bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deconvolving sequence features that discriminate between overlapping regulatory annotations
Authors: Kakumanu Akshay , Velasco Silvia , Mazzoni Esteban , Mahony Shaun 
Published: January 2017

AbstractGenomic loci with regulatory potential can be identified and annotated with various properties. For example, genomic sites may be annotated as being bound by a given transcription factor (TF) in one or more cell types. The same sites may be further labeled as being proximal or distal to known promoters. Given such a collection of labeled sites, it is natural to ask what sequence features are associated with each annotation label. However, discovering such label-specific sequence features is often confounded by overlaps between annotation labels; e.g. if regulatory sites specific to a given cell type are also more likely to be promoter-proximal, it is difficult to assess whether motifs identified in that set of sites are associated with the cell type or associated with promoters. In order to meet this challenge, we developed SeqUnwinder, a principled approach to deconvolving interpretable discriminative sequence features associated with overlapping annotation labels. We demonstrate the novel analysis abilities of SeqUnwinder using three examples. Firstly, we show SeqUnwinder’s ability to unravel sequence features associated with the dynamic binding behavior of TFs during motor neuron programming from features associated with chromatin state in the initial embryonic stem cells. Secondly, we characterize distinct sequence properties of multi-condition and cell-specific TF binding sites after controlling for uneven associations with promoter proximity. Finally, we demonstrate the scalability of SeqUnwinder to discover cell-specific sequence features from over one hundred thousand genomic loci that display DNase I hypersensitivity in one or more ENCODE cell lines.Availabilityhttps://github.com/seqcode/sequnwinder
Transposons modulate transcriptomic and phenotypic variation via the formation of circular RNAs in maize
Authors: Chen Lu , Zhang Pei , Fan Yuan , Huang Juan , Lu Qiong , Li Qing , Yan Jianbing , Muehlbauer Gary J. , Schnable Patrick S. , Dai Mingqiu , Li Lin 
Published: January 2017

AbstractCircular RNAs (circRNAs) are covalently closed, single-stranded RNA molecules. Recent studies in human showed that circRNAs can arise via transcription of reverse complementary pairs of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. To test our hypothesis, we performed circRNA-Seq on B73 seedling leaves and integrate these data with 977 publicly available mRNA-Seq datasets. We uncovered 1,551 high-confidence maize circRNAs, which show distinct genomic features as compared to linear transcripts. Comprehensive analyses demonstrated that LINE1-like elements (LLE) and their Reverse Complementary Pairs (LLERCPs) are significantly enriched in the flanking regions of circRNAs. Interestingly, the accumulation of circRNA transcripts increases, while the accumulation of linear transcripts decreases as the number of LLERCPs increases. Furthermore, genes with LLERCP-mediated circRNAs are enriched among loci that are associated with phenotypic variation. These results suggest that LLERCPs can modulate phenotypic variation by the formation of circRNAs. As a proof of concept, we showed that the presence/absence variation of LLERCPs could result in expression variation of one cicrRNA, circ352, and further related to plant height through the interaction between circRNA and functional linear transcript. Our first glimpse of circRNAs uncovers a new role for transposons in the modulation of transcriptomic and phenotypic variation via the formation of circRNAs.
Transcriptional repression by ApiAP2 factors is central to chronic toxoplasmosis
Authors: Radke Joshua B. , Worth Danielle , Hong Dong-Pyo , Huang Sherri , Sullivan William J. , Wilson Emma H. , White Michael W. 
Published: January 2017

AbstractBradyzoite differentiation is marked by major changes in gene expression resulting in a parasite that expresses a new repertoire of surface antigens hidden inside a modified parasitophorous vacuole called the tissue cyst. The factors that control this important life cycle transition are not well understood. Here we describe an importantToxoplasmatranscriptional repressor mechanism controlling bradyzoite differentiation that operates exclusively in the tachyzoite stage. The ApiAP2 factor, AP2IV-4, is a nuclear factor dynamically expressed in late S phase through mitosis/cytokinesis of the tachyzoite cell cycle. Remarkably, deletion of the AP2IV-4 locus resulted in the increased expression of bradyzoite mRNAs in replicating tachyzoites, and in two different genetic lineages we confirmed the misexpression of tissue cyst wall components (e.g. BPK1, MCP4, CST1) and the bradyzoite surface antigen SRS9 in the tachyzoite stage. In the murine animal model, the loss of AP2IV-4 had profound biological consequences. Type II prugniaud strain parasites lacking AP2IV-4 were unable to form tissue cysts in brain tissue and the absence of this factor also recruited a potent immune response characterized by increases inflammatory monocytes, IFN-γ and higher numbers of both CD8+ and CD4+ T-cells. Altogether, these results indicate that suppression of bradyzoite antigens by AP2IV-4 during acute infection is required forToxoplasmato establish a chronic infection in the immune-competent host.Author SummaryTheToxoplasmabiology that underlies the establishment of a chronic infection is developmental conversion of the acute tachyzoite stage into the latent bradyzoite-tissue cyst stage. Despite the important clinical consequences of this developmental pathway, the molecular basis of the switch mechanisms that control formation of the tissue cyst is still poorly understood. A fundamental feature of tissue cyst formation is the expression of bradyzoite-specific genes. Here we show the transcription factor AP2IV-4 directly silences bradyzoite mRNA and protein expression in the acute tachyzoite stage demonstrating that developmental control of tissue cyst formation is as much about when not to express bradyzoite genes as it is about when to activate them. Loosing the suppression of bradyzoite gene expression in the acute tachyzoite stage caused by deleting AP2IV-4 blocked the establishment of chronic disease in healthy animals through the pre-arming of the immune system suggesting a possible strategy for preventing chronicToxoplasmainfections.
A theoretical framework of external accounting communication
Authors: Merkl-Davies Doris M. , Brennan Niamh M. 
Published: January 2017

PurposeThe purpose of this paper is to provide a theoretical framework of external accounting communication in the form of a typology based on perspectives, traditions, and theories from the discipline of communication studies. The focus is accounting communication with external audiences via public written documents outside the audited financial statements, i.e., annual reports, press releases, CSR reports, websites, conference calls, etc.Design/methodology/approachThe theoretical framework is based on two broad research perspectives on accounting communication: (A) a functionalist-behavioural transmission perspective and (B) a symbolic-interpretive narrative perspective. Eight traditions of communication research are introduced which provide alternative ways of conceptualising accounting communication, namely (1) mathematical tradition, (2) socio-psychological tradition, (3) cybernetic/systems-oriented tradition, (4) semiotic tradition, (5) rhetorical tradition, (6) phenomenological tradition, (7) socio-cultural tradition, and (8) critical tradition. Exemplars of each tradition from prior accounting research, to the extent they have been adopted, are discussed. Finally, a typology is developed, which serves as a heuristic device for viewing similarities and differences between research traditions.FindingsPrior accounting studies predominantly focus on the role of discretionary disclosures in accounting communication in the functioning of the relationship between organisations and their audiences. Research is predominantly located in the mathematical, the socio-psychological, and the cybernetic/systems-oriented tradition. Accounting communication is primarily viewed as the transmission of messages about financial, environmental, and social information to external audiences. Prior research is mainly concerned with the communicator (e.g. CEO personality) and the message (e.g. intentions and effects of accounting communication). Research from alternative traditions is encouraged, which explores how organisations and their audiences engage in a dialogue and interactively create, sustain, and manage meaning concerning accounting and accountability issues.Originality/valueThe paper identifies, organises, and synthesises research perspectives, traditions, and associated theories from the communication studies literature in the form of a typology. The paper concludes with an extensive agenda for future research on accounting communication.
From “mad men” to “math men”
Authors: Viale Thierry , Gendron Yves , Suddaby Roy 
Published: January 2017

Purpose
The authors study how communication agencies became important sites for the rise of measurement expertise in the government of consumer conduct following the development of online consumption. The purpose of this paper is to focus on the processes by which digital measurement developed (within the agencies) as a new legitimate form of expertise, able to produce relevant and detailed knowledge about the government of web users.

Design/methodology/approach
The authors carried out a field examination in France, predicated on 100 interviews with actors involved in communication consultancy. Drawing on the concepts of governmentality and inter-jurisdictional experimentation, the authors examine how digital measurement expertise acquired legitimacy within agencies. The authors also analyze how contemporary technologies of measurement and surveillance, as operated by in-house digital experts, provide advertising specialists and advertisers with increasingly precise data on consumer conduct and thought.

Findings
The constitution and legitimization of digital measurement expertise was characterized by experimentation, culminating in the production of persuasive claims of tangibility concerning communication impact, and in relative agreement on the relevance of digital expertise in operating increasingly powerful technologies of measurement and surveillance.

Originality/value
While the role of experts in promoting and implementing neoliberal governmentality is emphasized in the literature, the study indicates that considerable work is needed to develop and legitimize expertise consequent with neoliberalism. Also, the analysis highlights that the spread of digital measurement expertise and knowledge production in the government of web users constitutes a noteworthy step in the neoliberalization of society. Behind the front of “free” conduct lies an increasingly powerful network of technologies and expertise aimed at rendering consumer conduct knowable and predictable.
Segment reporting in a developing economy: the Indian banking sector
Authors: Birt Jacqueline , Joshi Mahesh , Kend Michael 
Published: January 2017

Purpose
The purpose of this paper is to investigate the value relevance of segment information for both public and private sector banks in India. In doing so, this paper examines a rapidly developing economy and perhaps its most critical sector during this period of strong economic growth.

Design/methodology/approach
In this study uses the simplified Ohlson model, for a sample of 136 private sector and public sector banks for the period 2007-2010 in India.

Findings
The paper finds that public sector banks have higher share prices, higher earnings and more equity compared with private sector banks. Segment earnings data is highly value relevant for both sectors; however, segment equity data is only marginally value relevant for Indian banks. The number of segments is also value relevant and associated with higher share prices.

Originality/value
The results of this study contribute additional evidence to the literature on segment reporting by studying the effect of adoption of segment reporting in an emerging market. Findings from the paper are particularly relevant as India is currently in the process of changing its segment reporting requirements and moving to an IFRS-based segment standard.
Management of income statement variables to report small positive earnings numbers
Authors: Lee B. Brian , Shin Haeyoung , Vetter William , Kim Dong Wuk 
Published: January 2017

Purpose
Charting the earnings numbers reported by Korean firms produces a bell curve, but for a sharp discontinuity in the area surrounding zero. The purpose of this paper is to investigate if and how a large segment of Korean managers might manage accounting numbers to produce the observed result.

Design/methodology/approach
This study adopts an empirical research method using Korean listed firms as a sample. The primary focus of investigation is on major income statement variables that might produce the observed results in earnings from operations and net income.

Findings
Managers of Korean firms opportunistically use almost all income statement variables to influence earnings numbers. They manage revenues and selling, general & administrative expenses to report small positive earnings from operations, but manage non-operating gains (losses) to report small positive net income.

Research limitations/implications
This paper does not answer several questions related to loss avoidance. First, the paper did not examine which actions, such as discretionary accruals, opportunistic business decisions, or bogus transactions, were employed to affect line items on the income statement. Second, the paper did not investigate what specific incentives trigger Korean managers to report small positive earnings. Korean firms have traditionally raised capital by borrowing funds from creditors and governmental agencies. Thus, they may be concerned that reporting losses would reduce their borrowing capacity. Finally, corporate governance, such as CEO tenure and option grants may influence the extent of earnings management to avoid losses, but most corporate governance data for Korean companies must be manually collected. Accordingly, these subjects are left for future studies as well.

Originality/value
This study contributes to accounting literature by reporting how managers of Korean firms artificially coordinate major income statement variables and report small positive earnings figures, noting the differences between earnings management investigating methodology and ones used in previous studies.
Tie strength, green expertise, and interpersonal influences on the purchase of organic food in an emerging market
Authors: Chang Sheng-Hsiung , Chang Chin-Wen 
Published: January 2017

Purpose
Set in an emerging economy context, the purpose of this paper is to examine the determinants of green consumers’ purchase behavior on organic food by analyzing the impact of word-of-mouth (WOM) effects (i.e. tie strength, sender’s green expertise, receiver’s green expertise), conformity behaviors (i.e. normative interpersonal influence and informational interpersonal influence) on green purchase intention, and the relationship between green purchase intention and green purchase behavior.

Design/methodology/approach
Data were collected by self-administered questionnaire completed by respondents who had purchase experience of organic food in the last six months. The specific context of this study is green consumption for organic food in Taiwan. Data collection was implemented in a convenience sampling method. Among the 578 consumers who had filled the questionnaire, 147 did not have any purchase history of organic food, resulting in a final usable sample of 431 (response rate 74.57 percent) in Taiwan. The data were collected during a five-week period in late 2015.

Findings
Through structural equation modeling analysis, data were analyzed and the empirical results indicate that tie strength, sender’s green expertise, and receiver’s green expertise have a positive influence on green consumer’s susceptibility to informational interpersonal influences and normative interpersonal influences, separately. In addition, informational interpersonal influences and normative interpersonal influences both have a positive relationship on green purchase intention, which will further positively influence the green purchase behavior.

Originality/value
This study reminds marketers of the impact of WOM effects as well as interpersonal influences on consumers. It examines the impact of tie strength, senders’ green expertise, and receivers’ green expertise on green purchase intention and green purchase behavior. This study also explores the mediation effects of green consumers’ susceptibility to interpersonal influences. Consumers’ susceptibility to interpersonal influence is discussed in the marketing literature. However, few prior studies have explored its effect in the green setting. Last, few attempts have discussed the relationship between green purchase intention and green purchase behavior. This study contributes to the literature by examine the relationship between green purchase intentions and green purchase behavior.
A preliminary study on the quality and safety of street-vended warankasi (a Nigerian soft white cheese) from Ibadan, Oyo state, Nigeria
Authors: Adeyeye Samuel Ayofemi Olalekan 
Published: January 2017

Purpose
The purpose of this paper is to evaluate the quality and safety of street-vended warankasi, a Nigerian soft white cheese.

Design/methodology/approach
A total of 80 samples were collected in two batches of 40 samples each in January and June, 2015 from eight major markets from Ibadan, Oyo State, Nigeria. The samples were analyzed for the proximate components, quality indices (total soluble nitrogen, TSN and volatile fatty acid, VFA), and for the presence of pathogenic bacteria, Campylobacter jejuni (CJ), Listeria monocytogenes (LM), Mycobacterium tuberculosis (MT), Salmonella spp. (SS), Escherichia coli (EC), and Yersinia enterocolitica (YE), and heavy metals such as (lead (Pb), cadmium (Cd), mercury (Hg), and chromium (Cr) concentrations.

Findings
The results revealed that the values of moisture, protein, fat, crude fiber, and ash contents (%) of warankasi samples were in the range 46.26±1.41-51.24±1.61, 33.92±1.18-37.26±1.42, 6.74±0.64-8.33±0.96, 1.27±0.02-1.73±0.09, 1.31±0.03-1.78±0.08, respectively. The values of TSN (mgN/kg) and VFA (%) were in the range of 1.19+0.10-2.54+0.18, and 5.79+0.19-9.12+0.30, respectively. The results further revealed the presence of CJ and SS and the absence of LM, MT, EC, and YE from the warankasi samples. Heavy metals detected in all the warankasi samples were generally below the maximum acceptable limits set by the World Health Organization for Pb (0.3 ppm), Cd (0.2 ppm), Hg (0.2 ppm), and Cr (0.5 ppm) with the exemption of samples from Iwo Road and Ojoo which were higher than other samples.

Research limitations/implications
This research work was conducted between January and June, 2015 and better results could be obtained if the study had been done for a longer period of time.

Practical implications
The paper helps in showing the quality and microbial safety of street-vended warankasi and this may bring imperative information and general consciousness on the microbiological safety of warankasi.

Originality/value
Much has been done concerning warankasi processing but little work has been done concerning street-vended warankasi. Therefore, this study was carried out to assess it.
Organic and conventional milk – insight on potential differences
Authors: Smigic Nada , Djekic Ilija , Tomasevic Igor , Stanisic Nikola , Nedeljkovic Aleksandar , Lukovic Verica , Miocinovic Jelena 
Published: January 2017

Purpose
The purpose of this paper is to investigate if there is a difference in hygiene parameters of raw milk produced in organic and conventional farm of similar size. In parallel, the aim was to determine if there are differences in pasteurized organic and conventional milk samples delivered on the market.

Design/methodology/approach
Raw milk samples were analyzed for aerobic colony count (ACC), somatic cell count (SCC), acidity, temperature, fat and protein content. On the other side, final products of organic and conventional pasteurized milk with 2.8 percent declared milk fat were analyzed for Raman spectroscopy, color change and sensorial difference.

Findings
Results of raw milk analysis showed statistically significant differences in fat content, SCC, acidity, temperature and ACC (p<0.05). It is of note that ACC for organic milk were lower for approx. 1 log CFU/ml compared to conventional milk samples. Pasteurized organic milk samples had a significantly higher L* value than those samples originating from conventional farms, indicating that organic is “more white” compared to conventional milk. According to the results of triangle test, with 95 percent confidence no more than 10 percent of the population is able to detect a difference.

Research limitations/implications
A limitation of this research is the fact that good veterinary practices at farms, namely, animal health and adequate usage of medicine for treating the animals, animal welfare and animal feeding were not analyzed.

Originality/value
This study analyzed potential differences in organic and conventional milk at two important production stages of the milk chain – at receipt at dairy plant (raw milk) and perceived by consumers (final product).
Do labels influence purchase decisions of food products? Study of young consumers of an emerging market
Authors: Kumar Niraj , Kapoor Sanjeev 
Published: January 2017

Purpose
The purpose of this paper is to study the usage and influence of food labels by the young consumers of an emerging market where food labeling regulation is comparatively recent phenomenon.

Design/methodology/approach
A purposely developed questionnaire was administered to 300 randomly selected youths of age between 18 and 30 years. The first part of the questionnaire sought information on socio-demographic profile, whereas the second part of the questionnaire had questions related to consumers’ perception of importance, their reading behavior, and their responses on the information content of food labels. Appropriate statistical tools were used to analyze the data.

Findings
Results revealed that young Indian consumers attached considerable importance to the food labels and read it before making a final purchase decision. In addition to price, all the product attributes which had implications for the consumers’ health were considered as extremely important by the young consumers. Information regarding different important product attributes can be broadly clubbed in two categories, namely, “product specification” and “product quality.” The final decision to purchase a product based on the food labels varied significantly based on the consumers’ gender, age, food habit, and residential locality.

Research limitations/implications
Nature of study does not allow drawing a conclusion regarding the causal relationship between food labels and consumers’ purchase decisions.

Originality/value
As labeling regulation is a comparatively recent phenomenon in India, study of the usage and influence of food labels on young consumers’ purchase decision, a hitherto not much-studied subject, will contribute significantly to the literature on food labels.