bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants
Authors: Gagliano Sarah A. , Ravji Reena , Barnes Michael R. , Weale Michael E. , Knight Jo 
Published: August 2015

AbstractAlthough technology has triumphed in facilitating routine genome sequencing, new challenges have been created for the data-analyst. Genome-scale surveys of human variation generate volumes of data that far exceed capabilities for laboratory characterization. By incorporating functional annotations as predictors, statistical learning has been widely investigated for prioritizing genetic variants likely to be associated with complex disease. We compared three published prioritization procedures, which use different statistical learning algorithms and different predictors with regard to the quantity, type and coding. We also explored different combinations of algorithm and annotation set. As an application, we tested which methodology performed best for prioritizing variants using data from a large schizophrenia meta-analysis by the Psychiatric Genomics Consortium. Results suggest that all methods have considerable (and similar) predictive accuracies (AUCs 0.64–0.71) in test set data, but there is more variability in the application to the schizophrenia GWAS. In conclusion, a variety of algorithms and annotations seem to have a similar potential to effectively enrich true risk variants in genome-scale datasets, however none offer more than incremental improvement in prediction. We discuss how methods might be evolved for risk variant prediction to address the impending bottleneck of the new generation of genome re-sequencing studies.
CAMKII-conditional deletion of histone deacetylase 2 potentiates acute methamphetamine-induced expression of immediate early genes in the mouse nucleus accumbens
Authors: Torres Oscar V. , McCoy Michael T. , Ladenheim Bruce , Jayanthi Subramaniam , Brannock Christie , Tulloch Ingrid , Krasnova Irina N. , Cadet Jean Lud 
Published: August 2015

AbstractMethamphetamine (METH) produces increases in the expression of immediate early genes (IEGs) and of histone deacetylase 2 (HDAC2) in the rat nucleus accumbens (NAc). Here, we tested whether HDAC2 deletion influenced the effects of METH on IEG expression in the NAc. Microarray analyses showed no baseline differences in IEG expression between wild-type (WT) and HDAC2 knockout (KO) mice. Quantitative-PCR analysis shows that an acute METH injection produced time-dependent increases in mRNA levels of several IEGs in both genotypes. Interestingly, HDAC2KO mice displayed greater METH-induced increases in Egr1 and Egr2 mRNA levels measured at one hour post-injection. The levels of Fosb, Fra2, Egr1 and Egr3 mRNAs stayed elevated in the HDAC2KO mice 2 hours after the METH injection whereas these mRNAs had normalized in the WT mice. In WT mice, METH caused increased HDAC2 recruitment to the promoters some IEGs at 2 hours post injection. METH-induced prolonged increases in Fosb, Fra2, Egr1 and Egr3 mRNA levels in HDAC2KO mice were associated with increased enrichment of phosphorylated CREB (pCREB) on the promoters of these genes. Based on our observations, we hypothesize that HDAC2 may regulate the expression of these genes, in part, by prolonging the actions of pCREB in the mouse NAc.
Efficient nitrogen incorporation in ZnO nanowires
Authors: Stehr Jan E. , Chen Weimin M. , Reddy Nandanapalli Koteeswara , Tu Charles W. , Buyanova Irina A. 
Published: August 2015

AbstractOne-dimensional ZnO nanowires (NWs) are a promising materials system for a variety of applications. Utilization of ZnO, however, requires a good understanding and control of material properties that are largely affected by intrinsic defects and contaminants. In this work we provide experimental evidence for unintentional incorporation of nitrogen in ZnO NWs grown by rapid thermal chemical vapor deposition, from electron paramagnetic resonance spectroscopy. The incorporated nitrogen atoms are concluded to mainly reside at oxygen sites (NO). The NO centers are suggested to be located in proximity to the NW surface, based on their reduced optical ionization energy as compared with that in bulk. This implies a lower defect formation energy at the NW surface as compared with its bulk value, consistent with theoretical predictions. The revealed facilitated incorporation of nitrogen in ZnO nanostructures may be advantageous for realizing p-type conducting ZnO via N doping. The awareness of this process can also help to prevent such unintentional doping in structures with desired n-type conductivity.
STAT1 deficiency redirects IFN signalling toward suppression of TLR response through a feedback activation of STAT3
Authors: Kim Hun Sik , Kim Dong Chan , Kim Hong-Mi , Kwon Hyung-Joon , Kwon Soon Jae , Kang Suk-Jo , Kim Sun Chang , Choi Go-Eun 
Published: August 2015

AbstractInterferons (IFNs) potentiate macrophage activation typically via a STAT1-dependent pathway. Recent studies suggest a functioning of STAT1-independent pathway in the regulation of gene expression by IFN-γ, thus pointing to the diversity in cellular responses to IFNs. Many functions of IFNs rely on cross-regulation of the responses to exogenous inflammatory mediators such as TLR ligands. Here we investigated the contribution of STAT1-independent pathway to macrophage activation and its underlying mechanism in the context of combined stimulation of IFN and TLR. We found that TLR-induced production of inflammatory cytokines (TNF-α, IL-12) was not simply nullified but was significantly suppressed by signaling common to IFN-γ and IFN-β in STAT1-null macrophages. Such a shift in the suppression of TLR response correlated with a sustained STAT3 activation and attenuation of NF-κB signaling. Using a JAK2/STAT3 pathway inhibitor or STAT3-specific siRNA, blocking STAT3 in that context restored TNF-α production and NF-κB signaling, thus indicating a functional cross-regulation among STAT1, STAT3 and NF-κB. Our results suggest that STAT1 deficiency reprograms IFN signaling from priming toward suppression of TLR response via feedback regulation of STAT3, which may provide a new insight into the host defense response against microbial pathogens in a situation of STAT1 deficiency.
Metallic Sn spheres and SnO2@C core-shells by anaerobic and aerobic catalytic ethanol and CO oxidation reactions over SnO2 nanoparticles
Authors: Kim Won Joo , Lee Sung Woo , Sohn Youngku 
Published: August 2015

AbstractSnO2 has been studied intensely for applications to sensors, Li-ion batteries and solar cells. Despite this, comparatively little attention has been paid to the changes in morphology and crystal phase that occur on the metal oxide surface during chemical reactions. This paper reports anaerobic and aerobic ethanol and CO oxidation reactions over SnO2 nanoparticles (NPs), as well as the subsequent changes in the nature of the NPs. Uniform SnO2@C core-shells (10 nm) were formed by an aerobic ethanol oxidation reaction over SnO2 NPs. On the other hand, metallic Sn spheres were produced by an anaerobic ethanol oxidation reaction at 450 °C, which is significantly lower than that (1200 °C) used in industrial Sn production. Anaerobic and aerobic CO oxidation reactions were also examined. The novelty of the methods for the production of metallic Sn and SnO2@C core-shells including other anaerobic and aerobic reactions will contribute significantly to Sn and SnO2-based applications.
Development of LC-MS/MS analysis of cyclic dipeptides and its application to tea extract
Authors: Yamamoto Kenji , Hayashi Miki , Murakami Yuka , Araki Yoko , Otsuka Yuuki , Kashiwagi Takehiro , Shimamura Tomoko , Ukeda Hiroyuki 
Published: August 2015

Abstract
2,5-Diketopiperazines (DKPs), also called cyclic dipeptides, have been known to occur in various foods. Recently, DKPs have attracted attentions as bioactive components. There were some reports on analytical methods for DKPs, but the number of analyzed DKPs was only a part of all DKPs and the quantitative performance was not studied in detail. In this study, we selected 31 kinds of DKPs and developed a quantitative and simultaneous analytical method using LC-MS/MS. This method was applied to DKPs determination in Pu-erh tea, post-fermentation tea, and 18 kinds of DKPs were determined at concentration of 0.0017–0.11 ppm. As a result of spiked test, it was concluded that the developed method using LC-MS/MS was useful for estimating DKPs concentration in tea.
The pricing of community supported agriculture shares: evidence from New England
Authors: Sproul Thomas W. , Kropp Jaclyn D. , Barr Kyle D. 
Published: August 2015

Purpose
– Community supported agriculture (CSA) programs allow consumers to buy a share of a farm’s production while providing working capital and risk management benefits for farmers. Several different types of CSA arrangements have emerged in the market with terms varying in the degree to which consumers share in the farm’s risk. No-arbitrage principles of futures and options pricing suggest that CSA shares should be priced to reflect the degree of risk transfer. The paper aims to discuss these issues.

Design/methodology/approach
– The authors evaluate the three most common share types using a cross-sectional data set of 226 CSA farms from New England to determine if there is empirical evidence in support of the theoretical price relationship between share types.

Findings
– The degree of risk transfer from farmers to consumers has a significant effect on the share price. There are statistically significant returns to scale and higher prices for organics. Farm characteristics and product offerings predict which type of shares is offered for sale.

Research limitations/implications
– The data set does not contain information pertaining to actual deliveries, expected deliveries, variance of expected deliveries, or covariance information; thus differences in share prices could be due to differences in these uncontrolled factors.

Originality/value
– This paper provides empirical evidence that CSA share prices reflect the degree of risk transferred from the producer to the consumer. It also highlights challenges in conducting empirical work pertaining to CSA contracting.
Determinants of farm income
Authors: Beckman Jayson , Schimmelpfennig David 
Published: August 2015

Purpose– The recent fluctuations in farm income remind us of the boom-bust nature of the agricultural sector. To better understand these fluctuations in farm income, the purpose of this paper is to examine the relationship between farm income and influential factors from 1964 to 2010 allowing for structural breaks in the data.Design/methodology/approach– The authors estimate error-correction models for an overarching model and several sub-models at different scales based on their relationship with farm income: micro, meso, and macro. The authors then provide a series of impulse response functions (IRFs) that combine short- and long-run impacts in a rigorous framework indicating the response of farm income to shocks from any of the explanatory variables.Findings– Results indicate that prices paid (PP) and received by farmers, technological change, interest and exchange rates (ERs), gross domestic product (GDP) and land prices all influence farm income. Results using IRFs show how increases in farm income arise from shocks to prices received and GDP; while PP, interest rates, and land prices have a negative impact on farm income. Technological progress and ERs switch from having a negative short-run impact, to a positive long-run impact.Originality/value– This paper takes a fresh look at the single, overarching model for farm income determinants. The authors break this model into three separate levels, with results indicating that these sub-groups perform better than the one overarching model of all variables.
A process for building inter-organizational contextual ambidexterity
Authors: Lavikka Rita , Smeds Riitta , Jaatinen Miia 
Published: August 2015

Purpose– The purpose of this paper is to discover a three-step process for building contextual ambidexterity into inter-organizational IT-enabled service processes through developmental interventions.Design/methodology/approach– A longitudinal action research project was conducted. The empirical study consisted of three consecutive developmental interventions to support the collaborative development effort of an IT company and its customer network to efficiently serve their present and future customers. The data consists of process modeling and simulation workshop discussions, interviews, observation, and archival data. The development effort was studied for over a year.Findings– The study shows that the three developmental interventions acted as a process for balancing the exploration-exploitation tension in inter-organizational service processes. The sequential interventions facilitated the studied organizations in crossing the inter-organizational knowledge boundaries and creating shared domain knowledge, creating common understanding of the collaborative IT-enabled service processes, and co-developing the coordination mechanisms that are essential for the continuous exploration and exploitation of the new ideas in the future collaborative service processes. These three steps built capacity for the inter-organizational management system to achieve synergies between goals, resources, and activities in the inter-organizational collaboration.Originality/value– The study contributes to the understanding on the process of building inter-organizational ambidexterity. The study presents a three-step process for building inter-organizational contextual ambidexterity into the IT-enabled service processes through developmental interventions. Research on inter-organizational contextual ambidexterity is combined with research on coordination and knowledge management.
Exploring the tensions behind the adoption of mobile work practices in SMEs
Authors: Raguseo Elisabetta , Paolucci Emilio , Neirotti Paolo 
Published: August 2015

Purpose– The purpose of this paper is to understand the contextual conditions under which mobile forms of work are chosen by small and medium enterprises (SMEs) and the most relevant tensions that these firms should be able to face in order to be successful in the adoption of these forms of work.Design/methodology/approach– A survey analysis on 304 SMEs and an analysis of a collection of case studies were conducted to answer to the following research questions: what is the role of contextual conditions in shaping the way firms develop and use their mobile forms of work? Which tensions do SMEs need to manage when adopt a particular mobile form of work?Findings– In this paper, the authors found that SMEs choose different mobile forms of work according to the conditions under which they operate. For example, SMEs that adopt mobile forms of work for operational reasons are more capable of using IT to improve their external orientation. Moreover, the analysis of the configurations of mobile forms of work led to classify in a systematic way the managerial and organizational tensions, and to identify which tensions need to be managed in each mobile work configuration. For example, firms that adopt mobile work given individual employee requests need to manage human resource management tensions.Research limitations/implications– Future research should analyse in depth the jobs that are frequently engaged in mobility and the operational and strategic reasons of their mobility. Moreover, future research should analyse more in-depth companies’ capability of managing tensions discussed in this paper.Practical implications– Managers should understand that mobile work is an essential element in the organizational strategy of SMEs, since it is a way to manage more effectively externally oriented business processes. Also policy makers should provide financial support for programmes aimed at promoting the importance of mobile forms of work, since they allow achieving different objectives and saving. Further, demand-oriented policies and experiences about mobile work adoption should be shared.Originality/value– The authors found scant empirical evidence on understanding the contextual conditions under which SMEs choose different mobile forms of work, and the most relevant tensions that SMEs should deal with when they decide for the adoption of a particular mobile work configuration. The value of this paper consists in filling this research gap.
Assessing the field
Authors: Frawley Emily , McLean Davies Larissa 
Published: August 2015

Purpose– The purpose of this paper is to explore the interface between high-stakes testing, disciplinary knowledge and teachers’ pedagogy in English. The most prevalent standardized assessment form in the current Australian context is the National Assessment Program for Literacy and Numeracy (NAPLAN) undertaken each year by students in Years 3, 5, 7 and 9 in all Australian States and Territories. Understood in the context of the Global Educational Reform Movement (GERM) (Sahlberg, 2011, pp. 100-101) – the NAPLAN tests serve as a bi-partisan governmental response to a perceived need to improve the quality of teachers and schools in Australia.Design/methodology/approach– The authors draw on the key sociological constructs of Pierre Bourdieu (1995) to analyze the ways in which the writing component of the suite of NAPLAN tests serves to legitimize and idealize particular kinds of writing, writers and teachers of writing.Findings– The authors suggest that in the absence of current literacy policy and curriculum instability, this national test shapes the literacy field, influencing the direction of writing practices and pedagogy, and, therefore, subject English itself, in Australian classrooms.Originality/value– This assessment intervention is considered in the context of the history of writing, and addresses accordingly fundamental questions concerning the changing nature of the writing/writerly field, the impact of assessment on teachers’ conceptions of disciplinarity and pedagogical content knowledge and students’ experiences of writing and thinking in subject English.
Bringing innovation to conventional feedback approaches in EFL secondary writing classrooms
Authors: Lee Icy , Mak Pauline , Burns Anne 
Published: August 2015

Purpose
– The purpose of this paper is to examine how the teachers implemented innovative feedback approaches in their writing classroom and the extent to which the innovative feedback approaches impacted upon student attitude and performance in writing. In the writing classroom, teacher feedback serves as an assessment as well as a pedagogical tool to enhance the teaching and learning of writing. While there is no shortage of literature on the topic of feedback per se, there is scant research on teachers’ attempts to implement change to conventional feedback practices, as well as the impact of such feedback innovation on student learning. Drawing on data gathered from individual teacher interviews, student questionnaires, student focus group interviews, pre-and post-writing tests and classroom observations, this study seeks to explore two teachers’ change initiative in their writing feedback approaches.

Design/methodology/approach
– The study used multiple sources of data including individual teacher interviews, student questionnaires and student focus group.

Findings
– The results suggest that the innovative feedback approaches helped to enhance the motivation and writing performance of the students. The paper concludes with implications and insights to help teachers implement similar feedback innovations in their contexts.

Practical implications
– First, the findings suggest that focused written corrective feedback is a viable option for responding to student writing, especially for low proficiency students in English as a foreign language (EFL) contexts. Second, teachers might consider the option of removal or delay in the reporting of scores, where appropriate. Third, more intensive training might be necessary to help students improve their peer evaluation skills and their ability to write more constructive comments for their peers.

Originality/value
– The significance of the study lies in the contribution it can make to existing writing feedback research that pays insufficient attention to teacher feedback in real classroom contexts, uncovering the process through which teachers attempt to bring improvement to conventional feedback practices, as well as the impact of feedback innovation on student learning in naturally occurring classroom contexts.
“I had been given the space to grow”
Authors: Manuel Jackie , Carter Don 
Published: August 2015

Purpose
– This paper aims to provide a critical interpretative analysis of an innovative model of assessment in subject English in New South Wales, Australia. The purpose of this paper is to explore the theoretical and practical dimensions of assessment in the English Extension 2 course. This course forms part of suite of senior secondary English courses within the Higher School Certificate program that includes high-stakes external examination.

Design/methodology/approach
– The paper draws on methods of documentary analysis. It sits within the tradition of curriculum research that critiques pre-active curriculum documents as a primary source for interpreting the theoretical and pedagogical principles and assumptions encoded in such documents. A social constructionist approach informs the analysis.

Findings
– The model of assessment in the New South Wales (NSW) English Extension 2 course provides students with the opportunity to engage in sustained research and the production of a major piece of work. In its emphasis on student creativity, reflective practice, metacognition and independent research, the course exemplifies the ways in which the principle of assessing both process and product as organic is achievable in a context of high-stakes external examinations.

Originality/value
– In an era of high-stakes, external and standardised testing regimes, this paper challenges the normative definitions of assessment prevalent in secondary schools, particularly at the senior secondary level. The assessment model underpinning the NSW English Extension 2 course offers a robust alternative to the increasingly prescriptive models evident in current education policy and practice. The paper calls for renewed attention to the potential for such a model of authentic assessment to be considered in the assessment programs of other subjects constituting the curriculum.
“Resisting the rage for certainty”: dialogic assessment
Authors: Brindley Sue , Marshall Bethan 
Published: August 2015

Purpose– The purpose of this paper is to report on one UK secondary school English teacher and use his practice as a vehicle for exploring the classroom realities of dialogic assessment. Dialogic assessment, a term first proposed by Alexander (2004), is a position which seeks to synthesise the potentially powerful positions of both dialogic teaching and assessment for learning remains largely unexploited as an approach to developing effective teaching and learning.Design/methodology/approach– Using video classroom evidence and interview, the authors explore the parameters within which dialogic teaching and assessment can be developed, and investigate the opportunities and obstacles which developing dialogic assessment bring about.Findings– The authors develop a framework, drawing on the evidence, which demonstrates the development of dialogic assessment in the classroom.Originality/value– This paper is an original look at dialogic assessment within the upper secondary sector.