bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear couplings and energy transfers in micro- and nano-mechanical resonators: intermodal coupling, internal resonance and synchronization
Authors: Asadi Keivan , Yu Jun , Cho Hanna 
Published: July 2018

Extensive development of micro/nano-electromechanical systems (MEMS/NEMS) has resulted in technologies that exhibit excellent performance over a wide range of applications in both applied (e.g. sensing, imaging, timing and signal processing) and fundamental sciences (e.g. quantum-level problems). Many of these outstanding applications benefit from resonance phenomena by employing micro/nanoscale mechanical resonators often fabricated into a beam-, membrane- or plate-type structure. During the early development stage, one of the vibrational modes (typically the fundamental mode) of a resonator is considered in the design and application. In the past decade, however, there has been a growing interest in using more than one vibrational mode for the enhanced functionality of MEMS/NEMS. In this paper, we review recent research efforts to investigate the nonlinear coupling and energy transfers between multiple modes in micro/nano-mechanical resonators, focusing especially on intermodal coupling, internal resonance and synchronization.
This article is part of the theme issue ‘Nonlinear energy transfer in dynamical and acoustical systems’.
Nemo-like kinase regulates Progranulin levels in the brain through the microglial endocytosis-lysosomal pathway
Authors: Dong Tingting , Kokubu Hiroshi , Driessen Terri M. , Tejwani Leon , Lim Janghoo 
Published: July 2018

AbstractGenetic variants in Granulin (GRN), which encodes the secreted glycoprotein Progranulin (PGRN), are associated with several neurodegenerative diseases including frontotemporal lobar degeneration, neuronal ceroid lipofuscinosis, and Alzheimer’s disease. These genetic alterations manifest in pathological changes due to a reduction of PGRN expression; therefore, identifying a factor that can modulate PGRN levels in vivo would enhance our understanding of PGRN in neurodegeneration, and could reveal novel potential therapeutic targets. Here, we report that Nemo-like kinase (Nlk) regulates Pgrn levels and its associated neuropathophysiology. Genetic interaction studies in mice show that Grn heterozygote mice on an Nlk heterozygote background display pathological and behavioral phenotypes which mimic Grn knockout mice. Furthermore, biochemical and cell biological studies suggest that Nlk reduction promotes Pgrn degradation via the endocytosis-lysosomal pathway, specifically in microglia. Our results reveal a new mechanism for the regulation of Pgrn in the brain and provide insight into the pathophysiology of PGRN-associated diseases.
Expanded CAG/CTG Repeats Resist Gene Silencing Mediated by Targeted Epigenome Editing
Authors: Yang Bin , Borgeaud Alicia C. , Aeschbach Lorène , Rodríguez-Lima Oscar , Ruiz Buendía Gustavo A. , Cinesi Cinzia , Baubec Tuncay , Dion Vincent 
Published: July 2018

AbstractExpanded CAG/CTG repeat disorders affect over 1 in 2500 individuals worldwide. Potential therapeutic avenues include gene silencing and modulation of repeat instability. However, there are major mechanistic gaps in our understanding of these processes, which prevent the rational design of an efficient treatment. To address this, we developed a novel system, ParB/ANCHOR-mediated Inducible Targeting (PInT), in which any protein can be recruited at will to a GFP reporter containing an expanded CAG/CTG repeat. Using PInT, we found no evidence that the histone deacetylase HDAC5 or the DNA methyltransferase DNMT1 modulate repeat instability upon targeting to the expanded repeat, suggesting that their effect is independent of local chromatin structure. Unexpectedly, we found that expanded CAG/CTG repeats reduce the effectiveness of gene silencing mediated by HDAC5 or DNMT1 targeting. The repeat-length effect in gene silencing by HDAC5 was abolished by a small molecule inhibitor of HDAC3. Our results have important implications on the design of epigenome editing approaches for expanded CAG/CTG repeat disorders. PInT is a versatile synthetic system to study the effect of any sequence of interest on epigenome editing.
Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
Authors: Ostblom Joel , Nazareth Emanuel J.P. , Tewary Mukul , Zandstra Peter W. 
Published: July 2018

AbstractA growing body of evidence highlights the importance of the cellular microenvironment as a regulator of phenotypic and functional cellular responses to perturbations. We have previously developed cell patterning techniques to control population context parameters, and here we demonstrate Context-explorer (CE), a software tool to improve investigation of microenvironmental variables through colony level analyses. We demonstrate the capabilities of CE in the analysis of human and mouse pluripotent stem cells (hPSCs, mPSCs) patterned in colonies of defined size and shape in multi-well plates.CE employs a density-based clustering algorithm to identify cell colonies within micropatterned wells. Using this automatic colony classification methodology, we obtain accuracies comparable to manual colony counts in a fraction of the time. Classifying cells according to their relative position within a colony enables statistical analysis of radial spatial trends in protein expression within multiple colonies in the same treatment group. When applied to colonies of hPSCs, our analysis reveals a radial gradient in the expression of the pluripotency inducing transcription factors SOX2 and OCT4, and a similar trend in the intra-colony location of different cellular phenotypes. We extend these analyses to colonies of different sizes and shapes and demonstrate how the metrics derived by CE can be used to asses the patterning fidelity of micropatterned plates.We have incorporated a number of features to enhance the usability and utility of CE. To appeal to a broad scientific community, all of the software’s functionality is accessible from a graphical user interface, and convenience functions for several common data operations are included. CE is compatible with existing image analysis programs such as CellProfiler and extends the analytical capabilities already provided by these tools. Taken together, CE facilitates investigation of spatially heterogeneous cell populations in fundamental research and drug development validation programs.
Using eDNA to biomonitor the fish community in a tropical oligotrophic lake
Authors: Valdez-Moreno Martha , Ivanova Natalia V. , Elías-Gutiérrez Manuel , Pedersen Stephanie L. , Bessonov Kyrylo , Hebert Paul D.N. 
Published: July 2018

AbstractEnvironmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184-187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM and S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, 6 fish species represent new records for the study area, while 2 require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods were appropriate for its detection. We developed protocols that enabled the recovery of eDNA from tropical oligotrophic aquatic ecosystems, and confirmed their effectiveness in detecting diverse species of vertebrates including an invasive species of Amazon catfish.
PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping
Authors: Hernández Sánchez Luis Francisco , Burger Bram , Horro Carlos , Fabregat Antonio , Johansson Stefan , Njølstad Pål Rasmus , Barsnes Harald , Hermjakob Henning , Vaudel Marc 
Published: July 2018

AbstractBackgroundMapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers, e.g. gene sets, in pathway knowledgebases. However, the isoform and post-translational modification states of proteins are lost when converting input and pathways into gene-centric lists.FindingsBased on the Reactome knowledgebase, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input, and outputs the possibly affected biochemical reactions, subnetworks, and pathways.ConclusionsPathwayMatcher enables refining the network-representation of pathways by including isoform and post-translational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity and it becomes possible to distinguish interactions between different forms of the same protein.
Estimating the mechanism of farmers’ effective participation in Chinese rural land consolidation
Authors: Wang Wenxiong , Yu Lihong , Zhou Wei , Marcouiller David W. , Luo Bin 
Published: July 2018

Purpose
Effective farmer participation in the rural land consolidation process has become increasingly important because it improves results in rural land consolidation and land use efficiency. The purpose of this paper is to examine the mechanism of farmers’ effective participation in Chinese rural land consolidation.

Design/methodology/approach
The authors empirically assess farmers’ effective participation in the rural land consolidation process in ten counties of China’s Hubei province. Focusing on an effective decision-making model, the authors comprehensively evaluated farmer participation using surveys that incorporated an index system and analyzed survey results using a structural equation model to examine factors that influenced farmer’s effective participation.

Findings
The results of the study suggest that the correlations between farmers’ effective participation and the impacting factors the authors proposed were particularly strong. In addition, participation ability, participation opportunity and participation incentive are strongly associated with effective farmer participation. Thus, the authors highlight that incentives should be provided to encourage farmers’ effective participation in rural land consolidation.

Research limitations/implications
Because of the chosen approach and the set of the research object, the geographic context of the empirical survey work was limited; furthermore, the authors only studied the influencing factors at the individual level, leaving the interaction effects between governmental factors and farmer individual factors inadequately explained.

Originality/value
Despite those limitations, these results serve as an important reference for government agencies and stakeholder groups in rural land consolidation decision making.
Are organizational factors more prevailing than individual factors in mitigating employee fraud?
Authors: Said Jamaliah , Omar Normah , Rafidi Marhamah , Syed Yusof Sharifah Norzehan 
Published: July 2018

Purpose
This paper aims to examine whether individual factors (religiosity and ethical values) and organizational factors (ethical leadership and whistleblowing practices) contribute to employee fraud mitigation.

Design/methodology/approach
Guided by Corporate Integrity System Malaysia, this study developed and collected 101-questionnaire survey from Royal Custom officers.

Findings
The findings revealed that individual factors (religiosity and ethical values) significantly contribute to fraud reduction, and organizational factors (both ethical leadership and whistle blowing practices) do not significantly contribute to employee fraud mitigation.

Originality/value
This study serves as a useful guide to alert and educate employers, professionals, law enforcement officers and policymakers of the importance of individual and organizational factors in mitigating employee fraud. There is very little empirical research conducted on employee fraud in Malaysia. This research helps bring that to light.
In an ideal world who should carry the can for wrongdoing business?
Authors: Vanni Domitilla 
Published: July 2018

Purpose
This paper aims to analyze the main international rules against economic crime and to verify if Italian legislation provides for appropriate measures according to own needs at a national level.

Design/methodology/approach
The research uses a comparative approach by examining the existing legislations on a global, European and Italian level for finding analogies and differences between them.

Findings
The research has discovered a wide variation in the legislative interventions against economic crimes and in the kind of imposed sanctions. Nevertheless, there seems to be a trend toward penalties, with a high degree of uniformity between the different levels of protection.

Research limitations/implications
This paper aims to maintain a common international level in fighting against economic crime and to enforce the effectiveness of national regulations.

Practical implications
The achievement of a high level of protection, for public security and social cohesion to prevent and reduce economic crimes.

Social implications
This paper ensures a high level of security for the general public by taking action against money laundering, cybercrimes and other sorts of misconduct, as well as by intensifying preventive action against all kinds of economic crime through an effective global cooperation.

Originality/value
This is a fast-moving area of law, which continues to evolve for the variety of behaviors through which economic crime occurs, so different solutions to the problem can be found by national legislators who must be coordinated in a global context on the basis of an international standard of protection to which they more and more frequently have to conform their own rules.
Turning information quality into firm performance in the big data economy
Authors: Fosso Wamba Samuel , Akter Shahriar , Trinchera Laura , De Bourmont Marc 
Published: July 2018

Purpose
Big data analytics (BDA) increasingly provide value to firms for robust decision making and solving business problems. The purpose of this paper is to explore information quality dynamics in big data environment linking business value, user satisfaction and firm performance.

Design/methodology/approach
Drawing on the appraisal-emotional response-coping framework, the authors propose a theory on information quality dynamics that helps in achieving business value, user satisfaction and firm performance with big data strategy and implementation. Information quality from BDA is conceptualized as the antecedent to the emotional response (e.g. value and satisfaction) and coping (performance). Proposed information quality dynamics are tested using data collected from 302 business analysts across various organizations in France and the USA.

Findings
The findings suggest that information quality in BDA reflects four significant dimensions: completeness, currency, format and accuracy. The overall information quality has significant, positive impact on firm performance which is mediated by business value (e.g. transactional, strategic and transformational) and user satisfaction.

Research limitations/implications
On the one hand, this paper shows how to operationalize information quality, business value, satisfaction and firm performance in BDA using PLS-SEM. On the other hand, it proposes an REBUS-PLS algorithm to automatically detect three groups of users sharing the same behaviors when determining the information quality perceptions of BDA.

Practical implications
The study offers a set of determinants for information quality and business value in BDA projects, in order to support managers in their decision to enhance user satisfaction and firm performance.

Originality/value
The paper extends big data literature by offering an appraisal-emotional response-coping framework that is well fitted for information quality modeling on firm performance. The methodological novelty lies in embracing REBUS-PLS to handle unobserved heterogeneity in the sample.
The effects of students
Authors: Pinna Roberta , Carrus Pier Paolo , Musso Marta , Cicotto Gianfranco 
Published: July 2018

PurposeThe purpose of this paper is to investigate the role of university identification to explain students’ involvement in extra-role behaviours and turnover intentions. The theoretical model developed, specifies the relationships between university identity and identification and between identification and behavioural patterns.Design/methodology/approachData have been collected from a sample of 338 students from an Italian University. Then, they have been analysed adopting linear regression models (multiple when occurs) and a path analysis through structural equations models has been developed. The Sobel test has been used in the analysis to verify the mediator role of variables.FindingsThe results show that: the university identity perception of students have significant effect on university identification process; and student-university identification have significant effect on student’s advocacy, that is negatively related to turnover intention.Originality/valueThis paper provides support for the importance of brand management in higher educational context. Institutions would benefit from communicating their identities clearly, coherently and in a persuasive manner, emphasising those aspects of the university’s identity that students and future students will perceive as prestigious and similar to their identities.
SuhB, a small non‐coding RNA involved in catabolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA
Authors: García‐Romero Inmaculada , Förstner Konrad U. , Santero Eduardo , Floriano Belén 
Published: July 2018

SummaryGlobal dRNA‐seq analysis of transcription start sites combined with in silico annotation using Infernal software revealed the expression of 91 putative non‐coding sRNA in Sphingopyxis granuli TFA cells grown on different carbon sources. Excluding housekeeping sRNAs, only one additional sRNA, which belongs to the Rfam SuhB family (RF00519), was detected by Infernal but with an incorrect size according to the experimental results. SuhB is highly conserved across the Sphingopyxis genus. Expression data revealed that SuhB is present in rapidly growing TFA cells. A suhB deletion mutant exhibited de‐repression of tetralin degradation (thn) gene expression and higher amounts of their LysR‐type activator, ThnR, under conditions of carbon catabolite repression (CCR). Interaction between SuhB and the 5′UTR of thnR mRNA was demonstrated in vitro. Moreover, co‐immunoprecipitation experiments, combined with fluorescence measurements of gfp fusions to the 5′UTR of thnR mRNA and the phenotype of an hfq deletion mutant, suggest the involvement of Hfq in this interaction. Taken together, these data support an Hfq‐mediated repressive role for SuhB, on ThnR mRNA translation that prevents thn gene induction. SuhB, which is a highly conserved sRNA in the Sphingopyxis genus, is the first identified element directly involved in CCR of thn gene expression in S. granuli strain TFA.
Bioavailability of Isoflavone Metabolites After Korean Fermented Soybean Paste (Doenjang) Ingestion in Estrogen‐Deficient Rats
Authors: Lee Da‐Hye , Kim Min Jung , Park So‐Hyun , Song Eun‐Ji , Nam Yong‐Do , Ahn Jiyun , Jang Young‐Jin , Ha Tae‐Youl , Jung Chang Hwa 
Published: July 2018

AbstractDoenjang (DJ), a fermented soybean product used in soups, stews, and sauces, contains high quality proteins, fats, vitamins, minerals, and other functional ingredients, including isoflavones and saponins. This study investigated whether DJ improves the bioavailability of isoflavones compared to boiled soybean (BS) in sham‐operated or ovariectomized (OVX) rats. We also examined the effects of ovariectomy on the differences in bioavailability of isoflavones. BS and DJ were administered in sham‐operated and OVX rats, and blood samples were collected. Twenty‐six isoflavone‐derived metabolites were identified. Pharmacokinetic analysis revealed that T1/2 values of the individual isoflavone metabolites were most different in sham and OVX rats, even after the same sample treatment; however, Tmax values were significant different in a few metabolites such as daidzein 4′‐glucuronide, daidzein 4′‐sulfate, 2‐(4‐hydroxyphenyl)propionic acid, and benzoic acid. For most of the individual metabolites, Cmax was higher in both sham and OVX rats administered BS than those administered DJ. The AUC was generally lower in OVX rats than in sham rats. The AUC of daidzein and genistein in BS‐fed sham rats was approximately 1.7‐fold higher than those administered DJ, whereas glycitein was detected only in the DJ group. No significant differences in AUC of daidzein and genistein were observed between BS and DJ administration in OVX rats, although the total isoflavone content of DJ was lower; thus, DJ‐mediated isoflavone bioavailability was more effective in OVX rats. Similar tendencies were observed for phase II and gut‐mediated metabolites. These results suggested that DJ enhanced isoflavone bioavailability under estrogen deficiency, even when the total isoflavone content was decreased by fermentation.
Determination of Volatiles and Carotenoid Degradation Compounds in Red Pepper Fermented by Lactobacillus parabuchneri
Authors: Lee Sang Mi , Lee Joo Young , Cho Youn Jeung , Kim Moon Seok , Kim Young‐Suk 
Published: July 2018

AbstractRed pepper (Capsicum annuum L.) has been used as one of key ingredients in certain fermented foods due to it providing a unique hot and spicy sensation. In this study, volatile compounds—including degradation compounds of carotenoids—in fermented red pepper inoculated with Lactobacillus parabuchneri were investigated. In total, the contents of certain alcohols, benzene and its derivatives, esters, hydrocarbons, lactones, pyrazines, and terpenes were increased in red pepper inoculated with L. parabuchneri, while those of aldehydes, sulfur‐containing compounds, and ketones decreased during the fermentation period. The contents of some degradation compounds of carotenoids (β‐ionone, β‐cyclocitral, α‐ionone, and β‐damascenone) increased significantly with the fermentation period. In particular, the content of β‐damascenone—which could form by the degradation of neoxanthin—increased gradually during fermentation, but this compound was not detected in 0‐day samples. These findings indicate that the contents of certain volatiles—including degradation compounds of carotenoids—in fermented red pepper inoculated with L. parabuchneri can change markedly during the fermentation process.Practical ApplicationThis study investigated the changes of volatiles and carotenoids degradation compounds in fermented red pepper inoculated with Lactobacillus parabuchneri during fermentation. These results could be used to improve the quality of red pepper‐based products and in the development of certain fermented foods, including Gochujang (fermented red pepper paste) and kimchi.