen 2.1M CGH array generally had low validation rates with lower density arrays, while whole genome sequence data had the highest validation rate (>60%).Conclusions.This study represents the first comprehensive survey of the distribution, prevalence and characteristics of CNVR in sheep. Multiple approaches were used to detect CNV regions and it appears that the best method for verifying CNVR on a large scale involves using a combination of detection methodologies. The characteristics of the 3,488 autosomal CNV regions identified in this study are comparable to other CNV regions reported in the literature and provide a valuable and sizeable addition to the small subset of published sheep CNVs.
The effect of domain growth on spatial correlations
Authors: Ross Robert J. H. , Yates C. A. , Baker R. E. 
Published: February 2016

AbstractMathematical models describing cell movement and proliferation are important research tools for the understanding of many biological processes. In this work we present methods to include the effects of domain growth on the evolution of spatial correlations between agent locations in a continuum approximation of a one-dimensional lattice-based model of cell motility and proliferation. This is important as the inclusion of spatial correlations in continuum models of cell motility and proliferation without domain growth has previously been shown to be essential for their accuracy in certain scenarios. We include the effect of spatial correlations by deriving a system of ordinary differential equations that describe the expected evolution of individual and pair density functions for agents on a growing domain. We then demonstrate how to simplify this system of ordinary differential equations by using an appropriate approximation. This simplification allows domain growth to be included in models describing the evolution of spatial correlations between agents in a tractable manner.
How domain growth is implemented determines the long term behaviour of a cell population through its effect on spatial correlations
Authors: Ross Robert J. H. , Baker R. E. , Yates C. A. 
Published: February 2016

AbstractDomain growth plays an important role in many biological systems, and so the inclusion of domain growth in models of these biological systems is important to understanding how these biological systems function. In this work we present methods to include the effects of domain growth on the evolution of spatial correlations in a continuum approximation of a lattice-based model of cell motility and proliferation. We show that, depending on the way in which domain growth is implemented, different steady-state densities are predicted for an agent population. Furthermore, we demonstrate that the way in which domain growth is implemented can result in the evolution of the agent density depending on the size of the domain. Continuum approximations that ignore spatial correlations cannot capture these behaviours, while those that account for spatial correlations do. These results will be of interest to researchers in developmental biology, as they suggest that the nature of domain growth can determine the characteristics of cell populations.
Generation of mutation hotspots in ageing bacterial colonies
Authors: Sekowska Agnieszka , Wendel Sofie , Nørholm Morten H. H. , Danchin Antoine 
Published: February 2016

AbstractHow do ageing bacterial colonies generate adaptive mutants? Over a period of two months, we isolated on ageing colonies outgrowing mutants able to use a new carbon source, and sequenced their genomes. This allowed us to uncover exquisite details on the molecular mechanism behind their adaptation: most mutations were located in just a few hotspots in the genome and over time, mutations increasingly originated from 8-oxo-guanosine, formed exclusively on the transcribed strand.
Productive infection of field strains of avian coronavirus infectious bronchitis virus in chicken peripheral blood-derived monocytes
Authors: Zhang Yueting , Whittaker Gary R. 
Published: February 2016

AbstractThe avian coronavirus infectious bronchitis virus (IBV) typically infects the respiratory tract of chickens, but can also spread to other organs. However, the mechanisms of virus dissemination are presently unclear. We show that peripheral blood-derived monocytes/macrophages from chickens (chPBMC) are productively infected by clinical strains of IBV, accompanied by induction of apoptosis. Our data suggest that chPBMCs play a role in the dissemination of IBV, and may be important for viral pathogenesis.
Does the choice of nucleotide substitution models matter topologically?
Authors: Hoff Michael , Orf Stefan , Riehm Benedikt , Darriba Diego , Stamatakis Alexandros 
Published: February 2016

AbstractBackgroundIn the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all 203 possible nucleotide substitution models in the Maximum Likelihood (ML) setting under the common Akaike, corrected Akaike, and Bayesian information criteria. We address the question if model selection matters topologically, that is, if conducting ML inferences under the optimal, instead of a standard General Time Reversible model, yields different tree topologies. We also assess, to which degree models selected and trees inferred under the three standard criteria (AIC, AICc, BIC) differ. Finally, we assess if the definition of the sample size (#sites versus #sites × #taxa) yields different models and, as a consequence, different tree topologies.ResultsWe find that, all three factors (by order of impact: nucleotide model selection, information criterion used, sample size definition) can yield topologically substantially different final tree topologies (topological difference exceeding 10%) for approximately 5% of the tree inferences conducted on the 39 empirical datasets used in our study.ConclusionsWe find that, using the best-fit nucleotide substitution model may change the final ML tree topology compared to an inference under a default GTR model. The effect is less pronounced when comparing distinct information criteria. Nonetheless, in some cases we did obtain substantial topological differences.
Border Effect Between Hong Kong and Mainland China
Authors: Fan Simon C. , Wei Xiangdong , Wu Jia 
Published: February 2016

AbstractThis study applies newly developed methodologies to investigate the border effect between Hong Kong and mainland China. It makes three contributions to a better understanding of the border effect puzzle. First, the special relationship between mainland China and Hong Kong provides us with a unique opportunity to disentangle the factors underlying the observed border effect. Second, in addition to estimating the border effect between mainland China and Hong Kong, we also estimate that between the mainland provinces of Guangdong and Shanghai. This comparison between two types of border effects facilitates a better understanding of the extent of domestic market integration in China. Third, owing to the nature of our data and the new estimation approach we adopt, our estimated border effects are less subject to the measurement error‐related and estimation‐related biases commonly seen in previous studies. We find the estimated border effect between Hong Kong and mainland China to be approximately 266 km, which is substantially larger than that between Guangdong and Shanghai (1.3 km). Both are substantially smaller than the estimated border effects found in many previous studies.
State Capitalism: A New Perspective on Land Sale in China
Authors: Tian Wei , Sheng Liugang , Zhao Hongyan 
Published: February 2016

AbstractThis paper presents a new perspective for understanding the land sale behaviour of local governments in China, focusing on the ‘institutional trinity’ of the land market; namely, state ownership, economic performance‐based political promotion and the unbalanced fiscal structure. The paper argues that the main motivations of local government to sell land are to promote industrial growth and to enhance government fiscal capacity. These two hypotheses are tested using prefecture‐level data covering approximately 330 municipalities during the period of 1999–2007. The paper finds that industrial output and fiscal expenditure increase by approximately 1.8% and 1.0%, respectively, if the area of land sale doubles. Evidence also shows that land sale promotes industrial growth by boosting fixed asset investment and foreign direct investment. Interestingly, the paper also finds that the land‐sale strategy of local governments is more effective in the eastern provinces than in other regions.
New Structural Economics and Resource Financed Infrastructure
Authors: Lin Justin Yifu , Wang Yan 
Published: February 2016

AbstractThe world economy needs a growth‐lifting strategy, and infrastructure financing appears to hold the key. Two new development banks have been established: the New Development Bank and the Asian Infrastructural Investment Bank (AIIB). However, what conceptual framework will they formulate? This paper addresses infrastructural financing issues from the angle of structural transformation as a strategy for global development. Based on the new structural economics (Lin, , ) we stress the ‘real’ side of transforming natural resources to productive assets using the resource financed infrastructure. As one of the innovative instruments, this approach could, first, combine two otherwise isolated supply chains, resource extraction and infrastructure building, and, thereby, bring developmental results many years ahead of what other conventional approaches could. Second, this could serve as one of the ‘least‐cost’ options for developing countries, and benefit borrowers disproportionately due to its feature of ‘non‐recourse’ loans. Finally, in a low‐yield environment, the rate of return from investing in bottleneck‐releasing infrastructure could be attractive to many investors. Future prospects of development financing, including the ‘one belt one road’ initiative are discussed.
Microbial Safety of Wood in Contact with Food: A Review
Authors: Aviat Florence , Gerhards Christian , Rodriguez‐Jerez José‐juan , Michel Valérie , Bayon Isabelle Le , Ismail Rached , Federighi Michel 
Published: February 2016

AbstractFood packaging is multifunctional: it protects from harvest to table. Four main groups of materials for direct food contact are mentioned in the literature: wood, glass, plastic, and metal. In this review, the focus is on wooden packaging for direct contact with food. In Europe, wood as a food contact material is subject to European Regulation (EC) No 1935/2004 states that materials must not transfer their constituents to food. Today, wooden packaging, like other packaging materials, does not have a Europe‐wide harmonized specific regulation, so member countries legislate at different levels. Wood has been safely used for centuries in contact with food but is usually questioned because of its microbiological behavior compared with smooth surfaces. Based on a review of published conclusions from scientific studies over the last 20 y and after a description of the general properties of wooden packaging, we focus on the microbiological status of natural wood. Then, we discuss the parameters influencing the survival of microorganisms on wood. Finally, we report on the transfer of microorganisms from wood to food and the factors influencing this phenomenon. This review demonstrates that the porous nature of wood, especially when compared with smooth surfaces, is not responsible for the limited hygiene of the material used in the food industry and that it may even be an advantage for its microbiological status. In fact, its rough or porous surface often generates unfavorable conditions for microorganisms. In addition, wood has the particular characteristic of producing antimicrobial components able to inhibit or limit the growth of pathogenic microorganisms.
Salt Reduction in a Model High‐Salt Akawi Cheese: Effects on Bacterial Activity, pH, Moisture, Potential Bioactive Peptides, Amino Acids, and Growth of Human Colon Cells
Authors: Gandhi Akanksha , Shah Nagendra P. 
Published: February 2016

AbstractThis study evaluated the effects of sodium chloride reduction and its substitution with potassium chloride on Akawi cheese during storage for 30 d at 4 °C. Survival of probiotic bacteria (Lactobacillus acidophilus, Lactobacillus casei, and Bifidobacterium longum) and starter bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), angiotensin‐converting enzyme‐inhibitory and antioxidant activities, and concentrations of standard amino acids as affected by storage in different brine solutions (10% NaCl, 7.5% NaCl, 7.5% NaCl+KCl [1:1], 5% NaCl, and 5% NaCl+KCl [1:1]) were investigated. Furthermore, viability of human colon cells and human colon cancer cells as affected by the extract showing improved peptide profiles, highest release of amino acids and antioxidant activity (that is, from cheese brined in 7.5% NaCl+KCl) was evaluated. Significant increase was observed in survival of probiotic bacteria in cheeses with low salt after 30 d. Calcium content decreased slightly during storage in all cheeses brined in various solutions. Further, no significant changes were observed in ACE‐inhibitory activity and antioxidant activity of cheeses during storage. Interestingly, concentrations of 4 essential amino acids (phenylalanine, tryptophan, valine, and leucine) increased significantly during storage in brine solutions containing 7.5% total salt. Low concentration of cheese extract (100 μg/mL) significantly improved the growth of normal human colon cells, and reduced the growth of human colon cancer cells. Overall, the study revealed that cheese extracts from reduced‐NaCl brine improved the growth of human colon cells, and the release of essential amino acids, but did not affect the activities of potential bioactive peptides.