bluuebunny/crossref_metadata_2025_split huggingface dataset:
Empirical verification of the “TACT” framework for teaching rigour in qualitative research methodology
Authors: Daniel Ben Kei 
Published: March 2018

Purpose
The purpose of this paper is to present a framework intended to guide students and novice researchers in learning about the necessary dimensions for assessing the rigour of qualitative research studies. The framework has four dimensions – (T)rustworthiness, (A)uditability, (C)redibility and (T)ransferability. The development of TACT is informed by various discourses of rigour in the qualitative research methods literature. Results of an empirical verification of TACT suggests that postgraduate students and faculty learning qualitative research found the framework useful for learning rigour in qualitative research methods. TACT also serves as an important theoretical tool for setting directions for further discourses on teaching and learning critical aspects of rigour in qualitative research methodology.

Design/methodology/approach
The formal verification of the TACT started with a development of a rating tool. The tool consisted of a total of 16 items, 4 items per each dimension. The items were ranked on five-scale Likert points (1=very important, 2=important, 3=neutral, 4=less important, 5=not important). The instrument was piloted and tested for reliability revealing an overall Cronbach’s α (α=0.86), which indicates a good level of internal consistency (George and Mallery, 2003) among the dimensions. The tool was put online and sent out to participants enroled in workshops on “assessing rigour in qualitative research studies”.

Findings
Overall, participants found TACT to be a useful framework for learning different dimensions for assessing qualitative research. They saw various benefits associated with the use of the framework including providing a better process for undertaking and reporting outcomes of qualitative research and for exploring different dimensions of rigour. Participants also indicated that using TACT facilitates reflexivity and fosters dependability of research outcomes. They stated that TACT could help researchers think about their personal relationship with a phenomenon being studied as well as the quality of data collected. Others said that TACT allows researchers to think about achieving transference and gaining confidence in the research findings.

Research limitations/implications
TACT is best suited as a teaching toolkit in qualitative research methodology courses. It is also useful as a platform for fostering a shared language in undertaking peer-review of methodological dimensions of qualitative research studies.

Practical implications
Though a general framework for accessing rigour in qualitative research studies is highly desirable, the usefulness of TACT in rendering rigour is subject to a particular academic tradition.

Social implications
TACT facilitates the exploration of different dimensions for assessing the outcome of qualitative research.

Originality/value
TACT is a general framework drawn from the literature and teaching practice and empirically validated.
Influence of intersections on the performance of position-based routing protocols for VANETs
Authors: Mansoor Ali Mohammed , Sarea Adel Mohammed , Md Sabri Aznul Qalid 
Published: March 2018

Purpose
The vehicular ad hoc network (VANET) is an emerging area for smart cities as observed in last few decades. However, some hurdles for VANET exist that need to be resolved before its full implementation in smart cities. Routing is one of the main factors for having effective communication between smart vehicles that urgently needs to be addressed. One factor that affects communication between the vehicles is the intersection points that obstruct the communication. The paper aims to discuss these issues.

Design/methodology/approach
The conventional routing schemes fail to address the intersection problems that occur during the two points of communication. Therefore, this paper analyses the performance of existing position-based routing protocol for inter-vehicle ad hoc networks, considering the impact of a number of intersections. This simulation evaluates different position-based routing protocols such as Intersection-based Distance and Traffic-Aware Routing (IDTAR), Greedy Traffic-Aware Routing, Anchor-based Street and Traffic-Aware Routing and Geographic Source Routing, based on road topology and the number of intersections.

Findings
As a result, the protocol IDTAR has a lower end-to-end delay and high packet delivery ratio in terms of the number of intersections as a case study of smart cities. This concludes that IDTAR can be adaptive to smart cities communication, although some questions need to be considered in terms of its security, compatibility, reliability and robustness.

Practical implications
The role of VANET has been highlighted in smart cities due to its implications in day-to-day life. The vehicles in VANET are equipped with wireless communication nodes to provide network connectivity. Such types of network operate without the legacy infrastructure, as well as legacy client/servers.

Originality/value
Additionally, the study contributes to smart cities by measuring the performance of position-based routing protocols for VANETs.
Environmental-related patent technology transfer effectiveness
Authors: Ferreira João J. , Fernandes Cristina , Ratten Vanessa 
Published: March 2018

PurposeEnvironmental-related technology transfer is increasingly being viewed as a policy issue and a business goal to be pursued by countries in order to increase their global competitiveness. Despite this policy importance, the research analysing environmental-related technology transfer comparing international rates of participation is limited. The paper aims to discuss this issue.Design/methodology/approachThe authors analyse the Organisation for Economic Co-operation and Development (OECD) data using econometric analysis to compare environmental-related technology patents between Portugal and Australia in terms of environmental management, water-related adaptation, and climate change mitigation.FindingsThe results suggest that environmental-related patents, in turn, are always registered in greater numbers by Australia than by Portugal but with both countries outpaced by the OECD average.Research limitations/implicationsThe research implications are that Australia has more international cooperation around the development of environmental-related technology patents than Portugal.Practical implicationsThe authors find that overall these patents do not have any statistically significant effect on predicting gross domestic product growth but there has been a higher number of patents for Australia focusing on water-related adaptation technology than for Portugal, which may be a result of policies aimed at increasing effective use of water in Australia.Originality/valueThe results of the analysis suggest that the OECD member state cooperation increases the number of environmental-related technology patents and serves as a mechanism to facilitate internationalisation.
eDNA Sampler: A fully integrated environmental DNA sampling system
Authors: Thomas Austen C. , Howard Jesse , Nguyen Phong L. , Seimon Tracie A. , Goldberg Caren S. 
Published: March 2018

Abstract

Species monitoring using environmental DNA (eDNA) is a powerful new technique for natural resource scientists and the number of research groups employing eDNA detection is growing rapidly. However, current eDNA sampling technologies consist mainly of do‐it‐yourself solutions, and the lack of purpose‐built sampling equipment is limiting the efficiency and standardization of eDNA studies.

Here, we describe the first fully integrated sampling system (Smith‐Root eDNA Sampler) designed by a team of molecular ecologists and engineers for high‐throughput eDNA sample collection. It consists of a backpack portable pump that integrates sensor feedback, a pole extension with remote pump controller, custom‐made filter housings in single‐use packets for each sampling site and onboard sample storage. The system is optimized for sampling speed and replicability, while minimizing risk of contamination.

We present an example pilot study designed to identify optimal eDNA Sampler system parameter values (i.e. pump pressure, flow rate, filter pore size, sample volume) in a new sampling environment. We identified a peak in filtration efficiency at a flow rate threshold of 1.0 L/m, and found that 5 μm filters captured significantly more target eDNA than 1 μm filters. Results also suggest that high filtration pressures may reduce eDNA retention, which implies that pressure should be standardized to avoid biasing detection data.

Similar to the technological evolution of backpack electrofishers, eDNA sampling technology is in the process of transitioning from a nascent phase to professionally engineered research tools. Such innovations will be essential as eDNA monitoring becomes one of the industry standard methods used for species detection and management.
Shigella sonnei Does Not Use Amoebae as Protective Hosts
Authors: Watson Jayne , Jenkins Claire , Clements Abigail 
Published: March 2018

ABSTRACT

Shigella flexneri
and
Shigella sonnei
bacteria cause the majority of all shigellosis cases worldwide. However, their distributions differ, with
S. sonnei
predominating in middle- and high-income countries and
S. flexneri
predominating in low-income countries. One proposed explanation for the continued range expansion of
S. sonnei
is that it can survive in amoebae, which could provide a protective environment for the bacteria. In this study, we demonstrate that while both
S. sonnei
and
S. flexneri
can survive coculture with the free-living amoebae
Acanthamoebae castellanii
, bacterial growth is predominantly extracellular. All isolates of
Shigella
were degraded following phagocytosis by
A. castellanii
, unlike those of
Legionella pneumophila
, which can replicate intracellularly. Our data suggest that
S. sonnei
is not able to use amoebae as a protective host to enhance environmental survival. Therefore, alternative explanations for
S. sonnei
emergence need to be considered.

IMPORTANCE
The distribution of
Shigella
species closely mirrors a country's socioeconomic conditions. With the transition of many populous nations from low- to middle-income countries,
S. sonnei
infections have emerged as a major public health issue. Understanding why
S. sonnei
infections are resistant to improvements in living conditions is key to developing methods to reduce exposure to this pathogen. We show that free-living amoebae are not likely to be environmental hosts of
S. sonnei
, as all
Shigella
strains tested were phagocytosed and degraded by amoebae. Therefore, alternative scenarios are required to explain the emergence and persistence of
S. sonnei
infections.
Genome Sequence of Coxiella-Like Endosymbiont Strain CLE-RmD, a Bacterial Agent in the Cattle Tick (Rhipicephalus microplus) Deutsch Strain
Authors: Ramaiah Arunachalam , Dasch Gregory A. 
Published: March 2018

ABSTRACT

We report a partial genome sequence for the
Coxiella
-like endosymbiont strain CLE-RmD, assembled from metagenomics data obtained from the southern cattle tick (
Rhipicephalus microplus
) Deutsch strain.
Complete Genome Sequences of Six Measles Virus Strains
Authors: Phan My V. T. , Schapendonk Claudia M. E. , Oude Munnink Bas B. , Koopmans Marion P. G. , de Swart Rik L. , Cotten Matthew 
Published: March 2018

ABSTRACT
Genetic characterization of wild-type measles virus (MV) strains is a critical component of measles surveillance and molecular epidemiology. We have obtained complete genome sequences of six MV strains belonging to different genotypes, using random-primed next generation sequencing.
Draft Genome Sequence of Escherichia coli KL53
Authors: Soltys Katarina , Vavrova Silvia , Budis Jaroslav , Palkova Lenka , Minarik Gabriel , Grones Jozef 
Published: March 2018

ABSTRACT

Here, we report the draft genome sequence of a clinical isolate of the uropathogenic strain
Escherichia coli
KL53. A total of 5,083,632 bp was
de novo
assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes. Remarkable is the presence of the tellurite resistance (
ter
) operon on a plasmid.
Coxiella burnetii Subverts p62/Sequestosome 1 and Activates Nrf2 Signaling in Human Macrophages
Authors: Winchell Caylin G. , Dragan Amanda L. , Brann Katelynn R. , Onyilagha Frances I. , Kurten Richard C. , Voth Daniel E. 
Published: March 2018

ABSTRACT

Coxiella burnetii
is the causative agent of human Q fever, a debilitating flu-like illness that can progress to chronic disease presenting as endocarditis. Following inhalation,
C. burnetii
is phagocytosed by alveolar macrophages and generates a lysosome-like replication compartment termed the parasitophorous vacuole (PV). A type IV secretion system (T4SS) is required for PV generation and is one of the pathogen's few known virulence factors. We previously showed that
C. burnetii
actively recruits autophagosomes to the PV using the T4SS but does not alter macroautophagy. In the current study, we confirmed that the cargo receptor p62/sequestosome 1 (SQSTM-1) localizes near the PV in primary human alveolar macrophages infected with virulent
C. burnetii
. p62 and LC3 typically interact to select cargo for autophagy-mediated degradation, resulting in p62 degradation and LC3 recycling. However, in
C. burnetii
-infected macrophages, p62 was not degraded when cells were starved, suggesting that the pathogen stabilizes the protein. In addition, phosphorylated p62 levels increased, indicative of activation, during infection. Small interfering RNA experiments indicated that p62 is not absolutely required for intracellular growth, suggesting that the protein serves a signaling role during infection. Indeed, the Nrf2-Keap1 cytoprotective pathway was activated during infection, as evidenced by sustained maintenance of Nrf2 levels and translocation of the protein to the nucleus in
C. burnetii
-infected cells. Collectively, our studies identify a new p62-regulated host signaling pathway exploited by
C. burnetii
during intramacrophage growth.
Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut
Authors: Wu Jikang , Sabag-Daigle Anice , Borton Mikayla A. , Kop Linnea F. M. , Szkoda Blake E. , Deatherage Kaiser Brooke L. , Lindemann Stephen R. , Renslow Ryan S. , Wei Siwei , Nicora Carrie D. , Weitz Karl K. , Kim Young-Mo , Adkins Joshua N. , Metz Thomas O. , Boyaka Prosper , Gopalan Venkat , Wrighton Kelly C. , Wysocki Vicki H. , Ahmer Brian M. M. 
Published: March 2018

ABSTRACT

Salmonella enterica
elicits intestinal inflammation to gain access to nutrients. One of these nutrients is fructose-asparagine (F-Asn). The availability of F-Asn to
Salmonella
during infection is dependent upon
Salmonella
pathogenicity islands 1 and 2, which in turn are required to provoke inflammation. Here, we determined that F-Asn is present in mouse chow at approximately 400 pmol/mg (dry weight). F-Asn is also present in the intestinal tract of germfree mice at 2,700 pmol/mg (dry weight) and in the intestinal tract of conventional mice at 9 to 28 pmol/mg. These findings suggest that the mouse intestinal microbiota consumes F-Asn. We utilized heavy-labeled precursors of F-Asn to monitor its formation in the intestine, in the presence or absence of inflammation, and none was observed. Finally, we determined that some members of the class
Clostridia
encode F-Asn utilization pathways and that they are eliminated from highly inflamed
Salmonella
-infected mice. Collectively, our studies identify the source of F-Asn as the diet and that
Salmonella
-mediated inflammation is required to eliminate competitors and allow the pathogen nearly exclusive access to this nutrient.
Degradation of a Novel DNA Damage Response Protein, Tankyrase 1 Binding Protein 1, following Adenovirus Infection
Authors: Chalabi Hagkarim Nafiseh , Ryan Ellis L. , Byrd Philip J. , Hollingworth Robert , Shimwell Neil J. , Agathanggelou Angelo , Vavasseur Manon , Kolbe Viktoria , Speiseder Thomas , Dobner Thomas , Stewart Grant S. , Grand Roger J. 
Published: March 2018

ABSTRACT
Infection by most DNA viruses activates a cellular DNA damage response (DDR), which may be to the detriment or advantage of the virus. In the case of adenoviruses, they neutralize antiviral effects of DDR activation by targeting a number of proteins for rapid proteasome-mediated degradation. We have now identified a novel DDR protein, tankyrase 1 binding protein 1 (TNKS1BP1) (also known as Tab182), which is degraded during infection by adenovirus serotype 5 and adenovirus serotype 12. In both cases, degradation requires the action of the early region 1B55K (E1B55K) and early region 4 open reading frame 6 (E4orf6) viral proteins and is mediated through the proteasome by the action of cullin-based cellular E3 ligases. The degradation of Tab182 appears to be serotype specific, as the protein remains relatively stable following infection with adenovirus serotypes 4, 7, 9, and 11. We have gone on to confirm that Tab182 is an integral component of the CNOT complex, which has transcriptional regulatory, deadenylation, and E3 ligase activities. The levels of at least 2 other members of the complex (CNOT3 and CNOT7) are also reduced during adenovirus infection, whereas the levels of CNOT4 and CNOT1 remain stable. The depletion of Tab182 with small interfering RNA (siRNA) enhances the expression of early region 1A proteins (E1As) to a limited extent during adenovirus infection, but the depletion of CNOT1 is particularly advantageous to the virus and results in a marked increase in the expression of adenovirus early proteins. In addition, the depletion of Tab182 and CNOT1 results in a limited increase in the viral DNA level during infection. We conclude that the cellular CNOT complex is a previously unidentified major target for adenoviruses during infection.

IMPORTANCE
Adenoviruses target a number of cellular proteins involved in the DNA damage response for rapid degradation. We have now shown that Tab182, which we have confirmed to be an integral component of the mammalian CNOT complex, is degraded following infection by adenovirus serotypes 5 and 12. This requires the viral E1B55K and E4orf6 proteins and is mediated by cullin-based E3 ligases and the proteasome. In addition to Tab182, the levels of other CNOT proteins are also reduced during adenovirus infection. Thus, CNOT3 and CNOT7, for example, are degraded, whereas CNOT4 and CNOT1 are not. The siRNA-mediated depletion of components of the complex enhances the expression of adenovirus early proteins and increases the concentration of viral DNA produced during infection. This study highlights a novel protein complex, CNOT, which is targeted for adenovirus-mediated protein degradation. To our knowledge, this is the first time that the CNOT complex has been identified as an adenoviral target.
Ethnic differences in the progression of chronic kidney disease and risk of death in a UK diabetic population: an observational cohort study
Authors: Mathur Rohini , Dreyer Gavin , Yaqoob Magdi M , Hull Sally A 
Published: March 2018

ObjectiveTo determine ethnic differences in the progression of chronic kidney disease (CKD) and risk of end-stage renal failure (ESRF) and death in adults with type 2 diabetes mellitus (T2DM), and to identify predictors of rapid renal decline.DesignObservational community-based cohort study undertaken from 2006 to 2016 with nested case–control study.Setting135 inner London primary care practices contributing to the east London Database.ParticipantsGeneral practice-registered adults aged 25–85 years with established T2DM and CKD at baseline.OutcomesThe annual rate of renal decline was compared between white, south Asian and black groups, and stratified by proteinuria and raised blood pressure (BP) at baseline. Predictors of rapid renal decline were identified in a nested case–control study. Cox proportional hazards regression was used to determine ethnic differences in the risk of ESRF and death.ResultsAge–sex adjusted annual decline was greatest in the Bangladeshi population. There was stepwise increase in the rate of decline when stratifying the cohort by baseline proteinuria and BP control, with south Asian groups being most sensitive to the combined effect of proteinuria and raised BP after accounting for key confounders.The odds of rapid renal decline were increased for individuals of Bangladeshi, African and Caribbean ethnicity, those with hypertension, proteinuria, cardiovascular disease and with increasing duration of diabetes. Rapid progression was more frequent in younger age groups. Risk of developing ESRF was highest in the black group compared with the white group (HR 1.88, 95% CI 1.11 to 3.19). Risk of death from any cause was 29% lower in the south Asian group compared with the white group (HR 0.71, 95% CI 0.56 to 0.91).ConclusionsProteinuria and hypertension trigger accelerated estimated glomerular filtration rate decline differentially by ethnicity. Active monitoring of younger adults, who have greater odds of rapid progression and the most to gain from interventions, is essential.
Lifestyle advice to cancer survivors: a qualitative study on the perspectives of health professionals
Authors: Koutoukidis Dimitrios A , Lopes Sonia , Fisher Abigail , Williams Kate , Croker Helen , Beeken Rebecca J 
Published: March 2018

ObjectivesAdoption of healthy lifestyle behaviours has shown promising effectiveness in reducing the high morbidity burden of cancer survivors. Health professionals (HPs) are well suited to provide lifestyle advice but few survivors report receiving guidance from them. This study aimed to explore HPs’ perspective of lifestyle advice (on healthy eating, physical activity, smoking, and alcohol) for cancer survivors.DesignIn-depth semistructured qualitative interviews were conducted by telephone or face to face. Data were analysed using qualitative content analysis.Setting and participantsTwenty-one UK HPs working in secondary care with breast, prostate or colorectal cancer survivors were interviewed.ResultsThe overarching theme was that HPs’ desire to provide lifestyle advice was not necessarily matched by knowledge and action. Three main themes were identified: (1) survivorship-centred barriers to provision, (2) HP-centred barriers to provision, and (3) optimal delivery of lifestyle advice. Results suggested that HPs’ perceptions of survivors’ current status of practising health behaviours, their perceived socioeconomic barriers and ability to practise health behaviours, and HPs’ fear for potential loss of connection with the patient influenced provision of lifestyle advice. Further factors included HPs’ knowledge of healthy lifestyle guidelines, feeling that they were not the ‘right person’ to provide advice, and lack of time and resources. HPs stressed that the optimal delivery of lifestyle advice should (1) be tailored to the individual and delivered throughout the cancer journey, (2) be focused on small and achievable changes framed as part of their treatment regimen and (3) be cost-effective for wide-scale implementation.ConclusionsIncorporation of the identified barriers when developing HP training programmes and lifestyle interventions could increase the probability of successful behavioural change, and thus improve outcomes for cancer survivors.