bluuebunny/crossref_metadata_2025_split huggingface dataset:
The null morpheme EVAL
Authors: Rett Jessica 
Published: March 2015

AbstractThis chapter is the second installment of a history of the treatment of evaluativity in degree semantics. It introduces the null degree modifier EVAL proposed in Rett (2008), along with the broader empirical facts that originally motivated it. It introduces the relevance of markedness and semantic competition to the issue of evaluativity. It also discusses some problems with the EVAL account, including the absence of any overt counterparts of EVAL, the asymmetry in evaluativity between the matrix and embedded clauses of equatives, and the lack of uniformity across relative adjective antonym pairs. It ends by discussing a few proposed alternatives to POS and EVAL.
Implicature: A brief review
Authors: Rett Jessica 
Published: March 2015

AbstractThis chapter introduces a number of empirical and theoretical precursors to the analysis in Chapter 5. It introduces Grice’s (1975) taxonomy of signification, including his distinction between conventional and conversational implicature, and his distinction between generalized and particularized conversational implicature. It introduces Horn’s (1984) implementation of Grice’s theory, his “division of pragmatic labor,” which better captures the tension between Quantity and Manner considerations. And it draws from Katzir (2007) to formalize Quantity and Manner scales. It also exemplifies uninformativity-based Quantity implicatures and Manner implicatures in constructions unrelated to evaluativity, to illustrate how they behave in terms of their content and cancellability, and how they interact. These data will form a basis for comparison for the predictions made by the analysis in Chapter 4.
Family genome browser: visualizing genomes with pedigree information
Authors: Juan Liran , Liu Yongzhuang , Wang Yongtian , Teng Mingxiang , Zang Tianyi , Wang Yadong 
Published: March 2015

Abstract
Motivation: Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge.
Results: We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically.
Availability and implementation: The FGB is available at http://mlg.hit.edu.cn/FGB/.
Contact: ydwang@hit.edu.cn.
Test set bias affects reproducibility of gene signatures
Authors: Patil Prasad , Bachant-Winner Pierre-Olivier , Haibe-Kains Benjamin , Leek Jeffrey T. 
Published: March 2015

Abstract
Motivation: Prior to applying genomic predictors to clinical samples, the genomic data must be properly normalized to ensure that the test set data are comparable to the data upon which the predictor was trained. The most effective normalization methods depend on data from multiple patients. From a biomedical perspective, this implies that predictions for a single patient may change depending on which other patient samples they are normalized with. This test set bias will occur when any cross-sample normalization is used before clinical prediction.
Results: We demonstrate that results from existing gene signatures which rely on normalizing test data may be irreproducible when the patient population changes composition or size using a set of curated, publicly available breast cancer microarray experiments. As an alternative, we examine the use of gene signatures that rely on ranks from the data and show why signatures using rank-based features can avoid test set bias while maintaining highly accurate classification, even across platforms.
Availability and implementation: The code, data and instructions necessary to reproduce our entire analysis is available at https://github.com/prpatil/testsetbias.
Contact: jtleek@gmail.com or bhaibeka@uhnresearch.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
SiPAN: simultaneous prediction and alignment of protein–protein interaction networks
Authors: Alkan Ferhat , Erten Cesim 
Published: March 2015

Abstract
Motivation: Network prediction as applied to protein–protein interaction (PPI) networks has received considerable attention within the last decade. Because of the limitations of experimental techniques for interaction detection and network construction, several computational methods for PPI network reconstruction and growth have been suggested. Such methods usually limit the scope of study to a single network, employing data based on genomic context, structure, domain, sequence information or existing network topology. Incorporating multiple species network data for network reconstruction and growth entails the design of novel models encompassing both network reconstruction and network alignment, since the goal of network alignment is to provide functionally orthologous proteins from multiple networks and such orthology information can be used in guiding interolog transfers. However, such an approach raises the classical chicken or egg problem; alignment methods assume error-free networks, whereas network prediction via orthology works affectively if the functionally orthologous proteins are determined with high precision. Thus to resolve this intertwinement, we propose a framework to handle both problems simultaneously, that of SImultaneous Prediction and Alignment of Networks (SiPAN).
Results: We present an algorithm that solves the SiPAN problem in accordance with its simultaneous nature. Bearing the same name as the defined problem itself, the SiPAN algorithm employs state-of-the-art alignment and topology-based interaction confidence construction algorithms, which are used as benchmark methods for comparison purposes as well. To demonstrate the effectiveness of the proposed network reconstruction via SiPAN, we consider two scenarios; one that preserves the network sizes and the other where the network sizes are increased. Through extensive tests on real-world biological data, we show that the network qualities of SiPAN reconstructions are as good as those of original networks and in some cases SiPAN networks are even better, especially for the former scenario. An alternative state-of-the-art network reconstruction algorithm random walk with resistance produces networks considerably worse than the original networks and those reproduced via SiPAN in both cases.
Availability and implementation: Freely available at http://webprs.khas.edu.tr/∼cesim/SiPAN.tar.gz.
Contact: cesim@khas.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
Antibiotic penetration and bacterial killing in aPseudomonas aeruginosabiofilm model
Authors: Cao Bao , Christophersen Lars , Thomsen Kim , Sønderholm Majken , Bjarnsholt Thomas , Jensen Peter Østrup , Høiby Niels , Moser Claus 
Published: March 2015

AbstractObjectivesTreating biofilm infections successfully is a challenge. We hypothesized that biofilms may be considered as independent compartments with particular pharmacokinetics. We therefore studied the pharmacokinetics and pharmacodynamics of tobramycin in a seaweed alginate-embedded biofilm model.MethodsSeaweed alginate beads containing Pseudomonas aeruginosa were cultured in LB medium, sampled at day 1, 3, 5 or 7 and examined for the effect of treatment with tobramycin for 30 min. Treated beads were homogenized and the number of cfu was determined. The antibiotic concentration in the solution of homogenized beads was measured. Finally, beads were examined for live cells by Syto9 staining and for dead cells by propidium iodide staining using a confocal laser scanning microscope.ResultsThe antibiotic level in each bead was relatively stable (range 30–42 mg/L; MIC = 1.5 mg/L). There were fewer cfu in the tobramycin-treated beads than the non-treated beads (P &lt; 0.016) and bacterial killing was reduced as the culture period increased from 1 to 7 days. Throughout the study period, increasing size and more superficial positioning of the microcolonies within the beads were demonstrated by confocal laser scanning microscopy. More dead cells (measured by propidium iodide staining) were observed in the treated group of beads, which supports the results obtained by culture.ConclusionsThe present study, simulating the clinical pharmacokinetics of tobramycin, demonstrates fast absorption of tobramycin in an in vitro biofilm model. In addition, this model system enables parallel investigation of pharmacokinetics and pharmacodynamics, providing a model for testing new treatment strategies.
Third-generation cephalosporin resistance conferred by a chromosomally encoded blaCMY-23 gene in the Escherichia coli ST131 reference strain EC958
Authors: Phan Minh-Duy , Peters Kate M. , Sarkar Sohinee , Forde Brian M. , Lo Alvin W. , Stanton-Cook Mitchell , Roberts Leah W. , Upton Mathew , Beatson Scott A. , Schembri Mark A. 
Published: March 2015

Abstract

Objectives
Escherichia coli ST131 is a globally disseminated MDR clone originally identified due to its association with the blaCTX-M-15 gene encoding an ESBL. It is thus assumed that blaCTX-M-15 is the major determinant for resistance to β-lactam antibiotics in this clone. The complete sequence of EC958, a reference strain for E. coli ST131, revealed that it contains a chromosomally located blaCMY-23 gene with an upstream ISEcp1 element as well as several additional plasmid-encoded β-lactamase genes. Here, we examined the genetic context of the blaCMY-23 element in EC958 and other E. coli ST131 strains and investigated the contribution of blaCMY-23 to EC958 resistance to a range of β-lactam antibiotics.

Methods
The genetic context of blaCMY-23 and its associated mobile elements was determined by PCR and sequencing. Antibiotic susceptibility testing was performed using Etests. The activity of the blaCMY-23 promoter was assessed using lacZ reporter assays. Mutations were generated using λ-Red-recombination.

Results
The genetic structure of the ISEcp1-IS5-blaCMY-23 mobile element was determined and localized within the betU gene on the chromosome of EC958 and five other E. coli ST131 strains. The transcription of blaCMY-23, driven by a previously defined promoter within ISEcp1, was significantly higher than other β-lactamase genes and could be induced by cefotaxime. Deletion of the blaCMY-23 gene resulted in enhanced susceptibility to cefoxitin, cefotaxime and ceftazidime.

Conclusions
This is the first known report to demonstrate the chromosomal location of blaCMY-23 in E. coli ST131. In EC958, CMY-23 plays a major role in resistance to third-generation cephalosporins and cephamycins.
ASASSN-14cc: A likely helium analog of RZ Leonis Minoris
Authors: Kato Taichi , Hambsch Franz-Josef , Monard Berto 
Published: March 2015

AbstractWe identified that ASASSN-14cc is a very active dwarf nova spending approximately 60% of the time in outburst. Our long-term photometry revealed that the object shows long outbursts recurring with a period of 21–33 d and very brief short outbursts lasting less than 1 d. The maximum fading rate exceeds 2.8 mag d−1. The duration of the long outbursts is 9–18 d, comprising 50%–60% of the recurrence time of long outbursts. We detected 0.01560–0.01562 d (22.5 min) modulations during long outbursts, which we identified as superhumps. These features indicate that ASASSN-14cc has outburst parameters very similar to the extremely unusual dwarf nova RZ LMi but with a much shorter superhump period. All the observations can be naturally understood, considering that this object is a helium analog (AM CVn-type object) of RZ LMi. The highest outburst activity among AM CVn-type objects can be understood as the high-mass transfer rate expected for the orbital period giving a condition close to the stability limit of the accretion disk. In contrast to RZ LMi, this object shows little evidence for premature quenching of the superoutburst, which has been proposed to explain the unusual outburst parameters in RZ LMi.
Modeling the Anesthetic Effect of Ropivacaine after a Femoral Nerve Block in Orthopedic Patients
Authors: Gaudreault François , Drolet Pierre , Fallaha Michel , Varin France 
Published: March 2015

AbstractAbstract
A population pharmacokinetic–pharmacodynamic model was developed that describes the relationship between sensory response and the amount of ropivacaine remaining at the site of injection after single-dose injection for femoral nerve block. Simulation using the model suggests that following a bolus dose of 100 mg, 0.2% ropivacaine hydrochloride should be infused at least at 3 ml/h to maintain a complete sensory block for 48 h.

Background:
Even though ropivacaine is frequently used during orthopedic surgery, the relationship between plasma concentrations and degree of sensory anesthesia after a peripheral nerve block is currently unknown. The aim of this study was to characterize this relation using population pharmacokinetic–pharmacodynamic modeling.

Methods:
Femoral nerve block was performed by the anterior approach using a single injection (20 ml) of 0.5% ropivacaine hydrochloride in 20 patients scheduled for total knee arthroplasty under spinal anesthesia. Sensory thresholds in response to a gradual increase in transcutaneous electrical stimulation (primary endpoints), loss and recovery of ice-cold sensation, as well as total ropivacaine plasma concentrations were determined up to 4 days after administration of the local anesthetic. Using NONMEM (ICON, USA), sensory block was modeled by assuming an equilibration delay (k
e0) between amount in the depot and effect-site compartments.

Results:
Mean effect-site amount producing 90% of the maximum possible effect (AE
90) was estimated as 20.2 mg. At 2 × AE
90, the sigmoid E
max model predicted a mean onset time of 23.4 min and mean duration of 22.9 h. Interindividual variability (IIV) for AE
50 was 49%. Typical k
e0 half-life was 34.7 min (IIV = 52%) and steepness parameter 8.7 (IIV = 48%). None of the pharmacodynamic model parameters showed sex, age, or body weight dependency.

Conclusions:
A population pharmacokinetic/pharmacodynamic model was developed that quantitatively describes the sensory component of a femoral nerve block in orthopedic patients. Further clinical studies will be needed to validate the clinical relevance of this finding.
A 9-Year-Old Girl With Persistent Obsessive and Compulsive Behaviors in a Primary Care Pediatric Practice
Authors: Gist Lauren , Mathews Carol , Williams Katherine N. , Stein Martin T. 
Published: March 2015

CASE: Chloe is a 9-year-old gal whose mother made an initial visit to a new pediatrician for concerns about her behavior. Chloe is apprehensive about the visit and frequently hides behind her mother.
Her parents first noticed Chloe becoming angry and more emotional 3 years ago, which her parents did not initially understand. However, over the past year, she has started to have more worries and unusual behavior.
Chloe and her mother report that when she walks through doorways, she will almost always go back and walks through again. At home, she will walk through doorways multiple times and at school, she will pretend she forgot something so her friends do not notice. She often will not walk downstairs and occasionally her mother has to carry her. Clothes are problematic for Chloe. If her father touches something of a specific color and then touches Chloe, she will have to change her clothes or take a shower. Sometimes, she will never be able to wear those clothes again. She had a recent episode where she could not stop tapping a red paper, because if she stopped, she said it would burst into flame. During the 2 weeks before the pediatric visit, symptoms increased to the point that she is now refusing to go to school. When she stays home, she lays in 1 place all day.
Chloe is a fourth grade student. The family does not report academic concerns. She has friends. She denies any appetite or sleep problems. She endorses periods of sadness, lack of energy, and decreased interest in social activities, mostly because she worries and is embarrassed. She kept her behaviors hidden from her 5 siblings for the past year, and she talked only to her mother about them. She is worried her friends might discover her behaviors.
The family history is notable for multiple paternal family members with anxiety and bipolar disorder and depression on mother's side. A few months ago, Chloe's family adopted a 7-year-old child with special needs from China.
Her growth, vital signs, and physical examination are unremarkable. Her mother filled out the Short Mood and Feelings Questionnaire and the Screen for Child Anxiety-Related Emotional Disorders, which both had elevated scores.
Improving Nonattendance at Outpatient Pediatric Endoscopy Unit of a Tertiary Center
Authors: Kogan‐Liberman Debora , Rivas Yolanda , Thompson John , Tomer Gitit 
Published: March 2015

AbstractBackground and Objectives:Failure to attend pediatric outpatient endoscopic procedures leads to inefficient use of resources, longer wait‐list times, and delay in diagnoses. The causes for pediatric endoscopy nonattendance are not well studied. The aim of the study was to identify factors associated with failure to attend endoscopic procedures and to assess the value of quality improvement (QI) interventions implemented to improve pediatric endoscopy attendance.Methods:This was a continuous QI project. We collected nonattendance data from November 2011 to November 2013. Information collected included procedure type, age, sex, time on the waiting list, history of previous procedures, and reason for nonattendance. The following QI interventions were implemented sequentially: an appointment reminder letter, a telephone call 1 week before procedure, and creation of an electronic medical note dedicated to endoscopy appointment. Pareto charts and statistical process control charts were used for analysis.Results:From November 2011 to November 2013, we were able to decrease nonattendance from 17% to 11% (P = 0.005). No‐show rate was reduced from 5% to 0.9% (P = 0.00001). There was no significant difference between attendees and nonattendees in relation to sex, age, or having a previous procedure. Longer waiting time (33 vs 26 days) was associated with increased risk for nonattendance (P = 0.0007). The most common causes for nonattendance were illness (31.5%), followed by caregiver/patients who no longer wanted the procedure (17.7%), and patients who improved (12.9%).Conclusions:Applying QI methods and tools improved pediatric endoscopy attendance. Longer wait time for endoscopic procedures is associated with nonattendance. Given the increased pediatric endoscopy demand, strategies should be implemented to reduce wait time for pediatric endoscopy.
Tritrichomonas foetus infections in female beef cattle with abortion in Wyoming, USA
Authors: Yao Chaoqun 
Published: March 2015

Introduction:Bovine trichomoniasis has been endemic in the USA since its discovery in the 1930s. Testing of bulls used for reproduction is currently mandated in 26 states to control spread of the disease. Although individual head prevalence in Wyoming has decreased since 2000 when the state's regulation started, the herd prevalence remains steady and the disease continues to have a wide geographic distribution. One factor neglected in current regulations is the role of infected cows/heifers in transmission. The latter may harbourTritrichomonas foetus, the causative organism, up to a few weeks post‐abortion/parturition. This capacity enables them to spread the disease in spite of extensive bull testing.Case presentation:The purpose of the present study was to determine the prevalence among Wyoming beef cattle of detectableT. foetusinfection in cows/heifers with a history of abortion for which samples had been tested. This retrospective study included all submissions to the Wyoming State Veterinary Laboratory between 2000 and 2010. Cows/heifers with a history of abortion among Wyoming producers were tested for trichomoniasis. Overall prevalence was 9.7 %. Furthermore, 4.5 % of aborted foetuses were positive.Conclusion:Our data collectively demonstrates that a percentage of cows/heifers that recently experienced abortion are positive forT. foetusand may play an important role in maintaining endemicity of bovine trichomoniasis.
Investigations Concerning Cavitation and Frost Fatigue in Clonal 84K Poplar Using High-Resolution Cavitron Measurements
Authors: Feng Feng , Ding Fei , Tyree Melvin T. 
Published: March 2015

Abstract
Both drought and freezing-thawing of stems induce a loss of hydraulic conductivity (percentage loss of conductivity [PLC]) in woody plants. Drought-induced PLC is often accompanied by physical damage to pit membranes, causing a shift in vulnerability curves (cavitation fatigue). Hence, if cavitated stems are flushed to remove embolisms, the next vulnerability curve is different (shifted to lower tensions). The 84K poplar (Populus alba × Populus glandulosa) clone has small vessels that should be immune from frost-induced PLC, but results demonstrated that freezing-thawing in combination with tension synergistically increased PLC. Frost fatigue has already been defined, which is similar to cavitation fatigue but induced by freezing. Frost fatigue caused a transition from a single to a dual Weibull curve, but drought-fatigued stems had single Weibull curves shifted to lower tensions. Studying the combined impact of tension plus freezing on fatigue provided evidence that the mechanism of frost fatigue may be the extra water tension induced by freezing or thawing while spinning stems in a centrifuge rather than direct ice damage. A hypothesis is advanced that tension is enhanced as ice crystals grow or melt during the freeze or thaw event, respectively, causing a nearly identical fatigue event to that induced by drought.