bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable impact of Verticillium longisporum on oilseed rape yield in field trials in the United Kingdom
Authors: Depotter Jasper R. L. , Thomma Bart P.H.J. , Wood Thomas A. 
Published: October 2017

AbstractThe Verticillium genus comprises economically important plant pathogens that collectively affect a broad range of annual and perennial crops. Verticillium longisporum mainly infects brassicaceous hosts, including oilseed rape. The most conspicuous symptom of V. longisporum infection on oilseed rape is black stem striping that appears towards the end of the cropping season. Thus far, the impact of V. longisporum infection on oilseed yield remains unclear. Verticillium stem striping recently emerged as a new disease in UK and currently displays a widespread occurrence in England. In this study, we assessed the impact of Verticillium stem striping on British oilseed rape production. To this end, four cultivars (Incentive, Vision, Harper and Quartz) were grown in field plots with different levels of V. longisporum disease pressure at different locations over two consecutive years. Whereas Incentive and Vision developed relatively few stem striping symptoms, Harper and especially Quartz showed severe symptoms during these field experiments. Furthermore, higher inoculum levels induced more severe symptoms in these cultivars. Intriguingly, significant yield reductions upon V. longisporum infection only occurred in a single field trial on all tested oilseed rape cultivars. Thus we conclude that Verticillium stem striping does not consistently impact oilseed rape yield, despite the occurrence of abundant disease symptoms.
Distinguishing genetic correlation from causation across 52 diseases and complex traits
Authors: O’Connor Luke J. , Price Alkes L. 
Published: October 2017

AbstractMendelian randomization (MR) is widely used to identify causal relationships among heritable traits, but it can be confounded by genetic correlations reflecting shared etiology. We propose a model in which a latent causal variable mediates the genetic correlation between two traits. Under the latent causal variable (LCV) model, trait 1 isfully genetically causalfor trait 2 if it is perfectly genetically correlated with the latent causal variable, implying that the entire genetic component of trait 1 is causal for trait 2; it ispartially genetically causalfor trait 2 if it has a high genetic correlation with the latent variable, implying that part of the genetic component of trait 1 is causal for trait 2. To quantify the degree of partial genetic causality, we define thegenetic causality proportion(gcp). We fit this model using mixed fourth momentsE(α1α2) andE(α1α2) of marginal effect sizes for each trait, exploiting the fact that if trait 1 is causal for trait 2 then SNPs affecting trait 1 (large) will have correlated effects on trait 2 (largeα1α2), but not vice versa. We performed simulations under a wide range of genetic architectures and determined that LCV, unlike state-of-the-art MR methods, produced well-calibrated false positive rates and reliable gcp estimates in the presence of genetic correlations and asymmetric genetic architectures; we also determined that LCV is well-powered to detect a causal effect. We applied LCV to GWAS summary statistics for 52 traits (averageN=331k), identifying partially or fully genetically causal effects (1% FDR) for 59 pairs of traits, including 30 pairs of traits with high gcp estimates (gĉp > 0.6). Results consistent with the published literature included genetically causal effects on myocardial infarction (MI) for LDL, triglycerides and BMI. Novel findings included a genetically causal effect of LDL on bone mineral density, consistent with clinical trials of statins in osteoporosis. These results demonstrate that it is possible to distinguish between genetic correlation and causation using genetic data.
First draft genome assembly of an iconic clownfish species (Amphiprion frenatus)
Authors: Marcionetti Anna , Rossier Victor , Bertrand Joris A. M. , Litsios Glenn , Salamin Nicolas 
Published: October 2017

AbstractClownfishes (or anemonefishes) form an iconic group of coral reef fishes, particularly known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment.Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained a total of 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii BUSCOs (Benchmarking Universal Single-Copy Orthologs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies.This resource is valuable for the advancing of studies of the particular life-history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.
Oxidative pathways of deoxyribose and deoxyribonate catabolism
Authors: Price Morgan N. , Ray Jayashree , Iavarone Anthony T. , Carlson Hans K. , Ryan Elizabeth M. , Malmstrom Rex R. , Arkin Adam P. , Deutschbauer Adam M. 
Published: October 2017

AbstractUsing genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-D-ribose and 2-deoxy-D-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl-CoA and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonatein vitro. InPseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while inParaburkholderia bryophilaand inBurkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, inKlebsiella michiganensis. Of these four bacteria, onlyP. simiaerelies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase ofP. simiaeis either non-specific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase fromPseudomonas putidathat we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism.ImportanceDeoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not encode any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of human metabolism and is present in urine. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.
Physiological and pathological brain activation in the anesthetized rat produces hemodynamic-dependent cortical temperature increases that can confound the BOLD fMRI signal
Authors: Harris Samuel S. , Boorman Luke W. , Das Devashish , Kennerley Aneurin J. , Sharp Paul S. , Martin Chris , Redgrave Peter , Schwartz Theodore H. , Berwick Jason 
Published: October 2017

AbstractAnesthetized rodent models are ubiquitous in pre-clinical neuroimaging studies. However, because the associated cerebral morphology and experimental methodology results in a profound negative brain-core temperature differential, cerebral temperature changes during functional activation are likely to be principally driven by local inflow of fresh, core-temperature, blood. This presents a confound to the interpretation of blood-oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) data acquired from such models, since this signal is also critically temperature-dependent. Nevertheless, previous investigation on the subject is surprisingly sparse. Here, we address this issue through use of a novel multi-modal methodology in the urethane anesthetized rat. We reveal that sensory stimulation, hypercapnia and recurrent acute seizures induce significant increases in cortical temperature that are preferentially correlated to changes in total hemoglobin concentration, relative to cerebral blood flow and oxidative metabolism. Furthermore, using a phantom-based evaluation of the effect of such temperature changes on the BOLD fMRI signal, we demonstrate a robust inverse relationship between the two. These findings indicate that temperature increases, due to functional hyperemia, should be accounted for to ensure accurate interpretation of BOLD fMRI signals in pre-clinical neuroimaging studies.
Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis
Authors: Holland David O , Johnson Margaret E 
Published: October 2017

AbstractStoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that leftover proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles.
The impact of corporate governance code on earnings management in listed non-financial firms
Authors: Outa Erick Rading , Eisenberg Paul , Ozili Peterson K. 
Published: October 2017

PurposeThe purpose of this paper is to examine whether voluntary corporate governance (CG) code issued in 2002 constrain earnings management (EM) among listed non-finance companies in Kenya.Design/methodology/approachUsing a panel data of 338-firm year’s observations between 2005 and 2014, the authors test the hypothesis that CG constrains EM in non-finance firms listed in Kenya. The authors regress discretionary accruals (DA) against a developed Corporate Governance Index (CGI).FindingsThe overall results show that DA is not significantly related to CG suggesting the voluntary CG code does not deter EM in non-finance companies in Kenya.Practical implicationsEvidence of income decreasing\increasing accruals implies EM still exists among the listed firms. This suggests that policymakers may need to consider radical actions including alternative or new CG approaches and new institutions to improve the effectiveness of CG.Originality/valueThis study extends existing studies by including composite CG as possible explanatory variable for constraining EM. The authors contribute to the debate by demonstrating that the voluntary CG code in Kenya is not effective in constraining DA and therefore the current initiatives by the regulator to change the current CG code are appropriately directed.
Audit report qualification/modification
Authors: Moalla Hanen 
Published: October 2017

PurposeThe purpose of this paper is to investigate the influence of financial variables and especially profitability, loss in current year, loss in previous year, leverage and liquidity in predicting audit report qualifications (qualified audit opinion) and audit report modifications (qualified opinion or unqualified but with an explanatory paragraph).Design/methodology/approachThe authors used hand-collected data from financial statements and from auditors’ general reports of 76 non-financial publicly traded companies over a period of 11 years (2005-2015). A total of 545 audit reports were analyzed.FindingsThe results of panel logistic regression reported a positive relationship between liquidity, loss in the current year, loss in the previous year and a qualified audit report. A positive relationship was found between leverage and audit report modification. Also, the findings show that the Tunisian revolution did not affect the qualification or the modification of the audit report but qualifications decreased significantly during the period of the financial crisis.Practical implicationsThe research has practical implications and can help auditors in identifying factors motivating audit report qualification or audit report modification, mainly in periods of instability.Originality/valueThis study contributes to auditing research, since the authors know very little about the determinants of audit opinion in emerging and African markets. It constitutes an addition to previous knowledge about audit opinion in the context of Tunisia during two important periods: the financial crisis and revolution. This research is one of the rare studies analyzing qualifications and audit report modifications by considering both qualifications and explanatory paragraphs.
Accounting and governance in Africa – contributions and opportunities for further research
Authors: Soobaroyen Teerooven , Tsamenyi Mathew , Sapra Haresh 
Published: October 2017

Purpose
The purpose of this paper is to review and reflect on the contributions of the Journal of Accounting in Emerging Economies’ special issue on accounting and governance in Africa.

Design/methodology/approach
The themes and contributions from the accepted papers are identified and discussed in relation to prior research and potential for further studies.

Findings
Key aspects of boards and corporate governance (CG), audit reporting and quality and government accounting practices are revealed as mechanisms which, in some cases, did have some consequences in the African context. However, in other cases, accounting or governance mechanisms appear to be at the periphery of organizational practice and exhibit little influence on decision making and accountability.

Research limitations/implications
Whilst this paper does not provide a systematic review of the literature in the African context, it provides relating to special issue’s contributions on CG, audit and government accounting on the continent.

Originality/value
This special issue extends the burgeoning scholarship in African accounting and governance and provides directions and opportunities for future research.
Financial determinants of local government debt in New Zealand
Authors: Ehalaiye Dimu , Botica-Redmayne Nives , Laswad Fawzi 
Published: October 2017

PurposeThe purpose of this paper is to investigate the financial determinants of local government debt in New Zealand.Design/methodology/approachTo investigate the financial determinants of local government debt in New Zealand, the authors analyse the relationship between key financial variables with local government debt in New Zealand based on the theories of fiscal accountability and moral hazard using a panel data methodology, specifically the pooled ordinary least squares regression model.FindingsThe findings suggest that council income is the major financial determinant of local government borrowing in New Zealand rather than infrastructural spending and that during the global financial crises (GFC) borrowing levels of New Zealand local councils was not significantly impacted. However, the findings indicate that post the GFC, low interest rates have stimulated increased borrowing activity by New Zealand local governments to fund infrastructure.Originality/valueThis paper is the first to examine the determinants of local government debt in New Zealand. The findings of this study contribute to better understanding of local government/municipality debt in New Zealand and internationally by providing evidence on the financial determinants of debt of local governments and the indirect use of government policy to control local government borrowing. The findings of this study are anticipated to affect local government practices and national government policies in relation to local government finances.
Perceived accountability for local government infrastructure assets: the influence of stakeholders
Authors: Siriwardhane Pavithra , Taylor Dennis 
Published: October 2017

PurposeThe purpose of this study is to investigate the relationship between the degree of stakeholder salience and the degree of emphasis placed on accountability dimensions for infrastructure assets (IFAs) as perceived by mayors and chief executive officers (CEOs) of local government authorities (LGAs). Comparisons are drawn between the salience accorded to two broad stakeholder groups at the public level and at the government level.Design/methodology/approachPerceptions of mayors and CEOs are examined through a mail questionnaire survey administered among LGAs in Australia.FindingsOverall accountability for IFAs by the LGAs is influenced by the salience accorded to the demands and needs of public stakeholders (PSs) but not the salience accorded to government stakeholders (GS). It is evident that public and managerial accountabilities are impacted by PS salience, whereas political accountability is impacted by the salience of GS. Thus, it emphasises that the establishment and implementation of policies, processes and systems that render transparency and responsiveness to the public, as well as service quality and the disclosure of performance measures, are positively affected by the salience accorded to PS groups.Research limitations/implicationsThe results of the study may be affected by the inherent weaknesses associated with mail surveys.Practical implicationsAccountability of LGAs for IFAs to GS needs enhancement, specifically stronger policy incentives.Originality/valueThis paper contributes to the literature, providing evidence on how mayors and CEOs of LGAs perceive the salience of different stakeholders of IFAs and its impact on the perceived accountability.
Case‐control pharmacogenetic study of HCN1/HCN2 variants and genetic generalized epilepsies
Authors: Wu Shu‐Zhi , Ye Hua , Yang Xiao‐Guo , Lu Zhi‐Li , Qu Qiang , Qu Jian 
Published: October 2017

SummaryEpilepsy is a common complex neurological disorder, and some forms are resistant to drug treatment. The HCN1/HCN2 genes encode hyperpolarization‐activated cyclic nucleotide‐gated channels, which play important roles in the electrophysiology of neurons. We investigated the association between HCN1/HCN2 variants and drug resistance or the risk of genetic generalized epilepsies (GGEs). We used matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry to assess nine variants of HCN1/HCN2 in 284 healthy participants and 483 GGEs (279 drug‐responsive, 204 drug‐resistant). Frequencies of HCN2 rs7255568 and rs3752158 G alleles differed in GGEs and in controls (P = .039, P = .027, respectively). The frequency of HCN2 haplotype (CAC) was higher in patients than controls (P = .046). The frequency of the HCN1 rs10462087 CC+CT genotype was lower in patients with childhood absence epilepsy (CAE) than controls (P = .047). Rs7255568 was associated with the risk of CAE (P = .028) and juvenile myoclonic epilepsy (JME) (P = .02). Rs3752158 was associated with the risk of generalized tonic‐clonic seizures, JME, and febrile seizures (all P < .05). The frequency of the HCN2 haplotype (CAC) was higher in patients with JME (P = .015) and in those with febrile seizures (P = .024) than in controls. No significant association was found between HCN1/HCN2 alleles, genotypes or haplotypes, and drug resistance in patients. After Bonferroni's multiple comparisons correction, only the HCN2 rs3752158 C allele and GC+CC genotype frequencies in patients with JME were higher than those in controls (19.2% vs 11.6%, odds ratio (OR) = 1.71, 95% CI = 1.18‐2.32), P = .004 < 0.05/9; 36% vs 22.2%, OR = 1.62(1.18‐2.23), P = .003 < 0.05/9). Our study suggests that HCN2 rs3752158 is involved in the susceptibility to JME.
The presence of Philadelphia chromosome does not confer poor prognosis in adult pre‐B acute lymphoblastic leukaemia in the tyrosine kinase inhibitor era – a surveillance, epidemiology, and end results database analysis
Authors: Igwe Igwe J. , Yang Dongyun , Merchant Akil , Merin Noah , Yaghmour George , Kelly Kevin , Ramsingh Giridharan 
Published: October 2017

SummaryThe BCR‐ABL1 fusion gene is caused by a translocation between chromosomes 9 and 22, resulting in an abnormal chromosome 22 (Philadelphia chromosome; Ph). Prior to the introduction of tyrosine kinase inhibitors (TKI), the presence of BCR‐ABL1 conferred a poor prognosis in patients with acute lymphoblastic leukaemia (ALL). We compared the survival of Ph+ and Ph−ALL during the period when TKIs were universally available in the US for Ph+ALL, using a Surveillance, Epidemiology, and End Results (SEER) Database analysis. A total of 2694 patients with pre‐B ALL (206 Ph+ALL; 2488 Ph−ALL) aged ≥18 years, who were diagnosed between 2010 and 2014, were identified in SEER registries. The median overall survival (OS) was 32 months in Ph+ALL (95% confidence interval [CI] 18 months‐not reached) and 27 months (95% CI 24–30 months) in Ph−ALL (Log‐rank test P‐value 0·34). Older age was associated with worse prognosis in both Ph+ALL and Ph−ALL. Age‐adjusted OS was inferior in Hispanics and African‐Americans compared to non‐Hispanic whites. Survival of pre‐B ALL shows continued improvement with time. Philadelphia chromosome status does not confer poor prognosis in pre‐B ALL in the TKI era: prognostic factors in pre‐B ALL should be re‐evaluated in the light of this finding.