bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaMeta: Integrating metagenome analysis tools to improve taxonomic profiling
Authors: Piro Vitor C , Matschkowski Marcel , Renard Bernhard Y 
Published: May 2017

AbstractBackgroundMany metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g. read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools.ResultsWe propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases.ConclusionsIn a controlled case with simulated and real data we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install-c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at:https://github.com/pirovc/metameta
Comparative genomics sheds light on niche differentiation and the evolutionary history of comammoxNitrospira
Authors: Palomo Alejandro , Pedersen Anders G , Jane Fowler S , Dechesne Arnaud , Sicheritz-Pontén Thomas , Smets Barth F 
Published: May 2017

AbstractThe description of comammoxNitrospiraspp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria (β-AOB) in the environment, call into question the metabolic potential of comammoxNitrospiraand the evolutionary history of their ammonium oxidation pathway. We report four new comammoxNitrospiragenomes, constituting two novel species, and the first comparative genomic analysis on comammoxNitrospira.ComammoxNitrospirahas lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizingNitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to otherNitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to β-AOB, comammoxNitrospiragenomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammoxNitrospiraseems attuned to oligotrophy and hypoxia compared to β-AOB.β-AOBs are the clear origin of the ammonium oxidation pathway in comammoxNitrospira: reconciliation analysis indicates two separate earlyamoAgene transfer events from β-AOB to an ancestor of comammoxNitrospira, followed by clade specific losses. ForhaoA, one early transfer from β-AOB to comammoxNitrospirais predicted – followed by intra-clade transfers. We postulate that the absence of comammox genes in mostNitrospiragenomes is the result of subsequent loss.SignificanceThe recent discovery of comammox bacteria - members of theNitrospiragenus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammoxNitrospiraand related nitrifiers. Ammonium oxidation genes in comammoxNitrospirahad a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.
DisruptingPitx1regulatory topology results in overtly normal limb development
Authors: Sarro Richard , Emera Deena , Uebbing Severin , Dutrow Emily V. , Weatherbee Scott D. , Nottoli Timothy , Noonan James P. 
Published: May 2017

AbstractGene expression patterns during development are orchestrated in part by thousands of distant-acting transcriptional enhancers. However, identifying enhancers that are essential for expression of their target genes has proven challenging. Genetic perturbation of individual enhancers in some cases results in profound molecular and developmental phenotypes, but in mild or no phenotypes in others. Topological maps of long-range regulatory interactions may provide the means to identify enhancers critical for developmental gene expression. Here, we leveraged chromatin topology to characterize and disrupt the major promoter-enhancer interaction forPitx1, which is essential for hindlimb development. We found thatPitx1primarily interacts with a single distal enhancer in the hindlimb. Using genome editing, we deleted this enhancer in the mouse. Although loss of the enhancer completely disrupts the predominant topological interaction in thePitx1locus,Pitx1expression in the hindlimb is only reduced by ~14%, with no apparent changes in spatial distribution or evidence of regulatory compensation.Pitx1enhancer null mice did not exhibit any of the characteristic morphological defects of thePitx1−/−mutant. Our results indicate thatPitx1expression is robust to the loss of its primary enhancer interaction, suggesting disruptions of regulatory topology at essential developmental genes may have mild phenotypic effects.
Role ofChymotrypsin-like Elastase 1in Lung Physiology and in α1-Antitrypsin Deficiency
Authors: Joshi Rashika , Heinz Andrea , Fan Qiang , Guo Shuling , Monia Brett , Schmelzer Christian E.H. , Weiss Anthony S. , Batie Matthew , Parameswaran Harikrishnan , Varisco Brian M. 
Published: May 2017

Abstractα1-antitrypsin related lung disease (AAT-RLD) is the fourth leading indication for lung transplantation and is characterized by protease-mediated progressive emphysema that manifests in the 4thor 5thdecade of life.Chymotrypsin-like elastase 1(Cela1) is a digestive enzyme that binds to elastin in a stretch-dependent manner and is covalently neutralized by AAT. We hypothesized a role forCela1in AAT-RLD.Cela1-/-mice where phenotypically similar to wild type but had higher lung elastance and lacked stretch-inducible elastase activity. Wild-type mice administered anti-AAT oligo had reduced amounts of lung Cela1-AAT fusion protein in lung homogenate and spontaneously developed emphysema after 6 weeks.Cela1-/-mice administered anti-AAT oligo were completely protected from these emphysematous changes. Cela1 recombinant protein did not require propeptide cleavage for elastolysis, and its elastolytic profile was similar to that of other pancreatic elastases. Phylogenetic analysis of vertebrateCelapromoter and protein sequences showed that placental mammalCela1was distinct from otherCela’s, and that the placental mammal theCela1gene was invariantly conserved despite variable loss of otherCelagenes in non-carnivores. These data demonstrate that the pancreatic enzymeCela1has been evolutionarily co-opted for a role in reducing lung elastance in the placental mammal lineage and that its stretch-regulated expression and elastolytic activity is responsible for emphysema in the absence of its anti-protease: AAT.
Systematic effects of mRNA secondary structure on gene expression and molecular function in budding yeast
Authors: Wang Xia , Li Pidong , Gutenkunst Ryan N. 
Published: May 2017

AbstractDynamic control of gene expression is crucial for cellular adaptation to environmental challenges. mRNA secondary structure is known to be associated with mRNA and protein abundance, but little is known about how mRNA secondary structure affects gene expression dynamics. We report a genome-wide computational analysis of mRNA secondary structure, codon usage, and gene expression in budding yeast. We show that mRNA secondary structure combined with codon optimality regulates gene expression in multiple ways, from transcription to mRNA stability to translation. Moreover, we find that the effect of mRNA secondary structure on mRNA abundance is primarily mediated by transcription, not mRNA stability. Notably, genes with low mRNA secondary structure were substantially enriched for functions relevant to stress response, acting in the mitochondrion, endoplasmic reticulum, and ribosome. On the other hand, genes with high mRNA secondary structure were enriched for functions relevant to cellular maintenance, including macromolecular metabolism and biosynthesis. Our results suggest that mRNA secondary structure affects gene expression through coordination of multiple stages in protein biogenesis, with important consequences for stress response. The coupling of transcription to mRNA stability to translation makes concerted changes in mRNA and protein abundance possible and may amplify the effect of regulation to make quick responses to environmental variations.
Evaluation of ddRADseq for reduced representation metagenome sequencing
Authors: Liu Michael , Worden Paul , Monahan Leigh G. , DeMaere Matthew Z. , Burke Catherine M. , Djordjevic Steven P. , Charles Ian G. , Darling Aaron E. 
Published: May 2017

ABSTRACTBackground‘Who is doing what’ is the ultimate open question in microbiome study. Shotgun metagenomics is often applied to gain knowledge of functional roles for bacteria in microbial communities, where the data can be used to predict protein encoding genes and enzymatic pathways present in the community, sometimes leading to testable hypotheses for microbial function. We describe a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection.ResultsWe assessed the performance of the metagenomic ddRADseq approach by applying the method to human stool samples and generating sequence data. We evaluate the extent to which ddRADseq data provides an unbiased reduced representation for microbiome profiling.ConclusionAlthough ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
How to requisitely holistically consider internal gaps of business ethic
Authors: Nedelko Zlatko , Mulej Matjaz , Potocan Vojko 
Published: May 2017

PurposeThe aim of this paper is to report about a requisitely holistic examination of the business ethics, focused on internal gaps between company’s and employees’ ethics. Contribution considers reasons for emergence of business ethics’ internal gaps and their appearance forms.Design/methodology/approachThe authors specify and test model drawing upon modified versions of the ethics and management theory. In all, 1,125 responses were analyzed from an on-going survey conducted biannually among employees in Slovenian companies in the past decade.FindingsResults reveal that company’s real business ethics remained steady over the decade, while employees’ real business ethics have significantly improved. Significant differences exist between employees’ and company’s real business ethics and shape internal business ethics’ incompatibilities. Finally, results reveal a significant influence of employees’ real business ethics on company’s real business ethics.Research limitations/implicationsResearch is limited to postulated hypotheses, qualitative consideration of internal gaps of business ethics and quantitative analysis of business ethics’ development in the considered Slovenian companies in the past 10 years.Practical implicationsThe authors rethought the habit of separated consideration of managerial business ethics and employees’ ethics as well as the presumption about congruence between company’s and employees’ business ethics. The requisitely holistic understanding and consideration of internal gaps of business ethics is suggested.Originality/valueAvailable literature does not provide a similar model for a requisitely holistic consideration of internal gaps of business ethics. The study confirms the proposed model of business ethics gaps.
Research on integrated product service system driven by customer value based on ontology technology
Authors: Zhu Haihua , Li Jing , Gao James , Lu Weihua 
Published: May 2017

Purpose
With the customers’ increasing expectation on the product value, manufacturing enterprises around the world have made significant efforts to provide high value-added services in addition to their traditional product development and manufacturing business. For this reason, it is of great importance to research product service system. The purpose of this paper is to research on the key problem of integrated product service system (IPSS) design.

Design/methodology/approach
A value-oriented IPSS is developed, which is set up based on “requirements-functions-processes-structures” mapping model to give full consideration to customer value and service functions. An extended product-service blueprint, which stems from the service blueprint, is developed to describe product behaviors, service deliver processes, stakeholders’ activities and supporting activities. An ontology-based design support system is proposed to improve design efficiency and help designers making better-informed decisions. A computer-aided prototype system has been developed, and an initial attempt has been made to demonstrate the role of IPSS in the aerospace industry.

Findings
Many traditional design methods cannot effectively address the objects and processes integration problem of products and services. Moreover, both product and service should be considered in IPSS design, and both of them extremely depend on designers’ own experience and knowledge. Thus, a broader range of knowledge is required to understand product-service system (PSS) design.

Research limitations/implications
This research provides a solid foundation for PSS C and promotes an effective means for PSS design.

Originality/value
A customer value-oriented IPSS is presented. Customer requirements are considered during the design phase of PSS as well as both product and service knowledge.
Research on social e-commerce reputation formation and state-introduced model
Authors: Wei Chuang , Yu Zhao-Ji , Chen Xiao-Nan 
Published: May 2017

Purpose
This paper aims to solve the problem of information overload and reduce search costs. It proposes a social e-commerce online reputation formation model and community state-introduced model. A system dynamics trend simulation has been run to capture the relationship among the sellers, buyers, social e-commerce platforms and external environment to obtain an online reputation.

Design/methodology/approach
Empirical research relating to social e-commerce reputation has been used to confirm the influencing factors in social e-commerce, and a conceptual framework is developed for social e-commerce reputation formation. Thereafter, a trend simulation is generated to classify the relationship among the factors based on system dynamics. Also, the improved algorithm for community detection and a state-introduced model based on a Markov network are proposed to achieve better network partition for better online reputation management.

Findings
The empirical model captures the interaction effect of social e-commerce reputation and the state-introduced model to guide community public opinion and improve the efficiency of social e-commerce reputation formation. This helps minimize searching cost thereby improving social e-commerce reputation construction and management.

Research limitations/implications
There is no appropriate online reputation system to be constructed to test the relationship proposed in the study for a field experiment. Also, deeper investigation for the nodes’ attributes in social networks should be made in future research. Besides, researchers are advised to explore measurement for the reputation of a given seller by using social media data as from Twitter or micro blogs.

Originality/value
Investigations that study online reputation in the social e-commerce are limited. The empirical research figured out the factors which can influence the formation of online reputation in social e-commerce. An SD model was proposed to explain the factors interaction and trend simulation was run. Also, a state-introduced model was proposed to highlight the effect of nodes’ attributes on communities’ detection to give a deeper investigation for the online reputation management.
Game-theoretic analysis of Stackelberg oligopoly with arbitrary rank reflexive behavior of agents
Authors: Geraskin Mikhail 
Published: May 2017

Purpose
This paper aims to consider the problem of determining the equilibriums on oligopoly market in case of Stackelberg leader (leaders) and reflexive behavior of market agents.

Design/methodology/approach
This paper includes economic and mathematical modeling, optimization methods and game theory.

Findings
This paper explains models of reflexive games on oligopoly market, taking into account the diversity of agents’ reasoning about strategies of environing and equilibrium mechanisms for coincidence or opposition of agents’ reflexive reasoning on the same rank of reflection.

Research limitations/implications
This paper considers the oligopoly market with linear function of demand and costs of agents, the rational behavior of agents and the reflexive reasoning on the same rank of reflection. The set of agents’ reasoning about the environing strategies is considered as a set of market states for which the problem of agent’s optimal action choosing solves with the complete awareness.

Practical implications
Identification of reflexive behavior of environing allows agents to increase their market shares and profit.

Social implications
Oligopoly markets play a leading role in the world oil trade and reflexive behavior affects the market equilibrium.

Originality/value
In the paper, the mechanisms of equilibrium in reflexive games on the linear duopoly market for arbitrary rank reflection are developed.
Comprehension of handwriting development: Pen‐grip kinetics in handwriting tasks and its relation to fine motor skills among school‐age children
Authors: Lin Yu‐Chen , Chao Yen‐Li , Wu Shyi‐Kuen , Lin Ho‐Hsio , Hsu Chieh‐Hsiang , Hsu Hsiao‐Man , Kuo Li‐Chieh 
Published: May 2017

Background/aimNumerous tools have been developed to evaluate handwriting performances by analysing written products. However, few studies have directly investigated kinetic performances of digits when holding a pen. This study thus attempts to investigate pen‐grip kinetics during writing tasks of school‐age children and explore the relationship between the kinetic factors and fine motor skills.MethodsThis study recruited 181 children aged from 5 to 12 years old and investigated the effects of age on handwriting kinetics and the relationship between these and fine motor skills. The forces applied from the digits and pen‐tip were measured during writing tasks via a force acquisition pen, and the children's fine motor performances were also evaluated.ResultsThe results indicate that peak force and average force might not be direct indicators of handwriting performance for normally developing children at this age. Younger children showed larger force variation and lower adjustment frequency during writing, which might indicate they had poorer force control than the older children. Force control when handling a pen is significantly correlated with fine motor performance, especially in relation to the manual dexterity.Conclusions/significance of the studyA novel system is proposed for analysing school‐age children's force control while handwriting. We observed the development of force control in relation to pen grip among the children with different ages in this study. The findings suggested that manipulation skill may be crucial when children are establishing their handwriting capabilities.
MicroRNA‐128 promotes apoptosis in lung cancer by directly targeting NIMA‐related kinase 2
Authors: Zhao Dejian , Han Wenzheng , Liu Xia , Cui Dawei , Chen Yu 
Published: May 2017

BackgroundMicroRNA‐128 (miR‐128) serves as a regulator by inducing cancer cell apoptosis, differentiation, the epithelial‐to‐mesenchymal transition process, and tumor growth by mediating different targets. NIMA‐related kinase 2 (NEK2) is aberrantly expressed in lung cancer. The miR‐128/NEK2 pathway has been reported to predict prognosis in colorectal cancer; however, the determination of a relationship between miR‐128 and NEK2 in lung cancer has remained elusive. We explored the association between miR‐128 and NEK2 in lung cancer.MethodsMiR‐128 and NEK2 expression were examined in 15 lung cancer tissues by real time‐PCR. Lung cancer SK‐MES‐1 cells were transfected with miR‐128 mimic, an inhibitor or a negative control. MiR‐128 and NEK2 expression levels were detected using quantitative real time‐PCR and Western blot. SK‐MES‐1 cell apoptosis was performed by flow cytometry.ResultsCompared to adjacent non‐tumor tissues, miR‐128 was downregulated and NEK2 was upregulated in 15 lung cancer tissues. Lung cancer SK‐MES‐1 cells transfected with miR‐128 mimic induced a higher apoptotic rate than those transfected with the negative control. Dual luciferase assay further confirmed that NEK2 was a direct target of miR‐128 in lung cancer, and transfection with miR‐128 mimic could decrease the NEK2 protein level while the miR‐128 inhibitor increased NEK2 expression. Finally, the apoptotic effect of lung cancer cells induced by miR‐128 mimic could be reversed by NEK2 overexpression.ConclusionsNEK2 was regulated by miR‐128 in lung cancer and miR‐128 induced lung cancer cell apoptosis by mediating NEK2 expression.