bluuebunny/crossref_metadata_2025 huggingface dataset:
A template approach to quality improvement activity: a primary care example
Authors: Fawcett Christopher , Moriarty Helen , Perera Roshan
Published: June 2013

Introduction.
This paper demonstrates the use of a Quality Framework and Implementation Template to review processes for improving the quality and safety of opiate prescribing for chronic non-malignant pain (CNMP). Escalating use of prescription opiates for chronic pain is of national and international concern, with major implications for personal and public health as well as for patient safety and health service quality and safety.

Objectives.
This paper uses opiate prescribing for CNMP as a worked example to illustrate use of the Quality Framework for self-directed quality improvement in smaller specialist medical or community-based practices.

Methods.
An Implementation Template, comprising a series of focussed questions derived from the Quality Framework, was applied to one specific quality improvement activity arising from clinical practice (opiate prescribing for CNMP). This helped the practice team understand current systems and processes, identify actual and potential problems, and find possible solutions to institute interventions for change.

Conclusion.
The template approach to quality activity is very applicable within smaller specialist or community health service settings, enabling such health services to focus on their own quality improvement activities and address topics of importance to the practice in a systematic and productive manner.

What is known about the topic?
There are complex interactions and activities to be considered when undertaking quality improvement within community practice. Repeat opiate prescribing for CNMP is a significant issue for practices and patients.

What does this paper add?
This paper examines the specific case of improvements to quality and safety of repeat prescribing of opiates for CNMP in small clinics and other community-based health services. This example shows how users may utilise an Implementation Template to perform a systematic and comprehensive review of their systems and processes in relation to any chosen aspect of practice-based quality improvement activity. Services could apply these same principles to any topic of interest, or practice and/or organisational activity, to undertake systematic quality improvement.

What are the implications for practitioners?
The Implementation Template was designed for use by clinical practice teams. It will be helpful for practices that wish to undertake a quality improvement activity but lack the knowledge of how to proceed. Use of the template approach provides practice teams with the means to ensure that they consider the area of concern from all angles, and helps to uncover areas that might not otherwise have been considered.
Role of sea salt aerosols in the formation of aromatic secondary organic aerosol: yields and hygroscopic properties
Authors: Beardsley Ross , Jang Myoseon , Ori Baber , Im Yunseok , Delcomyn Carrie A. , Witherspoon Ned
Published: June 2013

Environmental context In the coastal and ocean environment, oil spills and ship movement can produce hazardous, organic aerosols. In this study, the role of sea salt in the formation processes of crude-oil-derived organic aerosols derived was explored, and it was found that sea salt can greatly increase the formation and growth of these toxic aerosols. Understanding of this process is crucial for evaluating the effect of oil spills and ship movements on air quality and human health. Abstract Dual, large (52m3), outdoor chambers were used to investigate the effect of aerosol aqueous phase chemistry on the secondary organic aerosol (SOA) yields of the photooxidation products of aromatic hydrocarbons in the coastal environment. Toluene and 1,3,5-trimethylbenzene were photochemically oxidised in the presence and absence of inorganic seeds (sea salt aerosol (SSA) or NaCl) at low NOx conditions. Overall, the presence of SSA, which was shown to contain water even at low relative humidities (RHs), led to higher SOA yields than the presence of NaCl seeds and the seedless condition. The results suggest that SOA yields in the coastal environment will be higher than those produced in terrestrial environment. To study the effect of SOA formation on the chemical composition of SSA, inorganic species were measured using a particle-into-liquid-sampler coupled to an ion chromatograph. The hygroscopic properties of the SSA internally mixed with SOA were analysed using a Fourier-transform infrared spectrometer. The fresh SSA shows a weak phase transition whereas no clear phase transition appeared in the aged SSA. The depletion of Cl– due to the accommodation of nitric acid and carboxylic acids on the surface of SSA coincides with changes in aerosol hygroscopic properties.
SO2 oxidation and nucleation studies at near-atmospheric conditions in outdoor smog chamber
Authors: Zhou Yang , Rosen Elias P. , Zhang Haofei , Rattanavaraha Weruka , Wang Wenxing , Kamens Richard M.
Published: June 2013

Environmental context
Nucleation, a fundamental step in atmospheric new-particle formation, is a significant source of atmospheric aerosols. Most
laboratory experiments investigate H2SO4 nucleation based on indoor chambers or flow tube reactors, and find discrepancies with field observations. Here a large outdoor smog chamber is used to study the relationship between SO2 and nucleation rates, and demonstrate the importance of aqueous phase oxidation of SO2 by H2O2 and other oxidants.

Abstract
Particle formation under different initial ambient background conditions was simulated in a dual outdoor smog chamber for the SO2 and O3–SO2 systems with and without sunlight, as well as a propylene–NOx–SO2–sunlight system. An exponential power of 1.37 between nucleation rates at 1nm (J1) and SO2 gas phase concentrations was obtained for the SO2–sunlight system and a minimum of 0.45ppbSO2 is required by this relationship to initiate nucleation (J1 is equal to 1cm–3s–1). An investigation of the O3–SO2–sunlight/dark system showed that the presence of O3 contributed to the particle nucleation and growth at night; however, it only enhanced the particle growth in the daytime when H2SO4 photochemistry was present. In the presence of an OH• scavenger, the O3–SO2 system did not show particle nucleation, suggesting that the scavenger cut off this pathway of SO2 oxidation. A lower nucleation rate and higher particle grow rate were also observed for SO2 oxidation in the presence of propylene and NOx. However a higher SO2 decay rate was obtained for the propylene system especially under high relative humidity, which was not observed in the O3–SO2 system. This suggests that aqueous phase oxidation of SO2 from H2O2, RO2• and other oxidants produced in the propylene–NOx system contribute to the particle growth.
Houston’s rapid ozone increases: preconditions and geographic origins
Authors: Couzo Evan , Jeffries Harvey E. , Vizuete William
Published: June 2013

Environmental context
Ozone pollution in Houston, Texas, has been a public health concern for decades. Unusually large hourly changes in observed ozone concentrations have been correlated with a greater likelihood of violating the federal air quality standard. We investigate the geographic and chemical origins of these large hourly increases, which should help regulators better control ozone violations.

Abstract
Many of Houston’s highest 8-h ozone (O3) peaks are characterised by increases in concentrations of at least 40ppb in 1h, or 60ppb in 2h. These rapid increases are called non-typical O3 changes (NTOCs). In 2004, the Texas Commission on Environmental Quality (TCEQ) developed a novel emissions control strategy aimed at eliminating NTOCs. The strategy limited routine and short-term emissions of ethene, propene, 1,3-butadiene and butene isomers, collectively called highly reactive volatile organic compounds (HRVOCs), which are released from petrochemical facilities. HRVOCs have been associated with NTOCs through field campaigns and modelling studies. This study analysed wind measurements and O3, formaldehyde (HCHO) and sulfur dioxide (SO2) concentrations from 2000 to 2011 at 25 ground monitors in Houston. NTOCs almost always occurred when monitors were downwind of petrochemical facilities. Rapid O3 increases were associated with low wind speeds; 75% of NTOCs occurred when the 3-h average wind speed preceding the event was less than 6.5kmh–1. Statistically significant differences in HCHO concentrations were seen between days with and without NTOCs. Early afternoon HCHO concentrations were greater on NTOC days. In the morning before an observed NTOC event, however, there were no significant differences in HCHO concentrations between days with and without NTOCs. Hourly SO2 concentrations also increased rapidly, exhibiting behaviour similar to NTOCs. Oftentimes, the SO2 increases preceded a NTOC. These findings show that, despite the apparent success of targeted HRVOC emission controls, further restrictions may be needed to eliminate the remaining O3 events.
The Miocene conifer flora of Balcombe Bay, Victoria, Australia
Authors: Lewis Emma K. , Drinnan Andrew N.
Published: June 2013

Fossil conifers from an early Miocene flora at Balcombe Bay near Melbourne, Australia, are described and illustrated. The most prominent elements are Araucaria balcombensis Selling emend. R.S.Hill and Dacrycarpus mucronatus P.M.Wells & R.S.Hill, and several other unidentified podocarp leaves are represented. Ovuliferous cones of D. mucronatus are described, along with isolated araucarian microsporophylls and podocarp pollen cones – both with pollen in situ. The floristic elements are similar to Eocene–Oligocene flora described from Tasmania, and indicate that these floras extended to now mainland Australia and persisted into the Miocene. They are indicative of a wetter and warmer climate than the present time.
A monographic account of Australian species of Amphiroa (Corallinaceae, Rhodophyta)
Authors: Harvey A. S. , Woelkerling W. J. , Huisman J. M. , Gurgel C. F. D.
Published: June 2013

The first Australia-wide monograph of Amphiroa (Corallinaceae, Rhodophyta) based on the morphological–anatomical species concept has confirmed the occurrence of nine species (A. anceps, A. beauvoisii, A. crassa, A. exilis, A. foliacea, A. fragilissima, A. gracilis, A. klochkovana, A. tribulus) and provides a basis for future molecular-systematics studies. A comparative analysis of 285 specimens from 121 localities, along with type material examinations, yielded clear evidence that nine characters associated with the vegetative system and tetrasporangial conceptacles were diagnostically significant at species level. Detailed accounts of each species are presented, along with an identification key, data on type specimens, species comparisons and biogeographic notes. A. foliacea is epitypified. Brief accounts of 34 additional taxa reported from Australia and at some stage ascribed to Amphiroa are included. Galaxaura versicolor and Amphiroa galaxauroides are heterotypic synonyms of A. anceps; recognition of A. anastomosans, A. ephedraea and A. nobilis as distinct species requires further evaluation; and A. dilatata and A. gaillonii are species of uncertain status. Amphiroa ephedraea is lectotypified. The remaining 27 names involve nomina nuda, illegitimate names, orthographic variants or taxa now excluded from Amphiroa.
Differences in access to healthcare and utilisation of HIV and sexually transmissible infection services between men who have sex with men and men who have sex only with women: results of the 2006–10 National Survey of Family Growth in the United States
Authors: Tao Guoyu , Hoover Karen W.
Published: June 2013

Background
Men who have sex with men (MSM) experience disparities in access to healthcare and have specific healthcare needs. Methods: We analysed data from the 2006–10 National Survey of Family Growth (NSFG) to examine differences in access to healthcare and HIV and sexually transmissible infection (STI) related health services by MSM and non-MSM among men in the United States aged 15–44 years who have ever had sex. MSM and sexually active MSM were identified in the NSFG as men who had ever had oral or anal sex with another man, or who had sex in the past 12 months with another man, respectively. Access was measured by the type of health insurance, having a usual place for receiving healthcare and type of usual place. Results: Of men aged 15–44 years who have ever had sex, there were no significant differences between MSM and non-MSM in the three access measures. MSM were more likely than non-MSM to receive HIV counselling (22.5% v. 8.3%) and STI testing (26.2% v. 15.6%) in the past 12 months, or to ever have had HIV testing (67.8% v. 44.6%). STI testing in the past 12 months was reported by 38.7% of sexually active MSM. Conclusion: Our findings show no significant differences in access to healthcare between MSM and non-MSM. MSM were more likely to receive HIV- and STI-related preventive services than non-MSM. However, the low STI testing rate among MSM highlights the need for interventions to increase STI testing, and HIV and STI counselling for MSM.
The potential impact of new generation molecular point-of-care tests on gonorrhoea and chlamydia in a setting of high endemic prevalence
Authors: Hui Ben B. , Wilson David P. , Ward James S. , Guy Rebecca J. , Kaldor John M. , Law Matthew G. , Hocking Jane S. , Regan David G.
Published: June 2013

Background Despite the availability of testing and treatment, bacterial sexually transmissible infections (STIs) continue to occur at endemic levels in many remote Indigenous communities in Australia. New generation molecular point-of-care (POC) tests have high sensitivity, comparable with conventional diagnostic tests, and have the potential to increase the impact of STI screening. Methods: We developed mathematical models of gonorrhoea (Neisseria gonorrhoeae) and chlamydia (Chlamydia trachomatis) transmission in remote Indigenous communities in Australia to evaluate screening and treatment strategies that utilise POC tests. Results: The introduction of POC testing with 95% sensitivity could reduce the prevalence of gonorrhoea and chlamydia from 7.1% and 11.9% to 5.7% and 8.9%, respectively, under baseline screening coverage of 44% per year. If screening coverage is increased to 60% per year, prevalence is predicted to be reduced to 3.6% and 6.7%, respectively, under conventional testing, and further reduced to 1.8% and 3.1% with the introduction of POC testing. Increasing screening coverage to 80% per year will result in a reduction in the prevalence of gonorrhoea and chlamydia to 0.6% and 1.5%, respectively, and the virtual elimination of both STIs if POC testing is introduced. Conclusions: Modelling suggests that molecular POC tests of high sensitivity have great promise as a public health strategy for controlling chlamydia and gonorrhoea. However, evaluation of the cost-effectiveness of POC testing needs to be made before widespread implementation of this technology can be considered.
Council-supported condom vending machines: are they acceptable to rural communities?
Authors: Tomnay Jane E. , Hatch Beth
Published: June 2013

BackgroundTwenty-four hour access to condoms for young people living in rural Victoria is problematic for many reasons, including the fact that condom vending machines are often located in venues and places they cannot access. Method: We partnered with three rural councils to install condom vending machines in locations that provided improved access to condoms for local young people. Councils regularly checked the machines, refilled the condoms and retrieved the money. They also managed the maintenance of the machine and provided monthly data. Results: In total, 1153 condoms were purchased over 12 months, with 924 (80%) obtained from male toilets and 69% (801 out of 1153) purchased in the second half of the study. Revenue of $2626.10 (AUD) was generated and no negative feedback from residents was received by any council nor was there any negative reporting by local media. Vandalism, tampering or damage occurred at all sites; however, only two significant episodes of damage required a machine to be sent away for repairs. Conclusions: Condom vending machines installed in rural towns in north-east Victoria are accessible to young people after business hours, are cost-effective for councils and have not generated any complaints from residents. The machines have not suffered unrepairable damage and were used more frequently as the study progressed.
An experimental study comparing linguistic phylogenetic reconstruction methods
Authors: Barbançon François , Evans Steven N. , Nakhleh Luay , Ringe Don , Warnow Tandy
Published: June 2013

This paper reports a simulation study comparing and evaluating the performance of different linguistic phylogeny reconstruction methods on model datasets for which the true trees are known. UPGMA performed least well, then (in ascending order) neighbor joining, the method of Gray & Atkinson and finally maximum parsimony. Weighting characters greatly improves the accuracy of maximum parsimony and maximum compatibility if the characters with high weights exhibit low homoplasy.
Indefinites, negation and Jespersen’s Cycle in the history of Low German
Authors: Breitbarth Anne
Published: June 2013

This paper offers a formal account of the diachronic changes in the interaction between indefinites in the scope of negation and the expression of sentential negation in the history of Low German. Different types of negative concord develop at the different historical stages. Parallel to that, the language underwent Jespersen’s Cycle. In addition, I argue that, against common belief, Jespersen’s Cycle is at best indirectly related to the type of interaction between indefinites and negation. Changes in the type of indefinites used in the scope of negation arise due to changes in the lexical properties of the indefinites involved, not as a result of changes in the expression of negation. Conversely, changes in the type of indefinites do not trigger changes in the expression of negation.
From Proto-Hungarian SOV to Old Hungarian Top Foc V X
Authors: Kiss Katalin É.
Published: June 2013

This paper argues that Hungarian underwent a word order change from SOV to Top Foc V X* prior to its documented history beginning in 1192. Proto-Hungarian SOV is reconstructed primarily on the basis of shared constructions of archaic Old Hungarian, and Khanty and Mansi, the sister languages of Hungarian. The most likely scenario of the change from head-final to head-initial was the spreading of right dislocation, and the reanalysis of right dislocated elements by new generations of speakers as arguments in situ. In Hungarian — as opposed to Khanty and Mansi — right dislocation was facilitated by the extension of differential object marking to all direct objects. The change in basic word order initiated the restructuring of other parts of Hungarian grammar as well, which is a still ongoing process.

[As of June 2015, this article is available as Open Access under a CC-BY-NC 4.0 license.]
The effects of biliteracy instruction on morphological awareness
Authors: Lyster Roy , Quiroga Jorge , Ballinger Susan
Published: June 2013

This classroom intervention study investigated the effects of biliteracy instruction on Grade 2 students’ morphological awareness in French and English. Three pairs of partner teachers (French/English) participating in a professional development project co-designed and implemented biliteracy tasks across their French and English classes, which together comprised a total of 80 students identified as dominant in either French or English or as French-English bilinguals. The biliteracy instruction integrated a linguistic focus on derivational morphology with a thematic focus on illustrated storybooks. Before and after the intervention, separate measures of morphological awareness in French and English were administered to a subsample of their students (n = 45) as well as to a comparison group of students (n = 20) not receiving the instruction. The experimental group significantly outperformed the comparison group in French, but not in English, yet when students’ language dominance was accounted for in the English measure, English-dominant students in the experimental group significantly outperformed their counterparts in the comparison group.
Teacher language awareness in content-based activity design
Authors: Lindahl Kristen , Baecher Laura , Tomaš Zuzana
Published: June 2013

With extensive numbers of English learners in public schools worldwide, content-based language instruction (CBI) is prevalent in the preparation of second language (L2) teaching professionals. This study investigated how aspects of Teacher Language Awareness (TLA) manifest as pre-service L2 teachers develop lesson plans for CBI contexts. The authors examined the interplay between three factors: the participants’ perceived utility of their teacher preparation coursework, the participants’ ability to identify language demands in a content-area text, and the types of pedagogical activities participants suggested for subsequent CBI lessons. Descriptive and qualitative data were obtained by combining a survey with a constructed lesson-planning task. Findings yielded paradoxical results pertaining to participants’ perceptions of language-focused coursework and their ability to apply TLA during CBI lesson plan development.
The nature of foreign language anxiety in elementary immersion program graduates
Authors: Wesely Pamela M.
Published: June 2013

This mixed methods study approached the issue of foreign language (FL) anxiety in a unique population of students in the U.S.: English-dominant students who had attended French or Spanish elementary immersion schools. One hundred thirty-one students from five immersion schools responded to surveys, and 33 of those students were interviewed. Data analysis procedures included a statistical analysis of the surveys, a theme analysis of the interviews, and an integrated consideration of the findings. It was found that the immersion students did experience some FL anxiety, but it was largely dependent on the situation and mediated by other aspects of being language learners. Their FL anxiety did not correlate with their decision whether or not to continue with the immersion program. Implications include a need to reexamine the importance of extracurricular learning experiences in immersion education, and a suggestion to expand FL anxiety research to different educational and methodological contexts.
The importance of classroom management in early language immersion
Authors: Slapac Alina , Dorner Lisa M.
Published: June 2013

This study examined the challenges and successes related to classroom management in a new French Immersion Elementary School (FIES). Framed by language immersion research and theories of culturally responsive classroom management (Weinstein, Curran, & Tomlinson-Clark, 2003), the study focuses on teachers’ decision-making processes in a one-way immersion setting. Using a case-study approach on one kindergarten classroom, qualitative data over one year included field notes from participant observation; transcripts of interviews and focus groups with teachers and administrators; classroom artifacts; and videotapes of classroom sessions. Results showed that classroom management was strongly shaped by several factors: the political context, lack of school-wide curricula and policies, built environment, and teachers’ prior experiences. The discussion examines how language educators and researchers must look beyond teachers’ beliefs and students’ cultures when devising solutions to social and behavioral challenges. Recommendations for new language immersion schools that deal with behavior management challenges are made.
Face in conflict
Authors: Bousfield Derek
Published: June 2013

Studies of conflict and conflict resolution rarely concern themselves with the ways in which conflictive situations are triggered. Corsaro and Rizzo (1990), in considering interpersonal conflict and aggression do suggest that conflict begins with one antagonist taking challenging opposition to an ‘antecedent event’. Further, within linguistics, even those studies which take a perspective on the role of language in the genesis, conduct, and consequences of mass violence (see the collection of papers in Dedaic and Nelson 2003) ignore the role that ‘face’ (Goffman 1967), and facework can have at any stage. The main contentions of this paper, therefore, are that the concept of “face” cannot be ignored at any level or stage of interaction, that face and identity whilst distinct and discrete concepts interlink, and, finally, that both concepts apply in instances of ethnic or international conflict and aggression. As such, it is argued that face and identity must henceforth be considered central to research or theorising on all aspects of aggression, conflict and conflict resolution.
“Uh. . . . not to be nitpicky,,,,,but…the past tense of drag is dragged, not drug.”
Authors: Hardaker Claire
Published: June 2013

This paper investigates the phenomenon known as trolling — the behaviour of being deliberately antagonistic or offensive via computer-mediated communication (CMC), typically for amusement’s sake. Having previously started to answer the question, what is trolling? (Hardaker 2010), this paper seeks to answer the next question, how is trolling carried out? To do this, I use software to extract 3,727 examples of user discussions and accusations of trolling from an eighty-six million word Usenet corpus. Initial findings suggest that trolling is perceived to broadly fall across a cline with covert strategies and overt strategies at each pole. I create a working taxonomy of perceived strategies that occur at different points along this cline, and conclude by refining my trolling definition.
Towards a cross-cultural pragmatic taxonomy of insults
Authors: Mateo José , Yus Francisco
Published: June 2013

The aim of this paper is to explain the use of insults from a relevance-theoretic perspective. To that end, our analysis takes into consideration four variables that, we believe, play a major role in how insults are produced an interpreted: (a) the conventional or innovative nature of the insult; (b) the underlying intentionality (to offend, to praise or to establish/maintain social bonding; (c) the in/correct interpretation of the insult, and (d) the addressee’s reaction or lack thereof. The combination of these variables generates a twenty four case taxonomy that can account for and describe the use of insults in any given (cross)-cultural context. The proposed taxonomy will be here described and exemplified.
Doppelformen von ēn- und ōn-Verben im Althochdeutschen
Authors: Heinzle Mirjam Marti
Published: June 2013

Bereits die früheste Überlieferung des Althochdeutschen zeigt, dass es schwache Verben gibt, die Flexionsformen nach zwei Paradigmen zeigen. Eine Reihe von althochdeutschen ēn-Verben (Klasse 3) hat Belege, die formal dem Flexionsparadigma der ōn-Verben (Klasse 2) angehören. Im vorliegenden
Beitrag wird diesen synonym nebeneinander stehenden Formen (sog. Doppelformen) in Bezug auf Überlieferung und Vorkommen nachgegangen. Insgesamt lassen sich zwanzig ēn-Verben ermitteln, die mehrfach Doppelformen nach der ōn-Flexion zeigen. Das Fränkische erweist sich dabei als Übergangszone zwischen dem Altsächsischen, das synchron bis auf wenige Ausnahmen keine ēn-Flexion kennt, und dem Oberdeutschen mit vielen ēn-Formen. Untersuchungsgrundlage ist das Gesamtkorpus aller bezeugten ēn-Verben des Althochdeutschen.
Cognitive Grammar and Dialogic Syntax
Authors: Zima Elisabeth
Published: June 2013

This paper relates the functional model of Dialogic Syntax and its key concept of resonance (Du Bois 2001 [2009]) to Cognitive Grammar (Langacker, 1987, 1991, 2001, 2008, 2009) with the aim of inquiring into the prospects, potential gains, and limitations of a Cognitive Grammar-inspired discourse analysis. First the two frameworks are compared from a theoretical point of view, focusing on how Du Bois’ account and Langacker’s Current Discourse Space Model (2001, 2008) deal with prior discourse as a resource for new usage events. In the subsequent case study, the theory is confronted with interactional data from Austrian parliamentary debates. Specific attention is paid to construal operations, more specifically viewpoint phenomena and subjectification, which are explored in relation to resonance activation. Drawing on detailed analyses that combine insights and concepts from Dialogic Syntax and Cognitive Grammar, strengths, shortcomings, and future challenges of Cognitive Grammar discourse studies are discussed.
Adding transparency to the identification of cross-domain mappings in real language data
Authors: Krennmayr Tina
Published: June 2013

In recent years much progress has been made in developing systematic protocols for finding linguistic metaphors in authentic language data. The description of conceptual structures, however, has not been placed on equally firm footing. One existing proposal, known as the five-step method, introduces systematicity to the process of determining conceptual structures of metaphors in discourse. However, it does not take sufficient steps to minimize intuition and to maximize transparency. This paper seeks to reduce these weaknesses by introducing the systematic use of dictionaries and a lexical database. The result is a more transparent and constrained method.
The Applicability of Mathematics: Beyond Mapping Accounts
Authors: Rizza Davide
Published: June 2013

In this article, I argue that mapping-based accounts of applications cannot be comprehensive and must be supplemented by analyses of other, qualitatively different, forms of application. I support these claims by providing a detailed discussion of the application of mathematics to a problem of election design that is prominent in social choice theory.
The Semantic View, If Plausible, Is Syntactic
Authors: Halvorson Hans
Published: June 2013

Halvorson argues that the semantic view of theories leads to absurdities. Glymour shows how to inoculate the semantic view against Halvorson’s criticisms, namely, by making it into a syntactic view of theories. I argue that this modified semantic-syntactic view cannot do the philosophical work that the original “language-free” semantic view was supposed to do.
In Defense of Reflection
Authors: Huttegger Simon M.
Published: June 2013

I discuss two ways of justifying reflection principles. First, I propose that an undogmatic reading of dynamic Dutch book arguments provides them with a sound foundation. Second, I show also that minimizing expected inaccuracy leads to a novel argument for reflection principles. The required inaccuracy measures comprise a natural class of functions that can be derived from a generalization of a condition known as propriety or immodesty. This shows that reflection principles are an essential feature not just of consistent degrees of belief but also of degrees of belief that approximate truth.
Short-time existence of the Ricci flow on noncompact Riemannian manifolds
Authors: Xu Guoyi
Published: June 2013

In this paper, we give the first detailed proof of the short-time existence of Deane Yang’s local Ricci flow. Then, using the local Ricci flow, we prove the short-time existence of the Ricci flow on noncompact manifolds, whose Ricci curvature has global lower bound and sectional curvature has only local average integral bound. The short-time existence of the Ricci flow on noncompact manifolds with bounded curvature was studied by Wan-Xiong Shi in the 1990s. As a corollary of our main theorem, we obtain the short-time existence part of Shi’s theorem in this more general context.
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
Authors: Hafez Dina , Ni Ting , Mukherjee Sayan , Zhu Jun , Ohler Uwe
Published: June 2013

Motivation: Pre-mRNA cleavage and polyadenylation are essential steps for 3′-end maturation and subsequent stability and degradation of mRNAs. This process is highly controlled by cis-regulatory elements surrounding the cleavage/polyadenylation sites (polyA sites), which are frequently constrained by sequence content and position. More than 50% of human transcripts have multiple functional polyA sites, and the specific use of alternative polyA sites (APA) results in isoforms with variable 3′-untranslated regions, thus potentially affecting gene regulation. Elucidating the regulatory mechanisms underlying differential polyA preferences in multiple cell types has been hindered both by the lack of suitable data on the precise location of cleavage sites, as well as of appropriate tests for determining APAs with significant differences across multiple libraries.

Results: We applied a tailored paired-end RNA-seq protocol to specifically probe the position of polyA sites in three human adult tissue types. We specified a linear-effects regression model to identify tissue-specific biases indicating regulated APA; the significance of differences between tissue types was assessed by an appropriately designed permutation test. This combination allowed to identify highly specific subsets of APA events in the individual tissue types. Predictive models successfully classified constitutive polyA sites from a biologically relevant background (auROC = 99.6%), as well as tissue-specific regulated sets from each other. We found that the main cis-regulatory elements described for polyadenylation are a strong, and highly informative, hallmark for constitutive sites only. Tissue-specific regulated sites were found to contain other regulatory motifs, with the canonical polyadenylation signal being nearly absent at brain-specific polyA sites. Together, our results contribute to the understanding of the diversity of post-transcriptional gene regulation.

Availability: Raw data are deposited on SRA, accession numbers: brain SRX208132, kidney SRX208087 and liver SRX208134. Processed datasets as well as model code are published on our website: http://www.genome.duke.edu/labs/ohler/research/UTR/

Contact: uwe.ohler@duke.edu
Effects of ocean acidification on hatch size and larval growth of walleye pollock (Theragra chalcogramma)
Authors: Hurst Thomas P. , Fernandez Elena R. , Mathis Jeremy T.
Published: June 2013

Hurst, T. P., Fernandez, E. R., and Mathis, J. T. 2013. Effects of ocean acidification on hatch size and larval growth of walleye pollock (Theragra chalcogramma). – ICES Journal of Marine Science, 70: 812–822. Rising atmospheric concentrations of CO2 are predicted to decrease the pH of high-latitude oceans by 0.3–0.5 units by 2100. Because of their limited capacity for ion exchange, embryos and larvae of marine fishes are predicted to be more sensitive to elevated CO2 than juveniles and adults. Eggs and larvae of walleye pollock (Theragra chalcogramma) were incubated across a broad range of CO2 levels (280–2100 µatm) to evaluate sensitivity in this critical resource species. Slightly elevated CO2 levels (∼450 µatm) resulted in earlier hatching times, but differences among egg batches were greater than those observed across CO2 treatments. Egg batches differed significantly in size-at-hatch metrics, but we observed no consistent effect of CO2 level. In three independent experiments, walleye pollock were reared at ambient and elevated CO2 levels through the early larval stage (to ∼30 days post-hatch). Across trials, there were only minor effects of CO2 level on size and growth rate, but fish in the ambient treatments tended to be slightly smaller than fish reared at elevated CO2 levels. These results suggest that growth potential of early life stages of walleye pollock is resilient with respect to the direct physiological effects of ocean acidification.
Evaluating deepwater fisheries management strategies using a mixed-fisheries and spatially explicit modelling framework
Authors: Marchal Paul , Vermard Youen
Published: June 2013

Marchal, P., and Vermard, Y. 2013. Evaluating deepwater fisheries management strategies using a mixed-fisheries and spatially explicit modelling framework. – ICES Journal of Marine Science, 70: 768–781. We have used in this study a spatially explicit bioeconomic modelling framework to evaluate management strategies, building in both data-rich and data-limited harvest control rules (HCRs), for a mix of deepwater fleets and species, on which information is variable. The main focus was on blue ling (Molva dypterygia). For that species, both data-rich and data-limited HCRs were tested, while catch per unit effort (CPUE) was used either to tune stock assessments, or to directly trigger management action. There were only limited differences between the performances of both HCRs when blue ling biomass was initialized at the current level, but blue ling recovered more quickly with the data-rich HCR when its initial biomass was severely depleted. Both types of HCR lead, on average, to a long-term recovery of both blue ling and saithe (Pollachius virens) stocks, and some increase in overall profit. However, that improvement is not sufficient to guarantee sustainable exploitation with a high probability. Blue ling CPUE did not always adequately reflect trends in biomass, which mainly resulted from fleet dynamics, possibly in combination with density-dependence. The stock dynamics of roundnose grenadier (Coryphaenoides rupestris), black scabbardfish (Aphanopus carbo) and deepwater sharks (Centrophorus squamosus and Centroscymnus coelolepis) were little affected by the type of HCR chosen to manage blue ling.
Krill biomass and aggregation structure in relation to tidal cycle in a penguin foraging region off the Western Antarctic Peninsula
Authors: Bernard Kim S. , Steinberg Deborah K.
Published: June 2013

Bernard, K. S., and Steinberg, D. K. 2013. Krill biomass and aggregation structure in relation to tidal cycle in a penguin foraging region off the Western Antarctic Peninsula. – ICES Journal of Marine Science, 70: 834–849

Antarctic krill are a key component of the diet of Adélie penguins inhabiting the Western Antarctic Peninsula (WAP), yet our understanding of the variability of krill distribution patterns within nearshore penguin feeding grounds is limited. A recent study of the foraging patterns of penguins breeding in the northern WAP suggests that tidal phase plays a role in foraging distance. We used acoustics to examine biomass and aggregation structure of krill in the penguin foraging grounds off Palmer Station during diurnal and semi-diurnal tides. Nearshore, integrated krill biomass during diurnal tides was significantly higher than during semi-diurnal tides. Krill aggregations were also shallower, closer together, and larger in dimension during diurnal tides. Conversely, krill aggregations had higher volumetric biomass and abundance during semi-diurnal tides. Further offshore, at the head of the Palmer Deep canyon, krill aggregations were similar to those observed nearshore during diurnal tides (i.e. shallow, close together, and large in dimension). Since krill aggregation structure strongly influences availability as a potential prey source, we suggest that foraging behavior of Adélie penguins in this region is strongly linked to the variability in nearshore krill aggregation structure as well as biomass.
Larval development of the barnacle Amphibalanus improvisus responds variably but robustly to near-future ocean acidification
Authors: Pansch Christian , Schlegel Peter , Havenhand Jonathan
Published: June 2013

Pansch, C., Schlegel, P., and Havenhand, J. 2013. Larval development of the barnacle Amphibalanus improvisus responds variably but robustly to near-future ocean acidification. – ICES Journal of Marine Science, 70: 805–811. Increasing atmospheric CO2 decreases seawater pH in a phenomenon known as ocean acidification. In two separate experiments we found that larval development of the barnacle Amphibalanus (Balanus) improvisus was not significantly affected by the level of reduced pH that has been projected for the next 150 years. After 3 and 6 days of incubation, we found no consistent effects of reduced pH on developmental speed or larval size at pH 7.8 compared with the control pH of 8.1. After 10 days of incubation, there were no net changes in survival or overall development of larvae raised at pH 7.8 or 7.6 compared with the control pH of 8.0. In all cases, however, there was significant variation in responses between replicate batches (parental genotypes) of larvae, with some batches responding positively to reduced pH. Our results suggest that the non-calcifying larval stages of A. improvisus are generally tolerant to near-future levels of ocean acidification. This result is in line with findings for other barnacle species and suggests that barnacles do not show the greater sensitivity to ocean acidification in early life history reported for other invertebrate species. Substantial genetic variability in response to low pH may confer adaptive benefits under future ocean acidification.
Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment
Authors: Ewing Brent , Hillier LaDeana , Wendl Michael C. , Green Phil
Published: June 2013

The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obtain the 3-billion-base human genome sequence by the target date of 2005. To reach this goal, improved automation will be essential, and it is particularly important that human involvement in sequence data processing be significantly reduced or eliminated. Progress in this respect will require both improved accuracy of the data processing software and reliable accuracy measures to reduce the need for human involvement in error correction and make human review more efficient. Here, we describe one step toward that goal: a base-calling program for automated sequencer traces,phred,with improved accuracy.phredappears to be the first base-calling program to achieve a lower error rate than the ABI software, averaging 40%–50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Consed: A Graphical Tool for Sequence Finishing
Authors: Gordon David , Abajian Chris , Green Phil
Published: June 2013

Sequencing of large clones or small genomes is generally done by the shotgun approach (Anderson et al. 1982). This has two phases: (1) a shotgun phase in which a number of reads are generated from random subclones and assembled into contigs, followed by (2) a directed, or finishing phase in which the assembly is inspected for correctness and for various kinds of data anomalies (such as contaminant reads, unremoved vector sequence, and chimeric or deleted reads), additional data are collected to close gaps and resolve low quality regions, and editing is performed to correct assembly or base-calling errors. Finishing is currently a bottleneck in large-scale sequencing efforts, and throughput gains will depend both on reducing the need for human intervention and making it as efficient as possible. We have developed a finishing tool, consed, which attempts to implement these principles. A distinguishing feature relative to other programs is the use of error probabilities from our programs phred andphrap as an objective criterion to guide the entire finishing process. More information is available athttp://www.genome.washington.edu/consed/consed.html.
Two one-dimensional linear zinc(II) polymers:catena-poly[[[2,6-bis(1H-benzimidazol-2-yl-κN3)pyridine]zinc(II)]-μ-pyridine-2,4-dicarboxylato-κ2O2:O4] andcatena-poly[[[2,6-bis(1H-benzimidazol-2-yl-κN3)pyridine]zinc(II)]-μ-pyridine-2,5-dicarboxylato-κ2O2:O5]
Authors: Xiang Jing
Published: June 2013

The solvothermal reactions of 2,6-bis(1H-benzimidazol-2-yl)pyridine (H2bpp) and hydrated ZnCl2in the presence of pyridine-2,4-dicarboxylic acid (2,4-pdcH2) or pyridine-2,5-dicarboxylic acid (2,5-pdcH2) afforded the title one-dimensional linear compounds, [Zn(C7H3NO4)(C19H13N5)]nor [Zn(2,4-pdc)(H2bpp)]n, (I), and [Zn(C7H3NO4)(C19H13N5)]nor [Zn(2,5-pdc)(H2bpp)]n, (II), respectively. The ZnIIcations in these compounds have closely comparable geometries and both are octahedrally coordinated by N4O2donor sets. The thermal stabilities have been investigated by thermogravimetric analysis (TGA) on the crystalline samples and their solid-state photoluminescence properties have been investigated at room temperature.
The Eden Principles in dementia respite care: carers’ experience
Authors: Downes Sandra
Published: June 2013

Purpose

The purpose of this paper is to report on outcomes for carers of people with dementia who use the services of Hawthorn House, a day respite centre in rural Western Australia that is based on the Eden Principles.

Design/methodology/approach

Quantitative and qualitative data from carers was collected and analysed. Quantitative data included the General Health Questionnaire‐12, Zarit Burden Interview, and Eden survey. Qualitative data was from semi‐structured interviews. Validation was confirmed and then simple statistics were generated from the quantitative data. Thematic analysis was used with the qualitative data.

Findings

Carers of people with dementia who use the services of Hawthorn House confirm that the Eden Principles are an integral part of Hawthorn House and report better than average health, less stress/burden and better quality of life. Many attribute this to the services they receive from Hawthorn House.

Research limitations/implications

Participants for the study were self‐selecting.

Practical implications

The paper provides verification that the Eden Principles can lead to meaningful and important benefits for carers of people with dementia.

Originality/value

This paper is the first to report on the use of the Eden Principles in a non full‐time respite centre for people with dementia in rural Australia. Further, it describes quantitative and qualitative data on quality of life outcomes for carers as a result of being associated with the centre.
Life story work – overcoming issues of consent and confidentiality
Authors: Pouchly Cara A. , Corbett Louise H. , Edwards Kati
Published: June 2013

Purpose

This is a discussion paper which aims to explore issues of consent and confidentiality when using life story work in clinical settings with older adults with dementia.

Design/methodology/approach

This is a discussion paper reviewing current research, policy, guidance from regulating bodies and government recommendations.

Findings

Life story work can be used in clinical practice without violating consent and confidentiality clauses in mental health practice when used appropriately.

Originality/value

This paper provides insights overcoming issues of consent and confidentiality with life story work in clinical practice, reducing the challenges reported by staff. Clinical recommendations are offered to both support and empower clinical staff, enabling the full benefits of this person‐centred tool to be utilised.