bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying transposon insertions in bacterial genomes through nanopore sequencing
Authors: Baltrus David A. , Medlen John , Clark Meara 
Published: September 2019

AbstractTransposon mutagenesis is a widely used tool for carrying out forward genetic screens across systems, but in some cases it can be difficult to identify transposon insertion points after successful phenotypic screens. As an alternative to traditional methods, we report on the efficacy of using an Oxford Nanopore’s MinION to identify transposon insertions through whole genome sequencing. We also report experiments using CRISPR-Cas to selectively target regions of the genome where a transposon has integrated. Our experiments provide a framework for understanding the efficiency of such techniques for carrying out forward genetic screens and point towards the ability to use CRISPR-based sequence capture to identify the insertion of particular regions of DNA across all genomes, which may enable Tn-Seq experiments using Nanopore based sequencing.
Tooth Shape Adaptations in Aglyphous Colubrid Snakes Inferred from 3D Geometric Morphometrics and Finite Element Analysis
Authors: Rajabizadeh Mahdi , Van Wassenbergh Sam , Mallet Christophe , Rücklin Martin , Herrel Anthony 
Published: September 2019

AbstractTo date there are few detailed and quantitative studies investigating the evolution of the tooth shape and function in Aglyphous snakes in relation to diet. To study dental adaptations to diet, a lineage that is of particular interest due to its large range of adult body sizes, is the one including dwarfed snakes of the genus Eirenis and their immediate sister group, whip snakes of the genus Dolichophis. A considerable evolutionary decrease in the size is observed from a Dolichophis-like ancestor to the miniature Eirenis, coupled with a considerable shift in their diet from a regime consisting mainly of endotherms with endoskeleton to ectotherms bearing a hard exoskeleton. Maxilla, palatine, pterygoid and dentary teeth were examined in an adult and a juvenile of Dolichophis schmidti, one Eirenis punctolineatus and one Eirenis persicus. 3D Geometric Morphometrics comparison revealed maxilla and palatine teeth of the E. persicus are blunt and conical shape while those teeth are sharp and elongated in E. punctatolineatus as well as the adult and juvenile D. schmidti. A similar difference could be noted for the pterygoid teeth. In contrast, the dentary teeth are not as different among the examined snakes. Blunt and conically shaped teeth, as observed in E. persicus, seem to be more adapted for biting hard bodied, arthropod prey, while sharp and elongated teeth in Dolichophis and E. punctatolineatus, are specialized for puncturing endotherm prey. The results of a finite element analysis confirms that during biting a hard bodied prey, the generated stresses in E. persicus tooth is mostly confined to the tip of the tooth and mostly well below the von Mises yield criterion the tooth. In contrary, D. schmidti tooth appears less well suited for biting a hard prey since the generated stresses widely distribute across the tooth with values roughly 2 to 3 times higher than the von Mises yield criterion of the tooth. A lower degree of specialization that was observed among the dentary teeth in the examined snakes suggest a similar functional constraint in pushing the prey against the upper tooth rows.
AstroDot: a new method for studying the spatial distribution of mRNA in astrocytes
Authors: Oudart Marc , Tortuyaux Romain , Mailly Philippe , Mazaré Noémie , Boulay Anne-Cécile , Cohen-Salmon Martine 
Published: September 2019

AbstractCells with a complex shape often use mRNA distribution and local translation to regulate distal functions. These mechanisms have recently been described in astrocytes, the processes of which contact and functionally modulate neighbouring synapses and blood vessels. In order to study the distribution of mRNA in astrocytes, we developed a three-dimensional histological method that combines mRNA detection viain situhybridization with immunostaining of the astrocyte-specific intermediate filament glial fibrillary acidic protein (GFAP). Three-dimensional confocal images were analyzed using AstroDot, a custom Image J plug-in developed in-house for the identification and quantification of mRNAs in GFAP-immunolabelled astrocyte somata, large processes and fine processes. The custom R package AstroStat was used to analyze the AstroDot results. Taking the characterization of mRNAs encoding the astrocyte-specific GFAP α and δ isoforms in the hippocampus as a proof of concept, we showed thatGfapα andGfapδ mRNAs mainly colocalized with GFAP in astrocyte processes.Gfapα mRNA was more abundant thanGfapδ mRNA, and was predominantly found in fine processes. Upon glial activation in the APPswe/PS1dE9 mouse model of Alzheimer’s disease, the same overall patterns were found but we noted strong variations inGfapα andGfapδ mRNA density and distribution as a function of the part of the hippocampus and the astrocyte’s proximity to beta-amyloid (Aβ) plaques. In astrocytes not associated with Aβ, Gfap α mRNA levels were only slightly elevated, and Gfap δ mRNA was distributed within the fine processes; these effects were more prominent in CA3 than in CA1. In contrast, levels of both mRNAs were markedly elevated in the fine processes of Aβ-associated astrocytes in both CA1 and CA3. In order to validate our new method, we confirmed thatRpl4mRNA (a ubiquitously expressed mRNA encoding the large subunit ribosomal protein 4) was present in large and fine processes in both astrocytes and microglia. In summary, we have developed a novel, reliable set of tools for characterizing mRNA densities and distributions in the somata and processes of astrocytes and microglia in physiological or pathological settings. Furthermore, our results suggest that intermediate filaments are crucial for distributing mRNA within astrocytes and for modulating specificGfapmRNA profiles in Alzheimer’s disease.
Prediction of best features in heterogeneous Lung adenocarcinoma samples using Least Absolute Shrinking and Selection Operator
Authors: Khaliq Ateeq Muhammed , Sharathchandra RG , Rajamohan Meenakshi 
Published: September 2019

AbstractThis study aims to create a tumor heterogeneity-based model for predicting the best features of lung adenocarcinoma (LUAD) in multiple cancer subtypes using the Least Absolute Shrinking and Selection Operator (LASSO). The RNA-Seq raw count data of 533 LUAD samples and 59 normal samples were downloaded from the TCGA data portal. Based on consensus clustering method samples was divided into two subtypes, and clusters were validated using silhouette width. Furthermore, we estimated subtypes for the abundance of immune and non-immune stromal cell populations which infiltrated cancer tissue. We established the LASSO model for predicting each subtype’s best features. Enrichment pathway analysis was then carried out. Finally, the validity of the LASSO model for identifying features was established by the survival analysis. Our study suggests that the unsupervised clustering and Machine learning methods such as LASSO model-based feature selection can be effectively used to predict relevant genes which might play an essential role in cancer diagnosis.
Analysis of South African universities and communities archives
Authors: Netshakhuma Nkholedzeni Sidney 
Published: September 2019

Purpose
The purpose of this study to investigate the relationships between South Africa (SA) universities and universities surrounding communities (USC) for preserving community histories and serve the universities’ mandate to support their local communities and support universities’ teaching and scholarship.

Design/methodology/approach
The study used a multiple case study approach through interviews. The population of the study comprised representatives from selected universities and their USC.

Findings
The findings revealed a lack of effective relationships between universities and USC to preserve communities’ histories. Hence, the communities’ archives are tools for teaching and scholarship. Relations between universities and USC are to be built on trust. Accountability and transparency are to be considered by both parties.

Research limitations/implications
The research is limited to selected SA universities, namely, University of Venda, Witwatersrand, Johannesburg, Pretoria and SA and USC. The findings are applicable to all SA universities and USC.

Practical implications
The relationship between universities and USC has a practical impact on the National archives of South Africa (NARSSA) to collect communities archives because it is in conflict with the mandate of NARSSA. The National Archives’ Act 43 of 1996 obliged NARSSA to collect and preserve communities’ archives on behalf of societies.

Social implications
Lack of universities and USC can lead to the loss of communities histories or archives.

Originality/value
This paper appears to be the first to research the relationship between SA universities and USC.
An IoMT-based geriatric care management system for achieving smart health in nursing homes
Authors: Tang Valerie , Choy K.L. , Ho G.T.S. , Lam H.Y. , Tsang Y.P. 
Published: September 2019

Purpose
The purpose of this paper is to develop an Internet of medical things (IoMT)-based geriatric care management system (I-GCMS), integrating IoMT and case-based reasoning (CBR) in order to deal with the global concerns of the increasing demand for elderly care service in nursing homes.

Design/methodology/approach
The I-GCMS is developed under the IoMT environment to collect real-time biometric data for total health monitoring. When the health of an elderly deteriorates, the CBR is used to revise and generate the customized care plan, and hence support and improve the geriatric care management (GCM) service in nursing homes.

Findings
A case study is conducted in a nursing home in Taiwan to evaluate the performance of the I-GCMS. Under the IoMT environment, the time saving in executing total health monitoring helps improve the daily operation effectiveness and efficiency. In addition, the proposed system helps leverage a proactive approach in modifying the content of a care plan in response to the change of health status of elderly.

Originality/value
Considering the needs for demanding and accurate healthcare services, this is the first time that IoMT and CBR technologies have been integrated in the field of GCM. This paper illustrates how to seamlessly connect various sensors to capture real-time biometric data to the I-GCMS platform for responsively supporting decision making in the care plan modification processes. With the aid of I-GCMS, the efficiency in executing the daily routine processes and the quality of healthcare services can be improved.
Consumer behavior in the omni-channel supply chain under social networking services
Authors: Yan Bo , Chen Yan-Ru , Zhou Xiao-Tai , Fang Jing 
Published: September 2019

Purpose
The purpose of this paper is to analyze how social networking services (SNSs) affect consumers’ behaviors on the omni-channel supply chain by using a reverse research method.

Design/methodology/approach
Initially, a questionnaire was administered to obtain data on the relationship between the perception factors of channels and consumer behavior. Subsequently, a structural equation model was constructed, and consumer behavior were determined in the omni-channel supply chain. Finally, the importance of various factors that affected consumer behavior in the omni-channel supply chain under SNSs was determined.

Findings
Conclusions affirm that a positive effect on consumer channel behaviors occurs when buyers obtain information from social network platforms. However, regardless of online, offline, or mobile terminal, shortcomings are indicated in consumers’ lack of feedback on purchased goods and the bias of feedback.

Originality/value
The study explored ways to efficiently apply SNSs in building the omni-channel supply chain. Meanwhile, corresponding suggestions were provided such that companies will know about consumer needs.
An assessment of effects of non-stationary operational conditions on wind turbine under different wind scenario
Authors: Hulio Zahid Hussain , Jiang Wei 
Published: September 2019

Purpose
The non-stationary operational wind loads vary in time and site and has remarkable effect on wind turbine drive train. The purpose of this paper is to determine the effects of wind class 3 and 7 on the life of wind turbine drive train. The two-wind class 3 and 7 are described by average wind speed and weight factor and effects of two variables on wind energy generation and wind turbine drive train studied.

Design/methodology/approach
The load distribution method is used to calculate stress range cycles for wind class 3 and 7. To determine the rise of force on wind turbine drive train, the load cycle method is proposed. The fatigue damage model is studied with respect to influence of different wind speeds and wind shear factor and then results analysed accordingly. Also sensitivity analysis has been carried out to assess the percentage of drop of energy generation and rise of tangential force for wind class 3 and 7. Linear fit method is used to determine the inclination of wind variation and wind shear of wind class 3 and 7. In this regard, two practical wind sites fall under the wind class 3 and 7 and 1.5 MW wind turbine have been taken in to account.

Findings
The results showed that the average rise of force on wind turbine drive train is 37.5% which can influence the drop in energy 34.7% for wind class 3. Similarly, the results of wind class 7 are showing that the average rise in force and drop in energy found to be 49.05% and 51.16%, respectively. The wind class 7 have higher tendency of wind fluctuations and weight factor that can cause a damage to wind turbine drive train components. The results showed that when wind speed increases to rated power 11.5 m/s the damages occurred and remain steady. Similarly, when weight factor increased from 0.18 to onwards the damage occurred. The increased wind loads increased the tangential loads on the wind turbine decreased life of the gearbox.

Originality/value
The results of study suggest that wind turbine should be design according to site specific wind environment for maximum energy generation and lowers the wind loads on the drive train component.
Intentions of entrepreneurship in sports science higher education: gender the moderator effect
Authors: Puyana Moisés Grimaldi , Gálvez-Ruiz Pablo , Sánchez-Oliver Antonio Jesús , Fernández Jerónimo García 
Published: September 2019

Purpose
The purpose of this paper is to understand the current relationship between factors such as desire and viability and entrepreneurial intention, using the Business Event Model as a point of analysis, as well as to understand the influence of gender as a moderating effect on entrepreneurial intention.

Design/methodology/approach
A total of 278 students from the Faculty of Education Sciences (University of Seville) were invited to participate with students carrying out degrees in Physical Activity and Sport Sciences.

Findings
There is a positive and similar relationship between desire and viability due to gender-related reasons. In the same way, this study presents a positive relationship in men and women, between desire and viability, desire and entrepreneurial intention and viability and entrepreneurial intention.

Practical implications
The public policies of the university should be oriented to the promotion of the desire perceived in women, carrying out sessions or training courses, where the speakers could be women leaders of companies. In addition, public policies should promote the perceived viability of men through training by providing technical resources on the operation of a company.

Social implications
This study provides theoretical knowledge on the entrepreneurial intentions of students at the University of Seville and therefore may help to improve policies aimed at promoting entrepreneurship.

Originality/value
This study provides clear practical implications for the management of students, and the findings facilitate the improvement of university policies designed to promote entrepreneurship in this type of student.
Porous ceramic foam loading titanium dioxide for photocatalytic degradation of the methyl orange solution
Authors: Guo Y.J. , Cheng W. , Liu P.S. 
Published: September 2019

Purpose
The purpose of this paper is to provide an investigation on a new kind of photocatalytic material, namely, the porous ceramic foam loading titanium dioxide, which can make an effective photocatalytic degradation of the methyl orange (MO) solution in the wastewater.

Design/methodology/approach
The natural zeolite powder has been used as the primary raw material to produce a sort of lightweight porous ceramic foam by impregnating polymer foam in slurry and then sintering. With the sol-gel method, a kind of open-cell reticular porous ceramic foam loading TiO2 film was obtained having a good photocatalytic action, and the resultant porous composite product presents the bulk density of 0.3~0.6 g/cm3 to be able to float on water.

Findings
The MO could tend to be completely degraded in the solution with a certain concentration by the TiO2-loaded ceramic foam irradiated with ultraviolet light, and this composite foam was found to have high degradation efficiency for the MO solution in a wide range of pH.

Originality/value
This work presents a TiO2-loaded ceramic foam that can effectively photo-catalyze to degrade the MO in water, and the degradation efficiency were examined under different conditions of the MO solution with various pH values.
Prediction of geometric characteristics in polycaprolactone (PCL) scaffolds produced by extrusion-based additive manufacturing technique for tissue engineering
Authors: Lee Jiwoon , Walker Jesse , Natarajan Sanjay , Yi Sung 
Published: September 2019

Purpose
Extrusion-based additive manufacturing (AM) has been considered as a promising technique to fabricate scaffolds for tissue engineering due to affordability, versatility and ability to print porous structures. The reliability and controllability of the printing process are necessary to produce 3D-printed scaffolds with desired properties and depend on the geometric characteristics such as porosity and pore diameter. The purpose of this study is to develop an analytical model and explore its effectiveness in the prediction of geometric characteristics of 3D-printed scaffolds.

Design/methodology/approach
An analytical model was developed to simulate the geometric characteristics of scaffolds produced by extrusion-based AM using fluid mechanics. Polycaprolactone (PCL) was chosen as a scaffold material and was assumed to be a non-Newtonian fluid for the model. The effectiveness of the model was verified through comparison with the experimental results.

Findings
A comparison study between simulation and experimental results shows that strut diameter, pore size and porosity of scaffolds can be predicted by using extrusion pressure, temperature, nozzle diameter, nozzle length and printing speed. Simulation results demonstrate that geometric characteristics have a strong relationship with processing parameters, and the model developed in this study can be used for predicting the scaffold properties for the extrusion-based 3D bioprinting process.

Originality/value
The present study provides a prediction model that can simulate the printing process by a simple input of processing parameters. The geometric characteristics can be predicted prior to the experimental verification, and such prediction will reduce the process time and effort when a new material or method is applied.
Antecedents of brand hate in the fast food industry
Authors: Hashim Sharizal , Kasana Sheraz 
Published: September 2019

PurposeThe purpose of this paper is to explore the concept of brand hate in detail which is the extreme negative emotion toward brands, by giving a comprehensive explanation concerning how brand hate evolves in consumers. More specifically, antecedents of brand hate are empirically assessed in this study.Design/methodology/approachThis study used primary data from 250 fast food brand consumers in Pakistan. Multiple regression analysis in SPSS was used to test the hypotheses related to the antecedents of brand hate.FindingsResults indicate that brand hate is instigated by five antecedents, which are negative past experience, symbolic incongruity, poor relationship quality, ideological incompatibility and rumor, with rumor being the biggest instigator.Originality/valueAntecedents of brand hate are assessed theoretically and empirically in this study which helps in understanding the true form of brand hate. More specifically, poor relationship quality and rumor are presented as the antecedents of brand hate according to the recommendations of the theory of hate.
From individuals to the organization
Authors: El-Awad Ziad 
Published: September 2019

Purpose
This study aims to develop a process model that details the mechanisms and learning processes by which entrepreneurial learning transpires at multiple levels in the organization. Using the transactive memory system (TMS) framework as a reference, the model specifies how individual streams of knowledge are routinized in nonhuman elements and, over time, become embedded in organizational routines and procedures.

Design/methodology/approach
The research uses a case-study methodology building on 18 in-depth semi-structured interviews, 20 h of non-participative observations and internal company documents.

Findings
The study demonstrates that knowledge is channeled from individuals to the organization via mechanisms that operate at the venture-team level – principally externalizing distinctions; rotating task work; co-constructing the task; and routinizing behavior. These mechanisms are fundamental for creating knowledge repertoires on which team members can build and for channeling different knowledge domains into the organization.

Originality/value
The study offers a dynamic view of entrepreneurial learning, underlining the structural and transactive components of TMS as being foundational for embedding knowledge in organizational routines and procedures.
Look to seedling heights, rather than functional traits, to explain survival during extreme heat stress in the early stages of subtropical rainforest restoration
Authors: Gardiner Ronald , Shoo Luke P. , Dwyer John M. 
Published: September 2019

Abstract

Ecological restoration is urgently needed to arrest and reverse land degradation, reinstate ecosystem services and recover threatened species. Tree planting is a commonly used strategy to restore forests; however, planted seedlings often experience low survival and slow growth during the establishment period. Critical evaluation of factors that lead to poor establishment is vital to improve practice but is often constrained by a lack of monitoring and reporting.

We took advantage of a large monitoring dataset (~7,000 native trees from 23 species) to interrogate an extensive suite of environmental conditions and plant characteristics that potentially contributed to poor survival and growth of seedlings in a restoration planting in southeast Queensland, Australia.

The initial height of planted seedlings strongly influenced survival and growth. Intermediate heights generally performed best and the optimal heights for different species were significantly but weakly modulated by functional traits including SLA, lamina area and leaf structure (compound vs. simple). Survival was lowest when seedlings were planted in high bulk density soils on hot days, and growth was fastest in plots with higher average elevation.

Synthesis and applications. In this large restoration experiment in Australia's subtropics, initial seedling height was a much stronger predictor of rainforest seedling survival than plant functional traits. We recommend planting rainforest seedlings between 25 and 35 cm tall, especially in restoration projects facing a high likelihood of hot weather during planting and establishment.