bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves
Authors: Regalado Julian , Lundberg Derek S. , Deusch Oliver , Kersten Sonja , Karasov Talia , Poersch Karin , Shirsekar Gautam , Weigel Detlef 
Published: October 2019

AbstractMicroorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, acquire nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of 16S rDNA and/or the internal transcribed spacer (ITS) of rDNA loci, but the decreasing cost of high-throughput sequencing has made shotgun metagenome sequencing increasingly accessible. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S rDNA and eukaryotic ITS1 amplicon data from 176 of these samples. The shotgun data were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. For shotgun and amplicon data, microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. We use the metagenome data, which captures the ratio of bacterial to plant DNA in leaves of wild plants, to scale the 16S rDNA amplicon data such that they reflect absolute bacterial abundance. We show that this cost-effective hybrid strategy overcomes compositionality problems in amplicon data and leads to fundamentally different conclusions about microbiome community assembly.
Pan-transcriptome-based Candidate Therapeutic Discovery for Idiopathic Pulmonary Fibrosis
Authors: Wang Yunguan , Yella Jaswanth K. , Ghandikota Sudhir , Cherukuri Tejaswini C. , Ediga Harshavardhana H. , Madala Satish K. , Jegga Anil G. 
Published: October 2019

ABSTRACTBACKGROUNDAlthough the advent of two FDA-approved therapies for idiopathic pulmonary fibrosis (IPF) has energized the field, their effects are largely suppressive than pulmonary fibrosis remission- or reversion-inducing. Hence, the pursuit for newer IPF therapeutics continues. Recent studies show that joint analysis of systems biology level information with drug-disease connectivity are effective in discovery of biologically relevant candidate therapeutics.METHODSPublicly available gene expression signatures from IPF patients are used to query large scale perturbagen signature library to discover compounds that can potentially reverse dysregulated gene expression in IPF. Two methods are used to calculate IPF-compound connectivity: gene expression-based connectivity and feature-based connectivity. Identified compounds are further prioritized based on their shared mechanism(s) of action.RESULTSWe identified 77 compounds as potential candidate therapeutics for IPF. Of these 39 compounds are either FDA-approved for other diseases or are currently in phase 2/3 clinical trials suggesting their repurposing potential for IPF. Among these compounds are multiple receptor kinase inhibitors (e.g., nintedanib, currently approved for IPF, and sunitinib), aurora kinase inhibitor (barasertib), EGFR inhibitors (erlotinib, gefitinib), calcium channel blocker (verapamil), phosphodiesterase inhibitors (roflumilast, sildenafil), PPAR agonists (pioglitazone), HDAC inhibitors (entinostat), and opioid receptor antagonists (nalbuphine). As a proof-of-concept, we performed in vitro validations with verapamil using lung fibroblasts from IPF and show its potential benefits in pulmonary fibrosis.CONCLUSIONSSince about half of the candidates discovered in this study are either FDA-approved or are currently in clinical trials for other diseases, rapid translation of these compounds as potential IPF therapeutics is feasible. Further, the generalizable, integrative connectivity analysis framework in this study can be readily adapted in early phase drug discovery for other common and rare diseases with transcriptomic profiles.
Making up ideal recruits
Authors: Gebreiter Florian 
Published: October 2019

PurposeThe purpose of this paper is to examine the role of graduate recruitment in the professional socialisation and subjectification of Big Four professionals.Design/methodology/approachThe paper draws on documentary data and interviews conducted at one British university. It adopts an interpretive perspective and is informed by Foucault’s work on technologies of power and technologies of the self.FindingsThe paper argues that the graduate recruitment practices of Big Four firms represent a series of examinations which produce the category of ideal recruits. It moreover suggests that this category serves as the ultimate objective of an ethical process whereby aspiring accountants consciously and deliberately seek to transform themselves into the type of subjects they aspire to be – ideal recruits.Research limitations/implicationsThe findings of the paper are primarily based on interviews conducted at one university. Future research could explore if students at other universities experience graduate recruitment in similar or different ways.Originality/valueThe paper highlights the constitutive role of graduate recruitment practices and shows that they can construct ideal recruits as much as they select them. It also shows that graduate recruitment is an important anticipatory socialisation mechanism that can compel aspiring accountants to learn how to look, sound and behave like Big Four professionals long before they join such organisations. Finally, the paper discusses its implications for the future of the profession, social mobility and the use of Foucault’s work on technologies of power and the self in studying subjectivity at elite professional service firms.
The tax gap as a public management instrument: application to wealth taxes
Authors: Durán-Cabré José M. , Esteller Moré Alejandro , Mas-Montserrat Mariona , Salvadori Luca 
Published: October 2019

PurposeThe purpose of this paper is to study the concept of tax gap, that is the difference between the total amount of taxes collected and the total tax revenues that would be collected under full tax compliance.Design/methodology/approachThe authors also present the methodology to estimate the gap for two taxes levied on wealth: the wealth tax and the inheritance and gift tax; both are administered in Spain by the regional tax authorities.FindingsThe authors point out that its estimation offers useful information about the relative size and nature of non-compliance, as well as its evolution over time. Likewise, the tax gap is a valuable instrument not only to define enforcement strategies of the tax administration but also to enhance its accountability. Nonetheless, the methodology used to estimate the tax gap and, consequently, the interpretation of the results is subject to limitations that are discussed in the paper.Originality/valueFinally, the paper provides the results of the estimations obtained from using microdata: 44.34 per cent gap in the wealth tax and 41.26 per cent in the inheritance and gift tax.
Managing environmental building performance through IT systems
Authors: Maslesa Esmir , Jensen Per Anker 
Published: October 2019

Purpose
This paper aims to disclose the role and features of various IT systems for environmental building performance (EBP) in facilities management.

Design/methodology/approach
The study focuses on IT systems used for facilities management in four organisations. The study is based on a maximum variance case study in which the selected organisations have different organisation type and portfolio size. Three organisations are from Denmark and one is from the UK.

Findings
Several IT systems can be used for managing EBP. EBP in IT systems is primarily reflected through energy management, with specific focus on monitoring and reporting electricity, heating and water consumption. Furthermore, greenhouse gas emissions related to energy consumption can be calculated in some IT systems, while other environmental categories like building materials and recycling potentials are not adequately supported by the systems covered in this study. Some IT systems offer additional features relating to EBP, such as waste management and space management, but the study shows that these features are not demanded at the current point.

Practical implications
The results can be used to support decision-making in organisations to improve EBP in facilities management by IT systems.

Originality/value
This study contributes with new knowledge on how IT systems are used in different organisations for managing EBP. The paper also shows how various IT systems can add value to real estate organisations and facilities management departments and support their business processes relating to EBP.
Challenges associated with the use of information and communication technologies in information sharing by fish farmers in the Southern highlands of Tanzania
Authors: Benard Ronald , Dulle Frankwell , Lamtane Hieromin 
Published: October 2019

Purpose
This paper aims to examine the challenges facing fish farmers in the use of information and communication technology (ICT) in information sharing on fish farming.

Design/methodology/approach
This study used both quantitative and qualitative methods. It involved 240 fish farmers who were randomly selected. Questionnaires, focus group discussions (FGDs), observation and key informant’s interviews were used as methods of data collection. Both descriptive and inferential statistics were used to analyse quantitative data, while content analysis was used for qualitative data.

Findings
It was found that the most frequently used ICTs by fish farmers in sharing agricultural information were mobile phones, radio and television. Also, the study revealed that major challenges facing fish farmers in sharing information include unfavourable radio or television broadcasting time, high cost of acquiring and maintenance of ICT facilities, lack of training on ICT, poor network connectivity and low level of literacy. Moreover, it was further found that there was negative significant relationship (P < 0.05) between challenges associated with the use and degree of ICT usage by fish farmers.

Originality/value
The study is original with the exception of areas where citations have been made. Besides, it provides awareness and understanding of the challenges facing fish farmers in ICT usage in information sharing on fish farming, and this will enable improvement of timely provision and access to relevant information and hence improved fish farming production.
Analysis of barriers in implementation of digital transformation of supply chain using interpretive structural modelling approach
Authors: Agrawal Prakash , Narain Rakesh , Ullah Inayat 
Published: October 2019

Purpose
Digital supply chain (DSC) is an agile, customer-driven and productive way to develop different forms of returns for companies and to leverage efficient approaches with emerging techniques and data analytics. Though the advantages of digital supply chain management (DSCM) are many, its implementation is quite slow for several reasons. The purpose of this paper is to identify the major barriers which hinder the adoption of DSC and to analyse the interrelationship among them. The barriers of DSC are explored on the basis of existing literature and experts’ opinion.

Design/methodology/approach
This paper uses the interpretive structural modelling (ISM) approach to develop a hierarchical structural model which shows the mutual dependence among the barriers of DSC. Cross-impact matrix multiplication applied to classification analysis was performed to represent these barriers graphically on the basis of their driving power and dependence.

Findings
The research demonstrates that the barriers “no sense of urgency”, “lack of industry specific guidelines”, “lack of digital skills and talent” and “high implementation and running cost” are the most significant barriers to digital transformation of supply chain. This paper also suggests some managerial implications to overcome the barriers which hinder the implementation of digital transformation of supply chain.

Practical implications
This paper assists managers and policymakers to understand the order in which these barriers must be tackled and adopts a roadmap for successful implementation of DSCM and reap its benefits.

Originality/value
This is one of the initial research studies which has analysed the barriers of DSC using ISM approach.
Effects of processing conditions on mechanical properties of PLA printed parts
Authors: Behzadnasab Morteza , Yousefi Ali Akbar , Ebrahimibagha Dariush , Nasiri Farahnaz 
Published: October 2019

Purpose
With recent advances in additive manufacturing (AM), polymer-based three-dimensional (3D) printers are available for relatively low cost and have found their way even in domestic and educational uses. However, the optimum conditions for processing and post-processing of different materials are yet to be determined. The purpose of this paper is to examine the effects of printing temperature, pattern and annealing conditions on tensile strength and modulus of samples printed with polylactic acid (PLA).

Design/methodology/approach
This study focuses on fused deposition modelling according to ISO/ASTM 52900 material extrusion AM. To print parts with maximum mechanical properties, the printing variables must be optimised. To determine the printing and annealing condition on physical and mechanical properties of PLA-based parts, dogbone-shaped tensile samples were printed at four different nozzle temperatures and five different filling patterns embedded in a 3D printing software. The samples were further annealed at three different temperatures for three different time intervals. The mechanical properties were evaluated and the changes in mechanical properties were analysed with the help of rheometrical measurements.

Findings
The results showed that printing condition has a significant influence on final properties, for example, the strain at break value increases with increasing nozzle temperature from 34 to 56 MPa, which is close to the value of the injected sample, namely, 65 MPa. While tensile strength increases with printing temperature, the annealing process has negative effects on the mechanical properties of samples.

Originality/value
The authors observed that traditional findings in polymer science, for example, the relationship between processing and annealing temperature, must be re-evaluated when applied in 3D printing because of major differences in processing conditions resulting from the layer-by-layer manufacturing.
Mutations in the CDSN gene cause peeling skin disease and hypotrichosis simplex of the scalp
Authors: van der Velden Jaap J. A. J. , van Geel Michel , Engelhart Jans J. , Jonkman Marcel F. , Steijlen Peter M. 
Published: October 2019

AbstractPeeling skin disease is a rare genodermatosis characterized by superficial exfoliation or peeling of the skin. Peeling skin disease is caused by biallelic mutations in CDSN as an autosomal recessive trait. Monoallelic mutations in CDSN have also been described in an autosomal dominant inherited genodermatosis: hypotrichosis simplex of the scalp. This disease is characterized by progressive hair loss of the scalp with onset after early childhood. Clinical data were obtained from a patient with lifelong generalized skin peeling and both his parents. The patient's parents did not suffer from skin peeling, but the mother had a history of thin scalp hair since early childhood. Mutation analysis in the patient showed compound heterozygous mutations in exon 2 of CDSN, a nonsense mutation c.598C>T (p.[Gln200*]), previously associated with hypotrichosis simplex of the scalp, and a frame‐shift mutation c.164_167dup (p.[Thr57Profs*6]), previously described in peeling skin disease. The p.(Gln200*) mutation was also found in the mother of the proband. Our study strengthens the previously established link between mutations in CDSN to peeling skin disease and hypotrichosis simplex of the scalp.
Oncolytic viruses: what to expect from their use in cancer treatment
Authors: Terrível Maria , Gromicho Catarina , Matos Ana Miguel 
Published: October 2019

AbstractOncolytic viruses are biologic agents able to selectively infect and destroy cancer cells while sparing the normal ones. Furthermore, they also stimulate the host immune system to combat the tumor growth and to promote tumor removal. This review thoroughly describes different types of viruses developed for targeting specific cancers, as well as the strategies to improve the efficacy and safety of oncolytic virotherapy. It also explores how their potential as anticancer agents may be enhanced through combination with other traditional therapies, such as chemotherapy or more recent approaches, such as checkpoint inhibitors. There are many oncolytic viruses currently being tested in clinical trials for the treatment of various types of cancer, suggesting that this approach could become the near future of the oncology field.
Rubber agroforestry in Thailand provides some biodiversity benefits without reducing yields
Authors: Warren‐Thomas Eleanor , Nelson Luke , Juthong Watinee , Bumrungsri Sara , Brattström Oskar , Stroesser Laetitia , Chambon Bénédicte , Penot Éric , Tongkaemkaew Uraiwan , Edwards David P. , Dolman Paul M. 
Published: October 2019

Abstract

Monocultural rubber plantations have replaced tropical forest, causing biodiversity loss. While protecting intact or semi‐intact biodiverse forest is paramount, improving biodiversity value within the 11.4 million hectares of existing rubber plantations could offer important conservation benefits, if yields are also maintained. Some farmers practice agroforestry with high‐yielding clonal rubber varieties to increase and diversify incomes. Here, we ask whether such rubber agroforestry improves biodiversity value or affects rubber yields relative to monoculture.

We surveyed birds, fruit‐feeding butterflies and reptiles in 25 monocultural and 39 agroforest smallholder rubber plots in Thailand, the world's biggest rubber producer. Management and vegetation structure data were collected from each plot, and landscape composition around plots was quantified. Rubber yield data were collected for a separate set of 34 monocultural and 47 agroforest rubber plots in the same region.

Reported rubber yields did not differ between agroforests and monocultures, meaning adoption of agroforestry in this context should not increase land demand for natural rubber. Butterfly richness was greater in agroforests, where richness increased with greater natural forest extent in the landscape. Bird and reptile richness were similar between agroforests and monocultures, but bird richness increased with the height of herbaceous vegetation inside rubber plots.

Species composition of butterflies differed between agroforests and monocultures, and in response to natural forest extent, while bird composition was influenced by herbaceous vegetation height within plots, the density of non‐rubber trees within plots (representing agroforestry complexity) and natural forest extent in the landscape. Reptile composition was influenced by canopy cover and open habitat extent in the landscape. Conservation priority and forest‐dependent birds were not supported within rubber.

Synthesis and applications. Rubber agroforestry using clonal varieties provides modest biodiversity benefits relative to monocultures, without compromising yields. Agroforests may also generate ecosystem service and livelihood benefits. Management of monocultural rubber production to increase inter‐row vegetation height and complexity may further benefit biodiversity. However, biodiversity losses from encroachment of rubber onto forests will not be offset by rubber agroforestry or rubber plot management. This evidence is important for developing guidelines around biodiversity‐friendly rubber and sustainable supply chains, and for farmers interested in diversifying rubber production.
MicroRNA‐147b suppresses the proliferation and invasion of non‐small‐cell lung cancer cells through downregulation of Wnt/β‐catenin signalling via targeting of RPS15A
Authors: Ning Qian , Pang Yamei , Shao Shan , Luo Minna , Zhao Lin , Hu Tinghua , Zhao Xinhan 
Published: October 2019

AbstractDeregulation of microRNAs (miRNAs) leads to malignant growth and aggressive invasion during cancer occurrence and progression. miR‐147b has emerged as one of the cancer‐related miRNAs that are dysregulated in multiple cancers. Yet, the relevance of miR‐147b in non‐small‐cell lung cancer (NSCLC) remains unclear. In the present study, we aimed to report the biological function and signalling pathways mediated by miR‐147b in NSCLC. Our results demonstrate that miR‐147b expression is significantly downregulated in NSCLC tissues and cell lines. Overexpression of miR‐147b decreased the proliferative ability, colony‐forming capability, and invasive potential of NSCLC cells. Notably, our study identified ribosomal protein S15A (RPS15A), an oncogene in NSCLC, as a target gene of miR‐147b. Our results showed that miR‐147b negatively modulates RPS15A expression in NSCLC cells. An inverse correlation between miR‐147b and RPS15A was evidenced in NSCLC specimens. Moreover, miR‐147b overexpression downregulated the activation of Wnt/β‐catenin signalling via targeting of RPS15A. Overexpression of RPS15A partially reversed the miR‐147b‐mediated antitumour effect in NSCLC cells. Collectively, these findings reveal that miR‐147b restricts the proliferation and invasion of NSCLC cells by inhibiting RPS15A‐induced Wnt/β‐catenin signalling and suggest that the miR‐147b/RPS15A/Wnt/β‐catenin axis is an important regulatory mechanism for malignant progression of NSCLC.
miR‐138 mediates sorafenib‐induced cell survival and is associated with poor prognosis in cholangiocarcinoma cells
Authors: Zheng Yingjie , Zhang Jingyu , Ye Bin 
Published: October 2019

AbstractCholangiocarcinoma is an aggressive malignancy with rapid invasion, metastasis and poor prognosis, however, the mechanism mediating its cholangiocarcinoma development needs further investigation. Here, we demonstrate that decreased miR‐138 in tumor tissues is related to the poor prognosis in patients, and that miR‐138 mediates sorafenib‐induced cell survival in cholangiocarcinoma cells. Moreover, miR‐138 negatively regulates SOX4 expression by specifically targeting its 3′ untranslated region (3′ UTR). As per our results, overexpression of SOX4 reversed sorafenib‐induced changes in cell viability and apoptosis. Furthermore, the elevated levels of SOX4 in the tumor tissues that correlated with poor prognosis. Overall, the present study reveals that miR‐138/SOX4 is involved in sorafinib‐mediated cell survival in cholangiocarcinoma cells, and is associated with poor prognosis.