bluuebunny/crossref_metadata_2025 huggingface dataset:
Other combinatory categorial frameworks
Authors: Barker Chris , Shan Chung-Chieh
Published: March 2015

Chapter 11 compares the tower fragment with two other combinatory approaches to scope and binding. The first comparison is with Jacobson’s variable‐free semantics. The tower system shares a number of methodological assumptions with variable‐free semantics, notably, the assumption that natural language analyses should be directly compositional. It also shares some specific hypotheses, such as the claim that pronouns denote identity functions. The second approach discussed is Steedman’s theory of scope as surface constituency. The surface constituency approach makes heavy use of function composition, which is not an essential element in the tower approach. Steedman’s account does not allow quantifiers to take scope from an in‐situ position that is not at the edge of its scope domain. We present data that suggests that this restriction is not empirically adequate.
Computational connections
Authors: Barker Chris , Shan Chung-Chieh
Published: March 2015

Chapter 12 discusses two computational topics. The first topic is one of the key inspirations for our approach, namely, Plotkin’s treatment of the call‐by‐name evaluation discipline versus the call‐by‐value evaluation discipline for a formal language (the untyped lambda calculus). Plotkin’s Continuation Passing Style technique allows explicit control over the evaluation order of an expression within a larger system that is order‐independent. We show the family resemblance between Plotkin’s CPS transforms and our combination schema. The second main topic of the chapter is of a more practical nature, and concerns the computational implementation of the tower system. We show how a refactoring of the type‐shifters into a slightly larger set of combinators guarantees that it is possible to build an efficient (decidable) implementation.
NLλ
Authors: Barker Chris , Shan Chung-Chieh
Published: March 2015

Chapter 13 introduces NL‐lambda, an innovative type‐logical grammar designed to explore the syntax and semantics of scope‐taking. NL‐lambda is a multi‐modal substructural logic in the tradition of Lambek. It is completely standard, with the exception of the addition of one unusual structural postulate characterizing the interaction between the merge mode (governing ordinary function/argument combination) and the continuation mode (governing scope‐taking). This postulate in effect introduces a kind of lambda abstraction in the syntax, and plays the role of a generalized form of Quantifier Raising. The syntactic categories of this logic are identical in form and in interpretation to the categories used throughout Part I. In the type‐logical approach, logical proofs play the role of syntactic derivations, and semantic interpretation follows automatically from the Curry‐Howard correspondence. Derivations are given illustrating how the logic provides an account of simple scope ambiguity.
Scope versus discontinuity: Anaphora, VPE
Authors: Barker Chris , Shan Chung-Chieh
Published: March 2015

Chapter 15 develops further applications of parasitic scope. There is a discussion of parasitic scope from a conceptual point of view, including a schematic diagram. NL‐lambda is compared with Morill et al.’s Discontinuous Lambek Grammar, a formal system that allows expressions to contain arbitrarily many points of discontinuity. In contrast, NL‐lambda achieves similar results while assuming that all expressions are contiguous constituents. Adapting an analysis from Morrill et al., we provide a parasitic scope analysis of pronoun binding and of verb phrase ellipsis. Derivations are given that show the interaction of pronoun binding with verb phrase ellipsis to provide an account of simple strict versus sloppy interpretations of VPE. A number of other parasitic scope analyses from the literature are briefly mentioned.
Formal properties of NLλ
Authors: Barker Chris , Shan Chung-Chieh
Published: March 2015

Chapter 17 explores the formal properties of NL‐lambda. This is done indirectly, by first studying NL‐CL, a type‐logical grammar with standard structural postulates. We prove that NL‐CL is sound and complete with respect to the usual class of relational models. We then prove that NL‐CL is conservative over NL (the non‐associative Lambek grammar). That is, a sequent in NL is a theorem in NL iff it is a theorem of NL‐CL. We then prove that NL‐CL is equivalent to a restricted version of NL‐lambda. We prove cut elimination for NL‐lambda. This clears the way for showing that NL‐lambda is decidable. In addition, we extend NL‐lambda to a still‐decidable version that handles syntactic displacement (which was handled in Part I by postulating silent expressions called gaps). We briefly mention a variant of NL‐CL that corresponds to unrestricted NL‐lambda.
Scope needsdelimitedcontinuations
Authors: Barker Chris , Shan Chung-Chieh
Published: March 2015

Chapter 18 discusses three other continuation‐based analyses of natural language: de Groote’s application of the lambda‐mu calculus to scope‐taking; Moortgat and Bernardi’s application of the Lambek‐Grishin calculus to scope‐taking; and de Groote’s continuation‐based grammar for dynamic anaphora. The main issue addressed throughout concerns the differences between undelimited continuations and delimited continuations. We argue that these approaches either do not allow sufficient variation in the result category of the expression over which a scope‐taker takes scope, or else require additional semantic mechanisms beyond the basic scope‐taking mechanism. We conclude that the expressive power of delimited continuations is essential for an adequate description of natural language. We also briefly discuss monads, a technique from functional programming related to continuations that has applications to natural language.
The Semantics of Evaluativity
Authors: Rett Jessica
Published: March 2015

The simplest form in which gradable adjectives are used—positive constructions, like John is tall—carry an additional semantic component, evaluativity, that is not part of the adjective’s lexicalized meaning. Evaluative constructions require that an entity instantiate a gradable predicate to a significantly high degree. This property holds of John is tall, but it fails to hold of some other adjectival constructions, like John is taller than Bill or John is 6 ft tall. The source of evaluativity has posed a challenge for semantic accounts of adjectives and adjectival constructions, which are tasked with explaining why the most basic use of gradable adjectives doesn’t reflect its core meaning. This book’s author's (2008) EVAL account capitalizes on notions of antonymy and markedness to account for the distribution of evaluativity across adjectival constructions, including the equative, which can be evaluative. This book sets these notions in a neo-Gricean framework of conversational implicature (Horn 1984; Levinson 2000). It presents an account of evaluativity across adjectival constructions as arising in some cases as a Quantity implicature (similar to the meaning attributed to tautologies like War is war) and in other cases as a Manner implicature (similar to the non-truth-conditional content of litotes like not uncommon). It attributes notable differences in where (i.e. matrix/subordinate clauses) and how (i.e. at-issue/not-at-issue content) evaluativity is encoded to the type of implicature and the question under discussion.
Introduction
Authors: Rett Jessica
Published: March 2015

This chapter presents the problem of evaluativity in the semantics of adjectival constructions. It previews the traditional account of evaluativity in positive constructions, and summarizes the implicature-based approach defended in the book. It introduces the rest of the chapters in the book and outlines the main themes, including the null morphemes POS and EVAL, implicature and the interaction between evaluativity and markedness, and extensions of the account of evaluativity as implicature.
The null morpheme EVAL
Authors: Rett Jessica
Published: March 2015

This 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

This 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

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

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

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

Objectives

Treating 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.

Methods

Seaweed 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.

Results

The 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 < 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.

Conclusions

The 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

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

We 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

Background 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.
Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades
Authors: McCleery Robert A. , Sovie Adia , Reed Robert N. , Cunningham Mark W. , Hunter Margaret E. , Hart Kristen M.
Published: March 2015

To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (
Python molurus bivittatus
) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range.
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.
The fate of a mutation in a fluctuating environment
Authors: Cvijović Ivana , Good Benjamin H. , Jerison Elizabeth R. , Desai Michael M.
Published: March 2015

Natural environments are never truly constant, but the evolutionary implications of temporally varying selection pressures remain poorly understood. Here we investigate how the fate of a new mutation in a fluctuating environment depends on the dynamics of environmental variation and on the selective pressures in each condition. We find that even when a mutation experiences many environmental epochs before fixing or going extinct, its fate is not necessarily determined by its time-averaged selective effect. Instead, environmental variability reduces the efficiency of selection across a broad parameter regime, rendering selection unable to distinguish between mutations that are substantially beneficial and substantially deleterious on average. Temporal fluctuations can also dramatically increase fixation probabilities, often making the details of these fluctuations more important than the average selection pressures acting on each new mutation. For example, mutations that result in a tradeoff between conditions but are strongly deleterious on average can nevertheless be more likely to fix than mutations that are always neutral or beneficial. These effects can have important implications for patterns of molecular evolution in variable environments, and they suggest that it may often be difficult for populations to maintain specialist traits, even when their loss leads to a decline in time-averaged fitness.
SCFJFK is a bona fide E3 ligase for ING4 and a potent promoter of the angiogenesis and metastasis of breast cancer
Authors: Yan Ruorong , He Lin , Li Zhongwu , Han Xiao , Liang Jing , Si Wenzhe , Chen Zhe , Li Lei , Xie Guojia , Li Wanjin , Wang Peiyan , Lei Liandi , Zhang Hongquan , Pei Fei , Cao Dengfeng , Sun Luyang , Shang Yongfeng
Published: March 2015

Loss of function/dysregulation of inhibitor of growth 4 (ING4) and hyperactivation of NF-κB are frequent events in many types of human malignancies. However, the molecular mechanisms underlying these remarkable aberrations are not understood. Here, we report that ING4 is physically associated with JFK. We demonstrated that JFK targets ING4 for ubiquitination and degradation through assembly of an Skp1–Cul1–F-box (SCF) complex. We showed that JFK-mediated ING4 destabilization leads to the hyperactivation of the canonical NF-κB pathway and promotes angiogenesis and metastasis of breast cancer. Significantly, the expression of JFK is markedly up-regulated in breast cancer, and the level of JFK is negatively correlated with that of ING4 and positively correlated with an aggressive clinical behavior of breast carcinomas. Our study identified SCFJFK as a bona fide E3 ligase for ING4 and unraveled the JFK–ING4–NF-κB axis as an important player in the development and progression of breast cancer, supporting the pursuit of JFK as a potential target for breast cancer intervention.
Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus
Authors: Hu Shi-Bin , Xiang Jian-Feng , Li Xiang , Xu Yefen , Xue Wei , Huang Min , Wong Catharine C. , Sagum Cari A. , Bedford Mark T. , Yang Li , Cheng Donghang , Chen Ling-Ling
Published: March 2015

In many cells, mRNAs containing inverted repeated Alu elements (IRAlus) in their 3′ untranslated regions (UTRs) are inefficiently exported to the cytoplasm. Such nuclear retention correlates with paraspeckle-associated protein complexes containing p54nrb. However, nuclear retention of mRNAs containing IRAlus is variable, and how regulation of retention and export is achieved is poorly understood. Here we show one mechanism of such regulation via the arginine methyltransferase CARM1 (coactivator-associated arginine methyltransferase 1). We demonstrate that disruption of CARM1 enhances the nuclear retention of mRNAs containing IRAlus. CARM1 regulates this nuclear retention pathway at two levels: CARM1 methylates the coiled-coil domain of p54nrb, resulting in reduced binding of p54nrb to mRNAs containing IRAlus, and also acts as a transcription regulator to suppress NEAT1 transcription, leading to reduced paraspeckle formation. These actions of CARM1 work together synergistically to regulate the export of transcripts containing IRAlus from paraspeckles under certain cellular stresses, such as poly(I:C) treatment. This work demonstrates how a post-translational modification of an RNA-binding protein affects protein–RNA interaction and also uncovers a mechanism of transcriptional regulation of the long noncoding RNA NEAT1.
Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex
Authors: Kapoor Prabodh , Bao Yunhe , Xiao Jing , Luo Jie , Shen Jianfeng , Persinger Jim , Peng Guang , Ranish Jeff , Bartholomew Blaine , Shen Xuetong
Published: March 2015

ATP-dependent chromatin remodeling complexes alter chromatin structure through interactions with chromatin substrates such as DNA, histones, and nucleosomes. However, whether chromatin remodeling complexes have the ability to regulate nonchromatin substrates remains unclear. Saccharomyces cerevisiae checkpoint kinase Mec1 (ATR in mammals) is an essential master regulator of genomic integrity. Here we found that the SWI/SNF chromatin remodeling complex is capable of regulating Mec1 kinase activity. In vivo, Mec1 activity is reduced by the deletion of Snf2, the core ATPase subunit of the SWI/SNF complex. SWI/SNF interacts with Mec1, and cross-linking studies revealed that the Snf2 ATPase is the main interaction partner for Mec1. In vitro, SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dpb11. The subunit requirement of SWI/SNF-mediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. Functionally, SWI/SNF-mediated Mec1 regulation specifically occurs in S phase of the cell cycle. Together, these findings identify a novel regulator of Mec1 kinase activity and suggest that ATP-dependent chromatin remodeling complexes can regulate nonchromatin substrates such as a checkpoint kinase.
A retrovirus packages nascent host noncoding RNAs from a novel surveillance pathway
Authors: Eckwahl Matthew J. , Sim Soyeong , Smith Derek , Telesnitsky Alice , Wolin Sandra L.
Published: March 2015

Although all retroviruses recruit host cell RNAs into virions, both the spectrum of RNAs encapsidated and the mechanisms by which they are recruited remain largely unknown. Here, we used high-throughput sequencing to obtain a comprehensive description of the RNAs packaged by a model retrovirus, murine leukemia virus. The major encapsidated host RNAs are noncoding RNAs (ncRNAs) and members of the VL30 class of endogenous retroviruses. Remarkably, although Moloney leukemia virus (MLV) assembles in the cytoplasm, precursors to specific tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs) are all enriched in virions. Consistent with their cytoplasmic recruitment, packaging of both pre-tRNAs and U6 snRNA requires the nuclear export receptor Exportin-5. Adenylated and uridylated forms of these RNAs accumulate in cells and virions when the cytoplasmic exoribonuclease DIS3L2 and subunits of the RNA exosome are depleted. Together, our data reveal that MLV recruits RNAs from a novel host cell surveillance pathway in which unprocessed and unneeded nuclear ncRNAs are exported to the cytoplasm for degradation.
Viral noncoding RNAs: more surprises
Authors: Tycowski Kazimierz T. , Guo Yang Eric , Lee Nara , Moss Walter N. , Vallery Tenaya K. , Xie Mingyi , Steitz Joan A.
Published: March 2015

Eukaryotic cells produce several classes of long and small noncoding RNA (ncRNA). Many DNA and RNA viruses synthesize their own ncRNAs. Like their host counterparts, viral ncRNAs associate with proteins that are essential for their stability, function, or both. Diverse biological roles—including the regulation of viral replication, viral persistence, host immune evasion, and cellular transformation—have been ascribed to viral ncRNAs. In this review, we focus on the multitude of functions played by ncRNAs produced by animal viruses. We also discuss their biogenesis and mechanisms of action.
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

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.
Transformational leadership and organisational performance
Authors: Katou Anastasia A.
Published: March 2015

Purpose

– The purpose of this paper is to investigate the serially mediating mechanisms of organisational justice, organisational trust, and employee reactions in the relationship between transformational leadership and organisational performance.

Design/methodology/approach

– The study is based on a national sample of 133 organisations from the public and private sectors in Greece and on data obtained from 1,250 employees at three hierarchical positions. The statistical method employed is structural equation modelling.

Findings

– The findings of the study suggest that responsive and supportive transformational leadership behaviour have a positive impact on organisational growth. Additionally, this impact is mediated by organisational procedural justice, organisational trust integrity and dependability, and organisational commitment.

Research limitations/implications

– The study does not allow for dynamic causal inferences because the data were collected using a questionnaire at a single point in time. Furthermore, the findings of the study may not generalise across borders, because the study was applied in the Greek context, which is experiencing a severe economic and financial crisis.

Practical implications

– The major message of the study to decision makers and practitioners is that leaders should work at fostering organisational commitment by improving perceptions of fairness and trust, consistent with the context where the organisation is activated.

Originality/value

– There is hardly any research that has been conducted to examine the serially mediating relationships of justice, trust, and employee reactions using multi-dimensional constructs in investigating the relationship between transformational leadership and organisational performance.
Anything but typical: how consumers evaluate origin products based on their cues
Authors: Spielmann Nathalie
Published: March 2015

Purpose

– A recent stream of research has focused on typicality associations – those that bring origins and products together. Most of the research has focused on typical products but atypical products have received very little attention, even though they are more and more present on the market. As it has yet to be reviewed, the relationship between intrinsic and extrinsic product cues and product evaluations is examined in this paper for typical and atypical origin products.

Design/methodology/approach

– Wine was used as the stimulus, and consumer evaluations of typical and atypical wines were reviewed. Consumers were segmented based on their knowledge of the product category. French respondents (n = 370) participated in an online questionnaire regarding the product cues they found most important, depending on if the wine was from the New World or the Old World.

Findings

– The results show that extrinsic cues are just as important as intrinsic cues in the evaluation of origin products, contrary to what prior research suggests. Furthermore, consumer knowledge moderates the evaluations of origin products; the results empirically confirms the theoretical country of origin – elaboration likelihood model (CoO-ELM) proposed by Bloemer et al. (2009) for atypical origin products, but show typical products are evaluated differently.

Originality/value

– This is the first study that empirically tests the CoO-ELM and includes the added dimension of typicality. The results allow for a better understanding of consumer perceptions of origin products and their cues.
Trust, behavior, and high school outcomes
Authors: Romero Lisa S.
Published: March 2015

Purpose

– The purpose of this paper is to contribute to the literature on student trust and to examine the relationship between student trust, behavior, and academic outcomes in high school. It asks, first, does trust have a positive effect on high school outcomes? Second, does trust influence student behavior, exerting an indirect effect on schooling outcomes? Third, are school size and student socioeconomic status (SES) antecedents of trust?

Design/methodology/approach

– A nationally representative sample of students attending public high schools in the USA (n=10,585) is drawn from the Educational Longitudinal Study. Structural equation modeling is used to examine the relationship between student trust, behavior and high school outcomes, controlling for SES, school size and prior achievement. Multiple measures of academic achievement are considered.

Findings

– There is a significant relationship between student trust, behavior and high school outcomes. Students who trust have fewer behavioral incidents and better academic outcomes with results suggesting that trust functions through behavior. This is true regardless of SES, school size or prior achievement.

Practical implications

– School leaders cannot change parental income or education, but can build trust. Developing and attending to student trust may not only mean that students are better behaved but, more importantly, are more successful academically.

Social implications

– In spite of decades of policy and legislation intended to improve schools, closing the achievement gap has proven elusive. One reason may be the relentless focus on physical artifacts of schooling, such as school organization, curriculum, testing and accountability, and a concomitant lack of attention to sociocognitive factors key to learning. Schools are social systems, and high levels of learning are unlikely to occur without a nurturing environment that includes trust.

Originality/value

– This research makes a valuable contribution by focussing on student trust in high schools and by illuminating the relationship between trust, behavior, and academic outcomes. Results suggest that trust impacts a broad range of high school outcomes but functions indirectly through behavior.
The centrality of ethical leadership
Authors: Ehrich Lisa C. , Harris Jessica , Klenowski Val , Smeed Judy , Spina Nerida
Published: March 2015

Purpose

– The central argument in this paper is that ethical school leadership is imperative in a context of increasing performance-driven accountability. The purpose of this paper is to focus on school principals’ perceptions of how they understand ethical leadership and how they lead the ethical use of data.

Design/methodology/approach

– This study utilises semi-structured interviews with six state school principals (one primary and six secondary) to explore their perceptions of ethical leadership practices; and how they balance current competing accountabilities in a context of performance-driven accountability.

Findings

– There were four key findings. First, principals used data to inform and direct their practices and their conversations with teachers. Second, while ethics was a central consideration in how principals’ led, practising in an ethical manner was identified as complex and challenging in the current context. Third, Starratt’s (1996) ethical framework proved to be relevant for interpreting principals’ practices. Finally, all of the principals referred to dilemmas they faced as a result of competing priorities and all used a variety of strategies to deal with these dilemmas.

Originality/value

– While there is a small body of research that explores school leaders’ understandings of ethical tensions and dilemmas, there is little research that has focused on school leaders’ understandings of the ethical use of data. This study, then, contributes to this area as it provides a discussion on school principals’ leadership practices in the current climate driven by data use.