bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving recovery of member genomes from enrichment reactor microbial communities using MinION–based long read metagenomics
Authors: Arumugam Krithika , Bessarab Irina , Liu Xianghui , Natarajan Gayathri , Drautz–Moses Daniela I. , Wuertz Stefan , Lauro Federico M. , Law Ying Yu , Huson Daniel H. , Williams Rohan B. H. 
Published: November 2018

AbstractNew long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes. While much progress has been made on cultured isolates, the ability of these methods to recover genomes of member taxa in complex microbial communities is less clear. Here we examine the ability of long read data to recover genomes from enrichment reactor metagenomes. Such modified communities offer a moderate level of complexity compared to the source communities and so are realistic, yet tractable, systems to use for this problem. We sampled an enrichment bioreactor designed to target anaerobic ammonium-oxidising bacteria (AnAOB) and sequenced genomic DNA using both short read (Illumina 301bp PE) and long read data (MinION Mk1B) from the same extraction aliquot. The community contained 23 members, of which 16 had genome bins defined from an assembly of the short read data. Two distinct AnAOB species from genus Candidatus Brocadia were present and had complete genomes, of which one was the most abundant member species in the community. We can recover a 4Mb genome, in 2 contigs, of long read assembled sequence that is unambiguously associated with the most abundant AnAOB member genome. We conclude that obtaining near closed, complete genomes of members of low-medium microbial communities using MinION long read sequence is feasible.
Healthful choices depend on the latency and rate of information accumulation
Authors: Sullivan Nicolette J. , Huettel Scott A. 
Published: November 2018

AbstractThe drift diffusion model (DDM) provides a parsimonious explanation of decisions across neurobiological, psychological, and behavioral levels of analysis. Although most DDM implementations assume that only a single value guides decisions, choices often involve multiple attributes that could make separable contributions to choice. Here, we fit incentive-compatible dietary choices to a multi-attribute, time-dependent drift diffusion model (mtDDM), in which taste and health could differentially influence the evidence accumulation process. We found that these attributes shaped both the relative value signal and the latency of evidence accumulation in a manner consistent with participants’ idiosyncratic preferences. Moreover, by using a dietary prime, we showed how a healthy choice intervention alters mtDDM parameters that in turn predict prime-dependent choices. Our results reveal that different decision attributes make separable contributions to the strength and timing of evidence accumulation – providing new insights into the construction of interventions to alter the processes of choice.
The innate immune DNA sensor cGAS is a negative regulator of DNA repair hence promotes genome instability and cell death
Authors: Jiang Hui , Panda Swarupa , Xue Xiaoyu , Liang Fengshan , Sung Patrick , Gekara Nelson O. 
Published: November 2018

ABSTRACTStringent regulation of DNA repair is essential for organismal integrity, but the mechanisms are not fully understood. Cyclic cGMP-AMP synthase (cGAS), the DNA sensor that alerts the innate immune system to the presence of foreign or damaged self-DNA in the cytoplasm is critical for the outcome of infections, inflammatory diseases and cancer. Besides this cytoplasmic function as an innate immune sensor, whether cGAS fulfills other biological roles remains unknown. Here we report that cGAS has a distinct role in the nucleus: it inhibits homologous recombination DNA repair (HR) thereby promoting genome instability and associated micronuclear generation and mitotic death. We show that cGAS-mediated inhibition of HR requires its DNA binding and oligomerization but not its catalytic activity or the downstream innate immune signaling events. Mechanistically, we show that cGAS impede RAD51-mediated DNA strand invasion, a key step in HR. These results uncover a new function of cGAS relevant for understanding its involvement in genome instability- associated disorders.
Population genomic analyses reveal a highly differentiated genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii
Authors: Geraldes Armando , Askelson Kenneth K. , Nikelski Ellen , Doyle Frank I. , Harrower William L. , Winker Kevin , Irwin Darren E. 
Published: November 2018

AbstractAccurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. In the western Canadian province of British Columbia, a subspecies of the northern goshawk (Accipiter gentilis laingi) is designated as Threatened under the Canadian Species at Risk Act. Historically, the range of this bird of prey has been ambiguous and its genetic distinctness from the other North American subspecies (Accipiter gentilis atricapillus) has not been well established. Given the uncertainty in using morphological traits to assign individual goshawks to these two subspecies, we analyzed genomic relationships in tens of thousands of single nucleotide polymorphisms identified using genotyping-bysequencing of high-quality genetic samples. This genome-wide analysis revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle genetic structuring among the remainder of our sampling sites within North America. Following from this analysis, we developed targeted genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing the addition of hundreds of low-quality samples to our analysis. This additional information confirmed that the distinct genetic cluster on Haida Gwaii is restricted to that archipelago. As thelaingiform was originally described as being based in Haida Gwaii, where the type specimen of that form is from, further study (especially of morphological traits) may indicate a need to restrict this name to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, our finding of a distinct Haida Gwaii genetic cluster along with the small and historically declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited bylaingi) show some subtle differentiation from other North American regions. We anticipate that these results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.
A stable, high refractive index, switching buffer for super-resolution imaging
Authors: Hartwich Tobias M.P. , Hin Chung Kenny Kwok , Schroeder Lena , Bewersdorf Joerg , Soeller Christian , Baddeley David 
Published: November 2018

AbstractdSTORM super-resolution imaging relies on switching buffers to enable dye molecules to enter and exit a metastable dark state. Current buffers have a very limited shelf life of approximately 1 day and poorly match sample refractive index, impacting negatively on measurement reproducibility and image fidelity. We present a buffer based on chemical, rather than enzymatic, oxygen scavenging which exhibits dramatically improved stability, switching speed, contrast, and index matching.
A new mechanism for ribosome rescue can recruit RF1 or RF2 to non-stop ribosomes
Authors: Goralski Tyler D. P. , Kirimanjeswara Girish S. , Keiler Kenneth C. 
Published: November 2018

AbstractBacterial ribosomes frequently translate to the 3’ end of an mRNA without terminating at an in-frame stop codon. In all bacteria studied to date, these non-stop ribosomes are rescued usingtrans-translation. In some species, genes required fortrans-translation are essential, but other species can survive withouttrans-translation because they express an alternative ribosome rescue factor, ArfA or ArfB.Francisella tularensiscells lackingtrans-translation are viable, butF. tularensisdoes not encode ArfA or ArfB. Transposon mutagenesis followed by deep sequencing (Tn-seq) identified a new alternative ribosome rescue factor, now named ArfT.arfTcan be deleted in wild-type cells but not in cells that lacktrans-translation activity. Over-expression of ArfT suppresses the slow growth phenotype in cells lackingtrans-translation and counteracts growth arrest caused bytrans-translation inhibitors, indicating that ArfT rescues non-stop ribosomesin vivo. Ribosome rescue assaysin vitroshow that ArfT promotes hydrolysis of peptidyl-tRNA on non-stop ribosomes in conjunction withF. tularensisrelease factors. Unlike ArfA, which requires RF2 for activity, ArfT can function with either RF1 or RF2. Overall, these results indicate that ArfT is a new alternative ribosome rescue factor with a distinct mechanism from ArfA and ArfB.ImportanceFrancisella tularensisis a highly infectious intracellular pathogen that kills more than half of infected humans if left untreated.F. tularensishas also been classified as a potential bioterrorism agent with the greatest risk for deliberate misuse. Recently, compounds that inhibit ribosome rescue have been shown to have antibiotic activity againstF. tularensisand other important pathogens. Like all bacteria that have been studied,F. tularensisusestrans-translation as the main pathway to rescue stalled ribosomes. However, unlike most bacteria,F. tularensiscan survive without any of the known factors for ribosome rescue. Our work identifies aF. tularensisprotein, ArfT, that rescues stalled ribosomes in the absence oftrans-translation using a new mechanism. These results indicate that ribosome rescue activity is essential inF. tularensisand suggest that ribosome rescue activity might be essential in all bacteria.
A New Method for Primary Culture of Mouse Dorsal Root Ganglion Neurons
Authors: Dong Tiantian , Li Shigang , Liu Wei , Yan Mengzhen , Yu Jie , Deng Xiaozhuo 
Published: November 2018

AbstractIn order to establish a simple and highly purified method for primary culture of mouse dorsal root ganglion neurons(DRGn), in this study, the DRGn of young mice were obtained by collagenase type I and trypsin digestion. Then the DRGn were obtained by immunocytochemical staining of mouse neuron specific enolase (NSE) monoclonal antibody, while using flow cytometry to further detect the positive rates of DRGn. The cultured primary DRGn grew well and had a purity of about 83.72%. The DRGn survival time was 60 days when cultured in DMEM medium containing nerve growth factor (NGF). The culture scheme is simple and stable, and a large number of high purity DRGn could be cultured, which provides a reliable model for further study of nerve cells.
Securitizations and accounting restatements
Authors: Wang Haiping , Zhang Jing 
Published: November 2018

Purpose
The purpose of this paper is to establish a direct link between securitizations and accrual-based earnings management by investigating whether financial statements in the periods of securitizations are more likely to be restated at a later time. In addition, this study examines whether the association between securitization and accounting restatements is more pronounced in the pre-financial crisis period and for banks with less independent or industry-specialized auditors.

Design/methodology/approach
This study covers a sample of bank holding companies with restatement information between 2001 and 2012. Using the incidence of material accounting restatements as a proxy for accrual earnings management, this study investigates whether securitizations are likely used as a tool for accrual earnings management. A logistic model is applied with standard errors clustered at the firm-year level. Various robustness tests are conducted to rule out the possibilities that the results are driven by unintentional reporting errors or endogeneity of the securitization decisions.

Findings
The empirical results reveal a positive and significant association between banks’ securitization activities and the likelihood of having accounting restatements. Moreover, this positive association is more pronounced in the pre-financial crisis period and for banks with less independent or industry-specialized auditors.

Research limitations/implications
The findings suggest that managers take advantage of discretions on accounting rules for securitizations to manage earnings. This evidence provides multi-dimension implications for standard setters and practitioners, as well as investors.

Originality/value
This is one of the very first papers to document evidence that accrual earnings management is involved in securitization.
Antecedents to the crisis: Mandeville, Smith, and Keynes
Authors: Wight Jonathan B. 
Published: November 2018

Purpose
The purpose of this paper is to present the methods of teaching about the global financial crisis (GFC) from a social economic perspective. Using primary texts from the history of economic thought, the moral underpinnings for collective social action are examined in times of economic depression. The deregulation of financial markets raises two questions: to what extent is deregulation the result of a misunderstanding about human nature and the behavioral lessons of social economics; and to what extend does deregulation ignore the moral lessons of Adam Smith’s invisible hand?

Design/methodology/approach
By reading sources including Mandeville, Smith, Keynes, Hayek and others, students form conclusions about the strengths and weaknesses of government interventions, both to fix, and to prevent, major recessions and depressions.

Findings
Two fallacies relating to financial market deregulation are that “greed is good” and that rational actors in the market will self-regulate leading to widespread prosperity. These moral beliefs supported financial liberalization, and ultimately contributed to financial institutions taking on enormous risks and losses that are ultimately socialized.

Originality/value
This paper innovatively uses readings from the history of economic thought to spark pedagogical discussions and debates about human nature and policymaking relevant to the GFC.
How do a buyer’s political ties affect the market-based selection of suppliers?
Authors: Yan Zebin , Lu Jiangyong 
Published: November 2018

PurposeAlthough the differential roles of political and business ties are recognized in the literature, the interplay between political and business ties remains unclear. This study aims to explore how political ties affect the formation of business ties with unfamiliar partners by analyzing how a buyer’s political ties affect the market-based selection of suppliers, an important channel through which the buyer forms business ties with unfamiliar suppliers.Design/methodology/approachA survey of 204 Chinese manufacturing firms was conducted to elucidate the relationship between political ties and the market-based selection of suppliers.FindingsThe findings suggest that buyers with strong political ties are more likely to engage in the market-based selection of suppliers; this positive relationship is diminished when social control is preferred over contractual control in the buyer’s supplier governance and is enhanced when technological uncertainty is high.Originality/valueFirst, this study sheds light on the interplay between political and business ties by revealing how the buyer’s political ties affect the formation of business ties with unfamiliar suppliers, as represented by the market-based selection of suppliers. Second, it uncovers the boundary conditions of the effect of political ties by revealing the moderating effect of social control preference and technological uncertainty. Third, it extends the interorganizational governance structure literature from its focus on the complement-substitute debate on social control and contractual control to examine the contingent effect of a hybrid governance structure.
Inhalation and dermal exposure to toluene among printing workers in a plastic bag factory
Authors: Phanprasit Wantanee , Songpek Kanchanok , Boonyayothin Vorakamol , Sujirarat Dusit 
Published: November 2018

Purpose
The purpose of this paper is to explore inhalation levels and dermal exposure to toluene among printing workers who wore no personal protective equipment; it is conducted in a plastic bag factory. Using a charcoal cloth pad (CCP) as a dermal sampler to assess skin permeation of liquid toluene is also investigated.

Design/methodology/approach
In total, 27 stationary air samples as well as urine and dermal samples were collected over 9 days from 11 printing workers. Six pieces of CCP were wrapped on each of the workers’ fingers for the dermal sample collection. Air samples were collected and analyzed according to NIOSH No. 1501, and 65 post-shift urine samples were collected and analyzed using gas chromatography equipped with headspace sampler (GC-HS/FID). Multiple linear regression was employed to analyze the association between the studied variables.

Findings
The mean (SD) urinary toluene (UTol) level was 13.42 (9.72) ug/L. Toluene on the CCP (TolCCP) was a meaningful predictor for UTol (p-value=0.027) with r and r2 values of 0.441 and 0.195, respectively. The r and r2 of the model using the toluene time-weighted average concentrations in air were 0.739 and 0.546, respectively. The absorbed dose of toluene determined from the TolCCP ranged from 1.05 to 91.94 mg, accounting for 12.3 percent of the threshold limit value (TLV).

Originality/value
Dermal exposure was insignificant when workers wore respirators, but when not, dermal absorption could contribute to the overall uptake and exposure above the TLV. Appropriate gloves should be assigned to the workers to reduce dermal exposure to toluene.
Empowerment through a teacher leadership academy
Authors: Visone Jeremy D. 
Published: November 2018

Purpose
The purpose of this paper is to examine the effectiveness of a teacher leadership academy (TLA) organized through a school district/university partnership in a small, US Suburban School District in increasing teachers’ participation in leadership activities.

Design/methodology/approach
TLA participants (n=11) were surveyed using the Teacher Leadership Activities Scale, and their results were compared to a control group of teachers in the district who were not participating in the TLA (n=12). Interviews and open-ended response items provided qualitative data to examine how the TLA contributed to teachers’ growth as leaders.

Findings
Results indicated that teachers in the TLA did increase participation in teacher leadership activities. Qualitative data revealed themes of many espoused benefits from TLA participation, including increased interactions with administrators, improved understanding of the obstacles associated with implementing changes, and expanded leadership capacity.

Research limitations/implications
Conditions that both enhanced and detracted from teacher leaders’ growth were identified and outlined, including formal leaders’ participation in TLA activities, material support for projects, and a supportive atmosphere (enhancers) and administrative roadblocks and the inability to remediate capacity issues for teacher leaders (detractors).

Originality/value
The conditions outlined above will assist those interested in creating TLAs in doing so with purpose and increased chance for buy in and success.
Procedure structuring for programming aircraft maintenance activities
Authors: Junqueira Viviane Souza Vilela , Nagano Marcelo Seido , Miyata Hugo Hissashi 
Published: November 2018

Purpose
This paper aims to exemplify the use of project management tools in the scheduling of aircraft maintenance activities. This process is known as maintenance, repair and overhaul and it has gained importance within the aeronautical sector due to its expected growth in the coming years; however, it also faces increasing competitiveness in its market. This fact gives rise to the need of acting in maintenance management and seeking lower costs while maintaining the quality of the service provided. The purpose of this paper is to propose the structuring of a procedure that aims to reduce the total maintenance time (downtime) and guarantee the delivery of the aircraft on time.

Design/methodology/approach
The paper, through a case study at a Brazilian aircraft maintenance center, used critical path method and critical chain project management, the latter being derived from the theory of constraints, with the purpose of analyzing resources systematically and synchronizing the activities in the precedence network.

Findings
As a result, it is shown that downtime can be reduced from 11 to 5 days and improvements are proposed to achieve greater market competitiveness.

Originality/value
This paper demonstrates the competitive advantage that resulted from the application of project management tools in the aircraft maintenance planning and execution.
Simulation of edge quality in fused deposition modeling
Authors: Armillotta Antonio 
Published: November 2018

Purpose
The purpose of this paper is to propose a method for simulating the profile of part edges as a result of the FDM process. Deviations from nominal edge shape are predicted as a function of the layer thickness and three characteristic angles depending on part geometry and build orientation.

Design/methodology/approach
Typical patterns of edge profiles were observed on sample FDM parts and interpreted as the effects of possible toolpath generation strategies. An algorithm was developed to generate edge profiles consistent with the patterns expected for any combination of input variables.

Findings
Experimental tests confirmed that the simulation procedure can correctly predict basic geometric properties of edge profiles such as frequency, amplitude and shape of periodic asperities.

Research limitations/implications
The algorithm takes into account only a subset of the error causes recognized in previous studies. Additional causes could be integrated in the simulation to improve the estimation of geometric errors.

Practical implications
Edge simulation may help avoid process choices that result in aesthetic and functional defects on FDM parts.

Originality/value
Compared to the statistical estimation of geometric errors, graphical simulation allows a more detailed characterization of edge quality and a better diagnosis of error causes.