bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digitalizing heterologous gene expression in Gram-negative bacteria with a portable on/off module
Authors: Calles Belén , Goñi-Moreno Angel , de Lorenzo Víctor 
Published: September 2019

ABSTRACTWhile prokaryotic promoters controlled by signal-responding regulators typically display a range of input/output ratios when exposed to cognate inducers, virtually no naturally occurring cases are known to have an off state of zero transcription—as ideally needed for synthetic circuits. To overcome this problem we have modelled and implemented simple digitalizer module that completely suppresses the basal level of otherwise strong promoters in such a way that expression in the absence of induction is entirely impeded. The circuit involves the interplay of a translation-inhibitory sRNA with the translational coupling of the gene of interest to a repressor such as LacI. The digitalizer module was validated with the strong inducible promotersPm(induced by XylS in the presence of benzoate) andPalkB(induced by AlkS/dicyclopropylketone) and shown to perform effectively both inE. coliand the soil bacteriumPseudomonas putida.The distinct expression architecture allowed cloning and conditional expression of e.g. colicin E3, one molecule of which per cell suffices to kill the host bacterium. Revertants that escaped ColE3 killing were not found in hosts devoid of insertion sequences, suggesting that mobile elements are a major source of circuit inactivationin vivo.
Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-promoting stromal components
Authors: Amini Parisa , Nassiri Sina , Malbon Alexandra , Markkanen Enni 
Published: September 2019

AbstractThe importance of cancer-associated stroma (CAS) for initiation and progression of cancer is well accepted. However, as stromal changes in benign forms of naturally occurring tumours are poorly understood, it remains unclear how CAS from benign and malignant tumours compare. Spontaneous canine mammary tumours are viewed as excellent models of human mammary carcinomas (mCA). We have recently reported highly conserved stromal reprogramming between canine and human mCA based on transcriptome analysis of laser-capture-microdissected FFPE specimen. To identify stromal changes between benign and malignant mammary tumours, we have analysed CAS and matched normal stroma from 13 canine mammary adenomas and compared them to 15 canine mCA. Our analyses revealed distinct stromal reprogramming even in small benign tumours. While similarities in stromal reprogramming exist, the CAS signature clearly distinguished adenomas from mCA, suggesting that it may reliably discriminate between benign and malignant tumours. We identified strongly discriminatory genes and found strong differential enrichment in several hallmark signalling pathways between benign and malignant CAS. The distinction between CAS from adenoma and mCA was further substantiated by differential abundance in cellular composition. Finally, to determine key players in CAS reprograming between adenomas and mCA, a network-based gene screening method identified modules of co-expressing genes with distinct expression profile in benign and malignant CAS, and revealed several hub genes as potential molecular drivers in CAS. Given the relevance of canine CAS as a model for the human disease, our approach identifies potential stromal drivers of tumour malignancy with implications for human mCA.Summary statementRNAsequencing-based analysis of stromal reprogramming between benign and malignant naturally occurring canine mammary tumours identifies potential molecular drivers in cancer-associated stroma that support tumour growth and malignancy.
Age-dependent neuroprotective effect of an SK3. channel agonist on excitotoxity to dopaminergic neurons in organotypic culture
Authors: Maldonado Oscar , Jenkins Alexandra , Belalcazar Helen M. , Hyman Katelynn M. , Cuervo Helena-Hernandez , Ladaga Giannina , Padilla Lucia , de Erausquin Gabriel A. 
Published: September 2019

AbstractWe evaluated the age-dependency of the neuroprotective effect of an small-conductance calcium activated potassium channel 3 (SK3) agonist, 1-EBIO, on AMPA excitoxicity to dopaminergic neurons (DN) in organotypic cultures. Most TH+ neurons were also SK3+. SK3+/TH-cells (DN+) were common at each developmental stage but more prominently at day in vitro (DIV) 8. Young DN+ neurons were small bipolar and fusiform, whereas mature ones were large and multipolar. Exposure of organotypic cultures to AMPA (100 μm, 16 h) had no effect on the survival of DN+ at DIV 8, but caused significant toxicity at DIV 15 (n=15, p=0.005) and DIV 22 (n=15, p<<0.001). These results indicate that susceptibility of DN to AMPA excitotoxicity is developmental stage-dependent in embryonic VM organotypic cultures. Immature DN+ (small, bipolar) were increased after AMPA (100 μm, 16 h) at DIV 8, at the expense of the number of differentiated (large, multipolar) DN+ (p=0.039). This effect was larger at DIV 15 (p<<<0.0001) and at DIV 22 (p<<<0.0001). At DIV 8, 30 μM 1-EBIO resulted in a large increase in DN+. At DIV 15, AMPA toxicity was prevented by exposure to 30 μM, but not 100 μM 1-EBIO. At DIV 22, excitotoxicity was unaffected by 30 μM 1-EBIO, and partially reduced by 100 μM 1-EBIO. The effects of the SK3. channel agonist 1-EBIO on the survival of SK3.-expressing dopaminergic neurons were concentrationdependent and influenced by neuronal developmental stage.
A single nucleotide polymorphism in the HOMER1 gene is associated with sleep latency and theta power in sleep electroencephalogram
Authors: Pedrazzoli Mario , Mazzotti Diego Robles , Ribeiro Amanda Oliveira , Mendes Juliana Viana , Bittencourt Lia Rita Azeredo , Tufik Sergio 
Published: September 2019

AbstractGlutamate is the most excitatory neurotransmitter in the central nervous system and it is involved in the initiation and maintaining of waking and rapid-eye-movement (REM) sleep. Homer proteins act in the trafficking and/or clustering of metabotropic glutamate receptors, and polymorphisms in the HOMER1 gene have been associated with phenotypes related to glutamate signaling dysregulation. In this study, we report the association of a single nucleotide polymorphism (SNP) in the HOMER1 gene (rs3822568) with specific aspects of sleep in a sample of the Brazilian population. To accomplish this, 1,042 individuals were subjected to a full-night polysomnography, and a subset of 983 subjects had rs3822568 genotyping data available. When compared with the A allele carriers, GG genotyped individuals showed higher sleep latency, lower sleep efficiency, reduced number of arousals per hour, lower apnea-hypopnea index (AHI) and lower theta spectral power. In summary, the present findings suggest that the rs3822568 polymorphism in the HOMER1 gene is associated with sleep EEG profiles and might have an impact on sleep quality and sleep structure, with potential to explain inter-individual variation in sleep homeostasis.
Reduced Kv3.1 Activity in Dentate Gyrus Parvalbumin Cells Induces Vulnerability to Depression
Authors: Medrihan Lucian , Umschweif Gali , Sinha Anjana , Reed Shayna , Gindinova Katherina , Sinha Subhash C. , Greengard Paul , Sagi Yotam 
Published: September 2019

AbstractParvalbumin (PV)-expressing interneurons are important for cognitive and emotional behaviors. These neurons express high level of p11, a protein associated with depression and action of antidepressants. Here we show that either specific deletion of p11 (p11 cKO) or chemogenetic inhibition in dentate gyrus (DG) PV neurons leads to anxiety-like behavior and susceptibility to depression in mice. DG PV neurons from p11 cKO mice showed reduced level and function of Kv3.1, and consequentially reduced capacity of high-frequency firing and altered short-term plasticity at synapses on granule cells. Activation of Kv3.1 or overexpression of the channel attenuated the vulnerability to depressive behavior.
The burden of deleterious variants in a non-human primate biomedical model
Authors: Ramensky Vasily , Jasinska Anna J. , Deverasetty Sandeep , Svardal Hannes , Zelaya Ivette , Jorgensen Matthew J. , Kaplan Jay Ross , Cline J. Mark , Zharikova Anastasia , Service Susan K. , Wilson Richard K. , Coppola Giovanni , Freimer Nelson B. , Warren Wesley C. 
Published: September 2019

ABSTRACTGenome sequencing studies of nonhuman primate (NHP) pedigree and population samples are discovering variants on a large and rapidly growing scale. These studies are increasing the utility of several NHP species as model systems for human disease. In particular, by identifying homozygous protein truncating variants (hPTVs) in genes hypothesized to play a role in causing human diseases, it may be possible to elucidate mechanisms for the phenotypic impact of such variants through investigations that are infeasible in humans. The Caribbean vervet (Chlorocebus aethiops sabaeus) is uniquely valuable for this purpose, as the dramatic expansion of its population following severe bottlenecks has enabled PTVs that passed through the bottleneck to attain a relatively high frequency. Using whole genome sequence (WGS) data from 719 monkeys of the Vervet Research Colony (VRC) extended pedigree, we found 2,802 protein-truncating alleles in 1,747 protein-coding genes present in homozygous state in at least one monkey. Polymorphic sites for 923 SNV hPTVs were also observed in natural Caribbean populations from which the VRC descends. The vervet genome browser (VGB) includes information on these PTVs, together with a catalog of phenotypes and biological samples available for monkeys who carry them. We describe initial explorations of the possible impact of vervet PTVs on early infant mortality.
The use of mutants and inhibitors to study sterol biosynthesis in plants
Authors: Vriese Kjell De , Pollier Jacob , Goossens Alain , Beeckman Tom , Vanneste Steffen 
Published: September 2019

ABSTRACTSterols are very well known for their important roles in membranes and signaling in eukaryotes. Plants stand out among eukaryotes by the large variety of sterols that they can produce, and employing them across a wide spectrum of physiological processes. Therefore, it is critical to understand the wiring of the biosynthetic pathways by which plants generate these distinct sterols, to allow manipulating them and dissect their precise physiological roles. Many enzymatic steps show a deep evolutionary conservation, while others are executed by completely different enzymes. Here, we review the complexity and variation of the biosynthetic routes of the most abundant phytosterols in the green lineage and how different enzymes in these pathways are conserved and diverged from humans,yeast and even bacteria. Based on their evolutionary conservation we discuss the use of human and yeast sterol biosynthesis inhibitors in plants, as an argument for the development of plant-tailored inhibitors of sterol biosynthesis.
DEA-ADALINE: an approach to improve the relative efficiency of 3PLs providers
Authors: Mohanty Mahamaya , Shankar Ravi 
Published: September 2019

PurposeBenchmarking is an approach to understand and evaluate the current position of different entities like third-party logistics (3PLs) service providers with respect to the best practices. The purpose of this paper is to develop an integrated approach to benchmark the 3PLs and minimize the transportation cost, operational cost, total carbon emissions and improve vehicle capacity utilization rate and demand management in an efficient manner.Design/methodology/approachConventional data envelopment analysis (DEA) is extended to develop an integrated approach involving DEA and adaptive linear neuron network (ADALINE). The proposed methodology is dichotomized to the benchmarking of DMUs using Charnes, Cooper, Rhodes ratio and, in the process, helps to suggest ways to reduce inefficiencies.FindingsThe approach also supports the decision makers to understand ways to increase the efficiency of decision-making units (DMUs) that are relatively inefficient for a set of 3PLs considered in this study. This is one of the potential researches as it studies how to improve the efficiency of inefficient DMUs.Research limitations/implicationsThe proposed approach would help the decision makers to better understand the complexities associated with the low-performing 3PLs. The application of the proposed DEA-ADALINE methodology is illustrated using a range of data set for 3PLs.Originality/valueThe paper examines and explains the value added to the conventional DEA model for obtaining the relative efficiencies with reference to the most efficient DMUs without any loss to the original characteristics of DEA and ADALINE.
A review of ICT-based applications to monitor environmental parameters
Authors: Habibi Shahryar 
Published: September 2019

Purpose
The purpose of this study is to implement environmental control systems; information and communication technologies based on user behavior for smart buildings and describe their definitions, technological advances, advantages and modern uses. It also highlights the complexity and difficulty of energy management and comfort via control devices.

Design/methodology/approach
This study reviews recent progress in control, information technologies, sensing and optimization in buildings and addresses the automation and environmental control systems of important parameters such as lighting, noise, temperature and humidity. It also explores the technological innovations and methods of management through sensors based on user behavior for the processes of optimization and control.

Findings
A proposed prototype has been developed by the combination of user behavior and control systems in buildings, mainly related to thermal comfort and energy use. This study addresses the development of a smart-comfort control system based on users’ behavior.

Originality/value
The main contribution of this study is the goal-driven development of an indoor quality apparatus for environmental monitoring data by using smart sensor systems. It can help users to monitor and control their environmental factors and provides functionalities for assessing comfortable ranges.
Social media – Changing the face of knowledge management
Authors: Irum Ayesha , Pandey Agrata 
Published: September 2019

Purpose
Social media (SM) is amongst the latest techniques employed by organizations in their knowledge management endeavors. The paper provides a brief overview of how SM platforms are utilized for the creation, dissemination, and retention of knowledge. The various stages of knowledge management as supported by social media, is mapped through a framework.

Design/methodology/approach
A list of research articles on “social media and knowledge management” have been read and reviewed. The insights are summarized and a framework is proposed.

Findings
The framework demonstrates how SM tools aid in the creation of new knowledge, knowledge exchange and storage of the knowledge footprint. They help to generate varied forms of knowledge from different stakeholders. The freely available information acts as a knowledge source for the third party. The virtual nature of digital platforms motivates employees to share knowledge more openly, leaving a digital trace that can be accessed anytime, thereby building on to the knowledge base.

Originality/value
The article highlights how SM can be essential in the knowledge management processes in the organization. It showcases the prominence of everyday organizational interactions and experiences which together build a knowledge-rich culture.
The comparison of preferred languages of appreciation between Singapore employees and US employees
Authors: White Paul , Hamrick Natalie , Liew Jasmine 
Published: September 2019

Purpose
Recent reports suggest Singapore employees especially value practical assistance in resolving work-related issues. As such, this study explored whether the appreciation language Acts of Service was chosen as the Primary Language of appreciation by Singapore employees at a higher frequency than U.S. employees.

Design/methodology/approach
Nine hundred sixty-seven Singapore employees completed the Motivating By Appreciation (MBA) Inventory, which assesses individuals’ preferred ways of being shown appreciation. A sample of 921 U.S. employees was created from the general MBA Inventory population that matched the Singapore employees group on age, gender and work setting.

Findings
Acts of Service (39 per cent) was virtually equivalent with Words of Affirmation (37 per cent) as the most preferred Language of Appreciation by the Singapore employees, whereas U.S. employees preferred Words of Affirmation at a significantly higher rate (40 per cent) than Acts of Service (26 per cent).

Research limitations/implications
Further research is needed before the findings should be generalized to all East Asian cultures, and additional research is needed before conclusions should be made regarding specific cultural differences in action items preferred.

Practical implications
Workplace leaders in Singapore need to be aware that understanding the work issues and providing practical assistance is highly valued by their employees and communicates appreciation as much as verbal and written praise. This emphasis on the desire for practical assistance is a cultural difference in comparison to their U.S. counterparts. Yet, in both cultures, the leader-employee interpersonal working relationship is a key factor that enables organizations to grow and work through changes successfully.

Originality/value
This is the first study to compare preferred appreciation languages of Singapore and US employees, and report Singapore employees especially value practical assistance in resolving work-related issues.
Evaluation on innovation efficiency of successor of Chinese listed family business based on DEA
Authors: Wang Qi , Wu Qiuming 
Published: September 2019

Purpose
The purpose of this study was to measure the innovative performance of a managed and owned mainland Chinese family business. The objective of the study was to assist an inheritor and/or successor of a family business and to find management problems in innovative activity.

Design/methodology/approach
To improve the innovative technical efficiency (TE) of the business, the study offers methods that enhance the allocation of resources to provide outcomes that improve the core competitiveness of the business and realize the sustainable development of the business. Innovation performance is a well-organized and efficient way of turning innovation input into innovation output. Human input, research and development expenditures measure innovation input. Patent output and other outputs, which include total labor productivity and asset liability ratios, measure innovation output. To complete the study’s task, the innovative performance of 46 Chinese listed family run and owned businesses were evaluated based on the data envelopment analysis and the Banker, Charnes and Cooper model.

Findings
The results of the study show that the overall TE of innovation in a Chinese family run and owned business is low and that the returns to scale of most such businesses is decreasing, and furthermore, that the overall innovation performance of is low.

Originality/value
The implications from the study further suggest that for business efficiency and increased profit a beneficiary of a Chinese family-owned business should optimize the firm’s size and resource allocation.
Importance measures for degrading components based on cooperative game theory
Authors: Cao Yingsai , Liu Sifeng , Fang Zhigeng 
Published: September 2019

Purpose
The purpose of this paper is to propose new importance measures for degrading components based on Shapley value, which can provide answers about how important players are to the whole cooperative game and what payoff each player can reasonably expect.

Design/methodology/approach
The proposed importance measure characterizes how a specific degrading component contributes to the degradation of system reliability by using Shapley value. Degradation models are also introduced to assess the reliability of degrading components. The reliability of system consisting independent degrading components is obtained by using structure functions, while reliability of system comprising correlated degrading components is evaluated with a multivariate distribution.

Findings
The ranking of degrading components according to the newly developed importance measure depends on the degradation parameters of components, system structure and parameters characterizing the association of components.

Originality/value
Considering the fact that reliability degradation of engineering systems and equipment are often attributed to the degradation of a particular or set of components that are characterized by degrading features. This paper proposes new importance measures for degrading components based on Shapley value to reflect the responsibility of each degrading component for the deterioration of system reliability. The results are also able to give timely feedback of the expected contribution of each degrading component to system reliability degradation.
Visualization of tax avoidance and tax rate convergence
Authors: Saka Chika , Oshika Tomoki , Jimichi Masayuki 
Published: September 2019

PurposeThis study aims to explore the evidence of the probability of firms’ tax avoidance and the downward convergence trend of national statutory tax rates and firms’ effective tax rates.Design/methodology/approachThis research employs exploratory data analysis using interactive data manipulation and visualization tools, namely, R with SparkR, dplyr, ggplot2 and googleVis (GeoChart and Motion Chart) packages. This analysis is based on the world-scale accounting data of all listed firms from 148 countries spanning 30 years.FindingsThe results reveal the following: three types of evidences on probability of firms’ tax avoidance, showing a non-random distribution of firms’ effective tax rates and return on assets, cross-sectional variation of firms’ effective tax rates in each country, and the trend of difference between effective tax rates and statutory tax rates, and the downward convergence trend of statutory tax rates and firms’ effective tax rates.Practical implicationsThe results highlight the prominent issues of world-scale tax avoidance and tax rate competition and facilitate a collaborative discussion between laymen and professionals using objective evidence.Originality/valueA novel methodology is adopted through the visualization of world-scale accounting data, which can facilitate a new perspective, revealing unexpected patterns and trends in otherwise hidden information. This study also highlights the importance of global consideration of firms’ tax avoidance and tax rate competition, using objective evidence.