bluuebunny/crossref_metadata_2025_split huggingface dataset:
The unique topologies ofN6-Adenosine methylation (m6A) in land-plant mitochondria and their putative effects on organellar gene-expression
Authors: Murik Omer , Chandran Sam Aldrin , Nevo-Dinur Keren , Sultan Laure D. , Best Corinne , Stein Yuval , Hazan Carina , Ostersetzer-Biran Oren 
Published: July 2019

SummaryMitochondria are the main source of ATP production and also contribute to many other processes central to cellular function. Mitochondrial activities have been linked with growth, differentiation and aging. As relicts of bacterial endosymbionts, these organelles contain their own genetic system (i.e., mitogenome or mtDNA). The expression of the mtDNA in plants is complex, particularly at the posttranscriptional level. Following transcription, the polycistronic pre-RNAs in plant mitochondria are processed into individual RNAs, which then undergo extensive modifications, as trimming, splicing and C→U editing, before being translated by organellar ribosomes. Our study focuses onN6-methylation of Adenosine ribonucleotides (m6A-RNA) in plant mitochondria. m6A is the most common modification in eukaryotic mRNAs. The biological significance of this highly dynamic modification is under investigation, but it’s widely accepted that m6A mediates structural switches that affect RNA stability and activity. By performing m6A-pulldown/RNA-seq (m6A-RIP-seq) analyses of Arabidopsis and cauliflower mitochondrial transcripts (mtRNAs), we provide with detail information on the m6A landscapes in angiosperms mitochondria. The results indicate that m6A targets different types of mtRNAs, including coding sequences, UTRs, introns and non-coding RNA species. While introns and noncoding-RNAs undergo multiple m6A modifications along the transcript, in mRNAs m6A-modifications are preferably positioned near start-codons, and may modulate the translatability of the m6A-modified transcripts.
Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity
Authors: Guilhot Robin , Rombaut Antoine , Xuéreb Anne , Howell Kate , Fellous Simon 
Published: July 2019

ABSTRACTEnvironmentally acquired microbial symbionts could contribute to host adaptation to local conditions like vertically transmitted symbionts do. This scenario necessitates symbionts to have different effects in different environments. We investigated this idea in Drosophila melanogaster, a species which communities of bacterial symbionts vary greatly among environments. We isolated four bacterial strains isolated from the feces of a D. melanogaster laboratory strain and tested their effects in two conditions: the ancestral environment (i.e. the laboratory medium) and a new environment (i.e. fresh fruit with live yeast). All bacterial effects on larval and adult traits differed among environments, ranging from very beneficial to marginally deleterious. The joint analysis of larval development speed and adult size further shows bacteria affected developmental plasticity more than resource acquisition. This effect was largely driven by the contrasted effects of the bacteria in each environment. Our study illustrates that understanding D. melanogaster symbiotic interactions in the wild will necessitate working in ecologically realistic conditions. Besides, context-dependent effects of symbionts, and their influence on host developmental plasticity, shed light on how environmentally acquired symbionts may contribute to host evolution.
Muscle overexpression of Klf15 via an AAV8-Spc5-12 construct does not provide benefits in spinal muscular atrophy mice
Authors: Ahlskog Nina , Hayler Daniel , Krueger Anja , Kubinski Sabrina , Claus Peter , Yáñez-Muñoz Rafael J , Bowerman Melissa 
Published: July 2019

ABSTRACTSpinal muscular atrophy (SMA) is a neuromuscular disease caused by loss of the survival motor neuron (SMN) gene. While there are currently two approved gene-based therapies for SMA, availability, high cost, and differences in patient response indicate that alternative treatment options are needed. Optimal therapeutic strategies will likely be a combination of SMN-dependent and -independent treatments aimed at alleviating symptoms in the central nervous system and peripheral muscles. Krüppel-like factor 15 (KLF15) is a transcription factor that regulates key metabolic and ergogenic pathways in muscle. We have recently reported significant downregulation of Klf15 in muscle of pre-symptomatic SMA mice. Importantly, perinatal upregulation of Klf15 via transgenic and pharmacological methods resulted in improved disease phenotypes in SMA mice, including weight and survival. In the current study, we designed an adeno-associated virus serotype 8 (AAV8) vector to overexpress a codon-optimised Klf15 cDNA under the muscle-specific Spc5-12 promoter (AAV8-Klf15). Administration of AAV8-Klf15 to severe Taiwanese Smn−/−;SMN2 or intermediate Smn2B/− SMA mice significantly increased Klf15 expression in muscle. We also observed significant activity of the AAV8-Klf15 vector in liver and heart. AAV8-mediated Klf15 overexpression moderately improved survival in the Smn2B/− model but not in the Taiwanese mice. An inability to specifically induce Klf15 expression at physiological levels in a time- and tissue-dependent manner may have contributed to this limited efficacy. Thus, our work demonstrates that an AAV8-Spc5-12 vector induces high gene expression as early as P2 in several tissues including muscle, heart and liver, but highlights the challenges of achieving meaningful vector-mediated transgene expression of Klf15.
Galectin-14 expression in ovarian cancer
Authors: Oliveira Fernandes de Araujo Lorenna , St-Pierre Yves 
Published: July 2019

AbstractGalectins (gal) are multifunctional proteins whose expression changes under different physiological or pathological conditions, including cancer. However, so far, most studies have focused on gal-1 and gal-3, and to a lesser extent to gal-7 and gal-9. We still know very little about other galectins, especially the recently discovered ones, such as gal-14, a prototype galectin highly expressed at the maternal-fetal interface. Here, usingin silicoandin vitroapproaches, we report a correlation betweenlgals14expression and ovarian cancer. We found that high expression of gal-14 mRNA in ovarian cancer cells is associated with a shorter survival. Consistent with this observation, we also found thatlgals14is preferentially expressed in high grade serous adenocarcinoma (HGSA) ovarian cancer. Ourin vitrodata with ovarian cancer cell lines confirmed thatlgals14is readily expressed in HGSA. Interestingly,de novoexpression of gal-14 in HEK-293 cells increased apoptosis, both at the basal level and following exposure to low doses of etoposide. Thus, although the study of this galectin is still in its infancy, we were able to provide novel insights into the expression patterns of this galectin and its involvement in cancer.
DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
Authors: Hong Hao , Jiang Shuai , Li Hao , Quan Cheng , Zhao Chenghui , Li Ruijiang , Li Wanying , Du Guifang , Yin Xiaoyao , Huang Yangchen , Li Cheng , Chen Hebing , Bo Xiaochen 
Published: July 2019

AbstractHi-C is commonly used to study three-dimensional genome organization. However, due to the high sequencing cost and technical constraints, the resolution of most Hi-C datasets is coarse, resulting in a loss of information and biological interpretability. Here we develop DeepHiC, a generative adversarial network, to predict high-resolution Hi-C contact maps from low-coverage sequencing data. We demonstrated that DeepHiC is capable of reproducing high-resolution Hi-C data from as few as 1% downsampled reads. Empowered by adversarial training, our method can restore fine-grained details similar to those in high-resolution Hi-C matrices, boosting accuracy in chromatin loops identification and TADs detection, and outperforms the state-of-the-art methods in accuracy of prediction. Finally, application of DeepHiC to Hi-C data on mouse embryonic development can facilitate chromatin loop detection with higher accuracy. We develop a web-based tool (DeepHiC,http://sysomics.com/deephic) that allows researchers to enhance their own Hi-C data with just a few clicks.Author summaryWe developed a novel method, DeepHiC, for enhancing Hi-C data resolution from low-coverage sequencing data using generative adversarial network. DeepHiC is capable of reproducing highresolution (10-kb) Hi-C data with high quality even using 1/100 downsampled reads. Our method outperforms the previous methods in Hi-C data resolution enhancement, boosting accuracy in chromatin loops identification and TADs detection. Application of DeepHiC on mouse embryonic development data shows that enhancements afforded by DeepHiC facilitates the chromatin loops identification of these data achieving higher accuracy. We also developed a user-friendly web server (http://sysomics.com/deephic) that allows researchers to enhance their own low-resolution Hi-C data (40kb-1 Mb) with just few clicks.
High throughput competitive fluorescence polarization assay reveals functional redundancy in the S100 protein family
Authors: Simon Márton A. , Ecsédi Péter , Kovács Gábor M. , Póti Ádám L. , Reményi Attila , Kardos József , Gógl Gergő , Nyitray László 
Published: July 2019

AbstractThe calcium-binding, vertebrate-specific S100 protein family consists of 20 paralogs in humans (referred as the S100ome), with several clinically important members. To assess their interactome, high-throughput, systematic analysis is indispensable, which allows one to get not only qualitative but quantitative insight into their protein-protein interactions (PPIs). We have chosen an unbiased assay, fluorescence polarization (FP) that revealed a partial functional redundancy when the complete S100ome (n=20) was tested against numerous model partners (n=13). Based on their specificity, the S100ome can be grouped into two distinct classes: promiscuous and orphan. In the first group, members bound to several ligands (>4-5) with comparable high affinity, while in the second one, the paralogs bound only one partner weakly, or no ligand was identified (orphan). Our results demonstrate that in vitro FP assays are highly suitable for quantitative ligand binding studies of selected protein families. Moreover, we provide evidence that PPI-based phenotypic characterization can complement the information obtained from the sequence-based phylogenetic analysis of the S100ome, an evolutionary young protein family.Author summaryFunctional similarity among a protein family can be essential in order to understand proteomic data, to find biomarkers, or in inhibitor design. Proteins with similar functions can compensate the loss-of-function of the others, their expression can co-vary under pathological conditions, and simultaneous targeting can lead to better results in the clinics. To investigate this property one can use sequence-based approaches. However, this path can be difficult. In the case of the vertebrate specific, evolutionary young, S100 family, phylogenetic approaches lead to ambiguous results. To overcome this problem, we applied a high-throughput biochemical approach to experimentally measure the binding affinities of a large number of S100 interactions. We performed unbiased fluorescence polarization assay, involving the complete human S100ome (20 paralogs) and 13 known interaction partners. We used this measured 20×13 (260) protein-protein interaction array to reveal the functional relationships within the family. Our work provide a general framework for studies focusing on phenotype-based domain classification.
Risk factors affecting the ability for earned value management to accurately assess the performance of infrastructure projects in Australia
Authors: Ibrahim Maan Nihad , Thorpe David , Mahmood Muhammad Nateque 
Published: July 2019

Purpose
The purpose of this paper is to investigate a set of risk-related factors influencing the earned value management (EVM) concept as an assessment technique in evaluating the progress of modern sustainable infrastructure construction projects.

Design/methodology/approach
A qualitative research approach has been adopted for identifying risk-related factors influencing EVM concept from a literature review and through interviewing industry personnel, followed by an inductive process to form sets of key factors and their measuring items.

Findings
EVM is a common method for assessing project performance. A weakness of this approach is that EVM assessment in its current form does not measure the impact of a number of project performance factors that result from the complexity of modern infrastructure construction projects, and thus does not accurately assess their impact in this performance. This paper discusses and explains a range of potential risk factors to evaluating project performance such as sustainability, stakeholder requirements, communication, procurement strategy, weather, experience of staff, site condition, design issues, financial risk, subcontractor, government requirements and material. In addition, their measuring items were identified.

Practical implications
This research assists projects managers to improve the evaluation process of infrastructure construction performance by incorporating a range of factors likely to impact on that performance and which are not included in current EVM calculations.

Originality/value
This research addresses the need to include in the EVM calculation a range of risk factors affecting the performance of infrastructure projects in Australia and therefore makes this calculation a more reliable tool for assessing project performance.
Computational investigation of laminar premixed hydrogen flame past a quenching mesh
Authors: Benim Ali Cemal , Pfeiffelmann Björn 
Published: July 2019

Purpose
The purpose of this study is the computational analysis of atmospheric, laminar, stoichiometric and premixed hydrogen-air flames in the presence of a quenching mesh. The assessment of the predictive capability of different reaction mechanisms, the clarification of the relative importance of the thermal and chemical effects for mesh quenching and the investigation of the influence of the mesh geometry on the quenching effectiveness are the focal points of the investigation.

Design/methodology/approach
The problem is posed as unsteady, two-dimensional. Differential governing equations are numerically solved by the finite volume method for the reacting hydrogen/air mixture, assuming an ideal gas behaviour. Thermal radiation and buoyancy are neglected. A coupled solver is used to treat the velocity-pressure coupling, along with a stiff-chemistry solver for the chemical kinetics. Second-order discretization schemes are used in space and time. A uniform grid resolution is used, where the grid independence in terms of the flame speed prediction is ensured in preliminary calculations for one-dimensional flames.

Findings
It is found that a detailed reaction mechanism is necessary for an accurate prediction. Meshes with round openings are found to be more effective that those with slit openings (SOs), by a factor of two in the maximum safe gap size. A perforated plate is observed to have a higher quenching potential compared to a wire mesh, for SOs. It is also found that the heat loss to the wall is the dominating quenching mechanism for the present problem, whereas adsorption of radicals plays a subordinate role.

Originality/value
In contrast to the previous studies in the field, a detailed reaction mechanism is applied instead of a single-step one, while still using the latter for comparison. The role of wall-radicals interaction for the quenching effectiveness of the mesh is addressed for the first time. Parametric studies are performed on the mesh geometry, which was not done before. Hydrogen is considered as fuel in contrast to the great majority of the previous work.
Corporate governance and the timeliness of audited financial statements
Authors: Mathuva David Mutua , Tauringana Venancio , Owino Fredrick J. Otieno 
Published: July 2019

PurposeThe nature of corporate governance (CG) mechanisms in an entity may influence the timeliness of the audited annual report. The purpose of this paper is to argue that the “quality” of CG in a firm has a significant association with the time it takes the audited annual report and financial statements to be released.Design/methodology/approachUsing a set of 543 firm-year observations over the period 2007–2016, the authors examine whether a validated CG-Index is associated with audit report delay (ARD). The authors employ both granular as well as aggregated approaches to the analyses. In addition, the authors include control variables known to have an association with ARD in the panel data regressions.FindingsThe findings, which are robust for self-selection among other checks, reveal that financial expertise in the audit committee, board size, board meetings and independence in the board are associated with longer ARDs. Some CG attributes such as board diversity (i.e. women and different nationalities in the board) are associated with improved timeliness of the annual reports. The results also reveal that a longer tenure for independent directors in the board is associated with a shorter ARD. Overall, the authors find that the composite CG score has a positive influence on the timeliness of annual reports.Research limitations/implicationsThe study focuses on listed companies in one developing country. Additional studies focusing on other jurisdictions could yield more results.Practical implicationsThe study is useful in highlighting those CG characteristics firms should focus on toward the attainment of timely corporate reporting to aid in decision making by users.Originality/valueThe study is unique since it emphasizes the importance of focusing on an aggregate CG-Index, and the contribution of the CG-Index toward the timeliness of annual reports.
Adopting situationally relevant modes of music information at different stages of information-seeking processes
Authors: Rousi Antti Mikael , Savolainen Reijo , Vakkari Pertti 
Published: July 2019

PurposeThe purpose of this paper is to elaborate the picture of situational relevance by examining how modes of music information are viewed as situationally relevant at different stages of information-seeking processes among music students.Design/methodology/approachEmpirical data of the present longitudinal study were collected in two phases by utilizing questionnaire and interview methods. Informants comprised of 14 university-level music students representing the fields of music performance, music education and music theory and composition. Modes of music information were approached through the information typology presented by Rousi, Savolainen and Vakkari.FindingsThe findings indicate that not only the modes of music information were seen as situationally relevant for different reasons by the three participating music student groups when at the beginning of their tasks, but also that the perceived situational relevance of the information modes underwent changes as their tasks progressed to focus formulation and post-focus stages.Research limitations/implicationsDue to the small number of participants, further research is needed to verify the results concerning the differences in information-seeking processes between diverse music student groups.Originality/valueThe paper showcases that approaching music information through frameworks that classify information sources at diverse levels of abstraction enables an accurate description of information-seeking processes and illuminates context-sensitive development of situational relevance of music information of diverse modes.
Citations to chemical databases in scholarly articles: to cite or not to cite?
Authors: Tomaszewski Robert 
Published: July 2019

PurposeChemical databases have had a significant impact on the way scientists search for and use information. The purpose of this paper is to spark informed discussion and fuel debate on the issue of citations to chemical databases.Design/methodology/approachA citation analysis to four major chemical databases was undertaken to examine resource coverage and impact in the scientific literature. Two commercial databases (SciFinder and Reaxys) and two public databases (PubChem and ChemSpider) were analyzed using the “Cited Reference Search” in the Science Citation Index Expanded from the Web of Science (WoS) database. Citations to these databases between 2000 and 2016 (inclusive) were evaluated by document types and publication growth curves. A review of the distribution trends of chemical databases in peer-reviewed articles was conducted through a citation count analysis by country, organization, journal and WoS category.FindingsIn total, 862 scholarly articles containing a citation to one or more of the four databases were identified as only steadily increasing since 2000. The study determined that authors at academic institutions worldwide reference chemical databases in high-impact journals from notable publishers and mainly in the field of chemistry.Originality/valueThe research is a first attempt to evaluate the practice of citation to major chemical databases in the scientific literature. This paper proposes that citing chemical databases gives merit and recognition to the resources as well as credibility and validity to the scholarly communication process and also further discusses recommendations for citing and referencing databases.
Does corporate governance affect dividend policy in India? Firm-level evidence from new indices
Authors: Pahi Debasis , Yadav Inder Sekhar 
Published: July 2019

Purpose
The purpose of this paper is to investigate the nexus between corporate governance and dividend policy of listed Indian firms.

Design/methodology/approach
Using new corporate governance stipulations, five new indices were constructed, namely, overall board governance index, board structure index, audit committee index, compensation committee index and nomination committee index. Using the newly developed indices, disclosure index and different firm-specific control variables, different panel Logit and Tobit regression models were estimated for 482 non-financial and non-utility listed firms during 2006–2017. Also, before the econometric analysis, mean difference test was conducted to examine the differences in dividend behaviour and corporate governance practices during pre- and post-Companies Act, 2013 and between payers and non-payers.

Findings
The overall evidence suggests that the firms having stronger corporate governance tend to pay higher dividends suggesting that the firm’s propensity to pay dividends increases with the improvement in corporate governance standards. Among the corporate governance indices board structure, audit committee and disclosure norms show a significant and positive relationship, whereas compensation committee and nomination committee show a positive but insignificant relationship with dividend policy. Control variables mostly had the expected impact on the dividends of the firms.

Practical implications
This study suggests that the establishment of the strong and effective corporate governance system is desirable to mitigate the agency conflicts between managers and shareholders and limit managers’ opportunistic behaviour in dividend payout policy.

Originality/value
This study is one of the latest studies to use several newly constructed indices on corporate governance mechanism based on new stipulations which bring new evidence on their specific impact on the dividend policy for an emerging market economy like India.