Search results for: Chris Patterson

Authors: Hasan Sungur, Evrim Baran, Benjamin Ahn, Aliye Karabulut Ilgu, Chris Rehmann, Cassandra Rutherford

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Engineering identity contributes to the professional and educational persistence of women engineers. A crucial factor contributing to the development of the engineering identity is recognition. Those without adequate recognition often do not succeed in positively building their identities. This research draws on Honneth’s recognition theory to identify factors impacting women civil engineers’ feelings of recognition as civil engineers. A survey was composed and distributed to 330 female alumni who graduated from the Department of Civil, Construction, and Environmental Engineering at Iowa State University in the last ten years. The survey items include demographics, perceptions of the identity of civil engineering, and factors that influence the recognition of civil engineering identities, such as views of society and family. Descriptive analysis of the survey responses revealed that the perceptions of civil engineering varied widely. Participants’ definitions of civil engineering included the terms: construction, design, and infrastructure. Almost half of the participants reported that the major reason to study civil engineering was their interest in the subject matter, and most reported that they were proud to be civil engineers. Many study participants reported that their parents see them as civil engineers. Treatment of institutions and the workplace were also considered as having a significant impact on the recognition of women civil engineers. Almost half of the participants reported that they felt isolated or ignored at work because of their gender. This research emphasizes the importance of recognition for the development of the civil engineering identity of women

Keywords: civil engineering, gender, identity, recognition

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Authors: Chris George, Adam Hamlin, Lily Pereg, Richard Charlesworth, Gal Winter

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Background: According to the ‘hygiene hypothesis’ the current rise in allergies and autoimmune diseases stems mainly from reduced microbial exposure due, amongst other factors, to urbanisation and distance from soil. However, this hypothesis is based on epidemiological and not biological data. Useful insights into the underlying mechanisms of this hypothesis can be gained by studying our interaction with soil. Soil microbiota may be directly ingested or inhaled by humans, enter the body through skin-soil contact or using plants as vectors. This study aims to examine the ability of soil microbiota to colonise the gut, study the interaction of soil microbes with the immune system and their potential protective activity. Method: The nutrition of the rats was supplemented daily with fresh or autoclaved soil for 21 days followed by 14 days of no supplementations. Faecal samples were collected throughout and analysed using 16S sequencing. At the end of the experiment rats were sacrificed and tissues and digesta were collected. Results/Conclusion: Results showed significantly higher richness and diversity following soil supplementation even after recovery. Specific soil microbial groups identified as able to colonise the gut. Of particular interest was the mucosal layer which emerged as a receptive host for soil microorganisms. Histological examination revealed innate and adaptive immune activation. Findings of this study reinforce the ‘hygiene hypothesis’ by demonstrating the ability of soil microbes to colonise the gut and activate the immune system. This paves the way for further studies aimed to examine the interaction of soil microorganisms with the immune system.

Keywords: gut microbiota, hygiene hypothesis, microbiome, soil

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Authors: Okpanachi Linus Odiji, Chris Ogwu Attah

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Election is no doubt widely assumed as one of the most suitable means of resolving political quagmires even though it has never been bereft of conflict which can manifest before, during, or after polls. What, however, advances democracy and promotes electoral integrity is the existence and effectiveness of institutional frameworks for electoral conflict management. Electoral conflicts are no doubt unique in the sense that they represent the struggles of people over the control of public resources. In most cases, the stakes involved are high and emotional that they do not only undermine inter-group relationship but also threaten national security. The need, therefore, for an effectively functional conflict management apparatus becomes imperative. While at the State level, there exist numerous governmental initiatives at various electoral stages aimed at managing conflicts, this paper examines the activities of the mass media, which is another prominent stakeholder in the electoral process. Even though media influence has increased tremendously in the last decade, researchers are yet to agree on its utility in the management of conflicts. Guided by the social responsibility theory of media reporting and drawing data from observed trends in Kogi state, the paper, which context analyses the 2019 gubernatorial election coverage in the state, observes both conflict escalation and de-escalation roles in the media. To mitigate conflict reporting misrepresentation, therefore, a common approach to conflict reporting should be designed and ordered by the National Broadcasting Commission as well as the Nigerian Press Council. This should be garnished with the training of journalists on conflict reporting and development of a standard conflict reporting procedure.

Keywords: conflict management, electoral conflict, mass media, media reporting

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Authors: Chris Schoborg, Morgan C. Wang

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In the realm of the National Football League (NFL), substantial dedication of time and effort is invested by both players and coaches in meticulously analyzing the game footage of their opponents. The primary aim is to anticipate the actions of the opposing team. Defensive players and coaches are especially focused on deciphering their adversaries' intentions to effectively counter their strategies. Acquiring insights into the specific play type and its intended direction on the field would confer a significant competitive advantage. This study establishes pre-snap information as the cornerstone for predicting both the play type (e.g., deep pass, short pass, or run) and its spatial trajectory (right, left, or center). The dataset for this research spans the regular NFL season data for all 32 teams from 2013 to 2022. This dataset is acquired using the nflreadr package, which conveniently extracts play-by-play data from NFL games and imports it into the R environment as structured datasets. In this study, we employ a recently developed machine learning algorithm, XGBoost. The final predictive model achieves an impressive lift of 2.61. This signifies that the presented model is 2.61 times more effective than random guessing—a significant improvement. Such a model has the potential to markedly enhance defensive coaches' ability to formulate game plans and adequately prepare their players, thus mitigating the opposing offense's yardage and point gains.

Keywords: lift, NFL, sports analytics, XGBoost

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Authors: Mirjana Ruppel, Rajendra Persad, Amit Bahl, Sanja Dogramadzi, Chris Melhuish, Lyndon Smith

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Multimodal image registration is a profoundly complex task which is why deep learning has been used widely to address it in recent years. However, two main challenges remain: Firstly, the lack of ground truth data calls for an unsupervised learning approach, which leads to the second challenge of defining a feasible loss function that can compare two images of different modalities to judge their level of alignment. To avoid this issue altogether we implement a generative adversarial network consisting of two registration networks GAB, GBA and two discrimination networks DA, DB connected by spatial transformation layers. GAB learns to generate a deformation field which registers an image of the modality B to an image of the modality A. To do that, it uses the feedback of the discriminator DB which is learning to judge the quality of alignment of the registered image B. GBA and DA learn a mapping from modality A to modality B. Additionally, a cycle-consistency loss is implemented. For this, both registration networks are employed twice, therefore resulting in images ˆA, ˆB which were registered to ˜B, ˜A which were registered to the initial image pair A, B. Thus the resulting and initial images of the same modality can be easily compared. A dataset of liver CT and MRI was used to evaluate the quality of our approach and to compare it against learning and non-learning based registration algorithms. Our approach leads to dice scores of up to 0.80 ± 0.01 and is therefore comparable to and slightly more successful than algorithms like SimpleElastix and VoxelMorph.

Keywords: cycle consistency, deformable multimodal image registration, deep learning, GAN

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Authors: Muhammed Ordu, Eren Demir, Chris Tofallis

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Over the past decade, the non-elective admissions in the UK have increased significantly. Taking into account limited resources (i.e. beds), the related service managers are obliged to manage their resources effectively due to the non-elective admissions which are mostly admitted to inpatient specialities via A&E departments. Geriatric medicine is one of specialities that have long length of stay for the non-elective admissions. This study aims to develop a discrete event simulation model to understand how possible increases on non-elective demand over the next 12 months affect the bed occupancy rate and to determine required number of beds in a geriatric medicine speciality in a UK hospital. In our validated simulation model, we take into account observed frequency distributions which are derived from a big data covering the period April, 2009 to January, 2013, for the non-elective admission and the length of stay. An experimental analysis, which consists of 16 experiments, is carried out to better understand possible effects of case studies and scenarios related to increase on demand and number of bed. As a result, the speciality does not achieve the target level in the base model although the bed occupancy rate decreases from 125.94% to 96.41% by increasing the number of beds by 30%. In addition, the number of required beds is more than the number of beds considered in the scenario analysis in order to meet the bed requirement. This paper sheds light on bed management for service managers in geriatric medicine specialities.

Keywords: bed management, bed occupancy rate, discrete event simulation, geriatric medicine, non-elective admission

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Authors: Nick Weir, Robert Stevens, Alan Hargreaves, Martin McGinnity, Chris Tinsley

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Hydrophobic materials have previously demonstrated the ability to elevate cell-cell interactions and promote the formation of neural networks whilst aligned nanofibers demonstrate the ability to induce extensive neurite outgrowth in an aligned manner. Hydrophobic materials typically elicit an immune response upon implantation and thus materials used for implantation are typically hydrophilic. Poly-L-lactic acid (PLLA) is a hydrophobic, non-immunogenic, FDA approved material that can be electrospun to form aligned nanofibers. Primary rat cortical neurons cultured for 10 days on aligned PLLA nanofibers formed 3D cell clusters, approximately 800 microns in diameter. Neurites that extended from these clusters were highly aligned due to the alignment of the nanofibers they were cultured upon and fasciculation was also evident. Plasma treatment of the PLLA nanofibers prior to seeding of cells significantly reduced the hydrophobicity and abolished the cluster formation and neurite fasciculation, whilst reducing the extent and directionality of neurite outgrowth; it is proposed that hydrophobicity induces the changes to cellular behaviors. Aligned PLLA nanofibers induced the formation of a structure that mimics the grey-white matter compartmentalization that is observed in vivo and thus represents a step forward in generating organoids or biomaterial-based implants. Upon implantation into the brain, the biomaterial architectures described here may provide a useful platform for both brain repair and brain remodeling initiatives.

Keywords: hydrophobicity, nanofibers, neurite fasciculation, neurite outgrowth, PLLA

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Authors: M. Patterson, R. Bond, K. Cowan, M. Mulvenna, C. Reid, F. McMahon, P. McGowan, H. Cormican

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This paper outlines the design of a simulator to allow for the optimisation of clinical workflows through a pathology laboratory and to improve the laboratory’s efficiency in the processing, testing, and analysis of specimens. Often pathologists have difficulty in pinpointing and anticipating issues in the clinical workflow until tests are running late or in error. It can be difficult to pinpoint the cause and even more difficult to predict any issues which may arise. For example, they often have no indication of how many samples are going to be delivered to the laboratory that day or at a given hour. If we could model scenarios using past information and known variables, it would be possible for pathology laboratories to initiate resource preparations, e.g. the printing of specimen labels or to activate a sufficient number of technicians. This would expedite the clinical workload, clinical processes and improve the overall efficiency of the laboratory. The simulator design visualises the workflow of the laboratory, i.e. the clinical tests being ordered, the specimens arriving, current tests being performed, results being validated and reports being issued. The simulator depicts the movement of specimens through this process, as well as the number of specimens at each stage. This movement is visualised using an animated flow diagram that is updated in real time. A traffic light colour-coding system will be used to indicate the level of flow through each stage (green for normal flow, orange for slow flow, and red for critical flow). This would allow pathologists to clearly see where there are issues and bottlenecks in the process. Graphs would also be used to indicate the status of specimens at each stage of the process. For example, a graph could show the percentage of specimen tests that are on time, potentially late, running late and in error. Clicking on potentially late samples will display more detailed information about those samples, the tests that still need to be performed on them and their urgency level. This would allow any issues to be resolved quickly. In the case of potentially late samples, this could help to ensure that critically needed results are delivered on time. The simulator will be created as a single-page web application. Various web technologies will be used to create the flow diagram showing the workflow of the laboratory. JavaScript will be used to program the logic, animate the movement of samples through each of the stages and to generate the status graphs in real time. This live information will be extracted from an Oracle database. As well as being used in a real laboratory situation, the simulator could also be used for training purposes. ‘Bots’ would be used to control the flow of specimens through each step of the process. Like existing software agents technology, these bots would be configurable in order to simulate different situations, which may arise in a laboratory such as an emerging epidemic. The bots could then be turned on and off to allow trainees to complete the tasks required at that step of the process, for example validating test results.

Keywords: laboratory-process, optimization, pathology, computer simulation, workflow

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Authors: Zhihao Zhao, Ali El-Nagger, Johnson Kau, Chris Olson, Douglas Tomlinson, Scott X. Chang

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One strategy to reduce CO₂ emissions from cement production is to reduce the amount of Portland cement produced by replacing it with supplementary cementitious materials (SCMs). Biochar is a potential SCM that is an eco-friendly and stable porous pyrolytic material. However, the effects of biochar addition on the performances of Portland cement composites are not fully understood. This meta-analysis investigated the impact of biochar addition on the 7- and 28-day compressive strength of Portland cement composites based on 606 paired observations. Biochar feedstock type, pyrolysis conditions, pre-treatments and modifications, biochar dosage, and curing type all influenced the compressive strength of Portland cement composites. Biochars obtained from plant-based feedstocks (except rice and hardwood) improved the 28-day compressive strength of Portland cement composites by 3-13%. Biochars produced at pyrolysis temperatures higher than 450 °C, with a heating rate of around 10 °C/min, increased the 28-day compressive strength more effectively. Furthermore, the addition of biochars with small particle sizes increased the compressive strength of Portland cement composites by 2-7% compared to those without biochar addition. Biochar dosage of < 2.5% of the binder weight enhanced both compressive strengths and common curing methods maintained the effect of biochar addition. However, when mixing the cement, adding fine and coarse aggregates such as sand and gravel affects the concrete and mortar's compressive strength, diminishing the effect of biochar addition and making the biochar effect nonsignificant. We conclude that appropriate biochar addition could maintain or enhance the mechanical performance of Portland cement composites, and future research should explore the mechanisms of biochar effects on the performance of cement composites.

Keywords: biochar, Portland cement, constructure, compressive strength, meta-analysis

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Authors: Azadeh Rouhandeh, Chris Joslin, Zhen Qu, Yuu Ono

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The centre of rotation of the hip joint is needed for an accurate simulation of the joint performance in many applications such as pre-operative planning simulation, human gait analysis, and hip joint disorders. In human movement analysis, the hip joint center can be estimated using a functional method based on the relative motion of the femur to pelvis measured using reflective markers attached to the skin surface. The principal source of errors in estimation of hip joint centre location using functional methods is soft tissue artefacts due to the relative motion between the markers and bone. One of the main objectives in human movement analysis is the assessment of soft tissue artefact as the accuracy of functional methods depends upon it. Various studies have described the movement of soft tissue artefact invasively, such as intra-cortical pins, external fixators, percutaneous skeletal trackers, and Roentgen photogrammetry. The goal of this study is to present a non-invasive method to assess the displacements of the markers relative to the underlying bone using optical motion capture data and tissue thickness from ultrasound measurements during flexion, extension, and abduction (all with knee extended) of the hip joint. Results show that the artefact skin marker displacements are non-linear and larger in areas closer to the hip joint. Also marker displacements are dependent on the movement type and relatively larger in abduction movement. The quantification of soft tissue artefacts can be used as a basis for a correction procedure for hip joint kinematics.

Keywords: hip joint center, motion capture, soft tissue artefact, ultrasound depth measurement

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Authors: Lemar Blake, Chris Oura, Ayanna C. N. Phillips Savage

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Improved DNA sequencing technology has greatly enhanced bacterial identification, especially for organisms that are difficult to culture. Mycobacteriosis with consistent hyphema, bilateral exophthalmia, open mouth gape and ocular lesions, were observed in various fish populations at the School of Veterinary Medicine, Aquaculture/Aquatic Animal Health Unit. Objective: To identify the species of Mycobacterium that is affecting aquarium fish at the School of Veterinary Medicine, Aquaculture/Aquatic Animal Health Unit. Method: A total of 13 fish samples were collected and analyzed via: Ziehl-Neelsen, conventional polymerase chain reaction (PCR) and real-time PCR. These tests were carried out simultaneously for confirmation. The following combination of conventional primers: 16s rRNA (564 bp), rpoB (396 bp), sod (408 bp) were used. Concatenation of the gene fragments was carried out to phylogenetically classify the organism. Results: Acid fast non-branching bacilli were detected in all samples from homogenized internal organs. All 13 acid fast samples were positive for Mycobacterium via real-time PCR. Partial gene sequences using all three primer sets were obtained from two samples and demonstrated a novel strain. A strain 99% related to Mycobacterium marinum was also confirmed in one sample, using 16srRNA and rpoB genes. The two novel strains were clustered with the rapid growers and strains that are known to affect humans. Conclusions: Phylogenetic analysis demonstrated two novel Mycobacterium strains with the potential of being zoonotic and one strain 99% related to Mycobacterium marinum.

Keywords: polymerase chain reaction, phylogenetic, DNA sequencing, zoonotic

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Authors: Mitra Shokrollahi, Mia Stanic, Anisha Hundal, Janet N. Y. Chan, Defne Urman, Chris A. Jordan, Anne Hakem, Roderic Espin, Jun Hao, Rehna Krishnan, Philipp G. Maass, Brendan C. Dickson, Manoor P. Hande, Miquel A. Pujana, Razqallah Hakem, Karim Mekhail

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Current models suggest that DNA double-strand breaks (DSBs) can move to the nuclear periphery for repair. It is unclear to what extent human DSBs display such repositioning. Here we show that the human nuclear envelope localizes to DSBs in a manner depending on DNA damage response (DDR) kinases and cytoplasmic microtubules acetylated by α-tubulin acetyltransferase-1 (ATAT1). These factors collaborate with the linker of nucleoskeleton and cytoskeleton complex (LINC), nuclear pore complex (NPC) protein NUP153, the nuclear lamina and kinesins KIF5B and KIF13B to generate DSB-capturing nuclear envelope tubules (dsbNETs). dsbNETs are partly supported by nuclear actin filaments and the circadian factor PER1 and reversed by kinesin KIFC3. Although dsbNETs promote repair and survival, they are also co-opted during poly (ADP-ribose) polymerase (PARP) inhibition to restrain BRCA1-deficient breast cancer cells and are hyper-induced in cells expressing the aging-linked lamin A mutant progerin. In summary, our results advance understanding of nuclear structure-function relationships, uncover a nuclear-cytoplasmic DDR and identify dsbNETs as critical factors in genome organization and stability.

Keywords: DNA damage response, genome stability, nuclear envelope, cancer, age-related disorders

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Authors: Shruti Malviya, Chris Bowler

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Environmental processes acting at multiple spatial scales control marine diatom community structure. However, the contribution of local factors (e.g., temperature, salinity, etc.) in these highly complex systems is poorly understood. We, therefore, investigated the diatom community organization as a function of environmental predictors and determined the relative contribution of various environmental factors on the structure of marine diatoms assemblages in the world’s ocean. The dataset for this study was derived from the Tara Oceans expedition, constituting 46 sampling stations from diverse oceanic provinces. The V9 hypervariable region of 18s rDNA was organized into assemblages based on their distributional co-occurrence. Using Ward’s hierarchical clustering, nine clusters were defined. The number of ribotypes and reads varied within each cluster-three clusters (II, VIII and IX) contained only a few reads whereas two of them (I and IV) were highly abundant. Of the nine clusters, seven can be divided into two categories defined by a positive correlation with phosphate and nitrate and a negative correlation with longitude and, the other by a negative correlation with salinity, temperature, latitude and positive correlation with Lyapunov exponent. All the clusters were found to be remarkably dominant in South Pacific Ocean and can be placed into three classes, namely Southern Ocean-South Pacific Ocean clusters (I, II, V, VIII, IX), South Pacific Ocean clusters (IV and VII), and cosmopolitan clusters (III and VI). Our findings showed that co-occurring ribotypes can be significantly associated into recognizable clusters which exhibit a distinct response to environmental variables. This study, thus, demonstrated distinct behavior of each recognized assemblage displaying a taxonomic and environmental signature.

Keywords: assemblage, diatoms, hierarchical clustering, Tara Oceans

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Authors: Professor Jo Angouri, Polina Mesinioti, Chris Turner

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In order for a group of ad-hoc professional to perform as a team, a shared understanding of the problem at hand and an agreed action plan are necessary components. This is particularly significant in complex, time sensitive professional settings such as in trauma emergencies. In this context, team briefings prior to the patient arrival (pre-briefings) constitute a critical event for the performance of the team; they provide the necessary space for co-constructing a shared understanding of the situation through summarising information available to the team: yet the act of summarising is widely assumed in medical practice but not systematically researched. In the vast teamwork literature, terms such as ‘shared mental model’, ‘mental space’ and ‘cognate labelling’ are used extensively, and loosely, to denote the outcome of the summarising process, but how exactly this is done interactionally remains under researched. This paper reports on the forms and functions of pre-briefings in a major trauma centre in the UK. Taking an interactional approach, we draw on 30 simulated and real-life trauma emergencies (15 from each dataset) and zoom in on the use of pre-briefings, which we consider focal points in the management of trauma emergencies. We show how ad hoc teams negotiate sharedness of future orientation through summarising, synthesising information, and establishing common understanding of the situation. We illustrate the role, characteristics, and structure of pre-briefing sequences that have been evaluated as ‘efficient’ in our data and the impact (in)effective pre-briefings have on teamwork. Our work shows that the key roles in the event own the act of summarising and we problematise the implications for leadership in trauma emergencies. We close the paper with a model for pre-briefing and provide recommendations for clinical practice, arguing that effective pre-briefing practice is teachable.

Keywords: summarising, medical emergencies, interaction analysis, shared/mental models

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Authors: Steve Fish, Chris Lambert

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Cumbria is a geo-political county in Northwest England within which the Lake District National Park, a UNESCO World Heritage site is located. Whilst the area has a formidable reputation for natural beauty and historic assets, the innovation ecosystem is described as ‘patchy’ for a number of reasons. The county is one of the largest in England by area and is sparsely populated. This paper describes the needs, development and delivery of an SME business-support programme funded by the European Regional Development Fund, Lancaster University and the University of Cumbria. The Cumbria Innovations Platform (CUSP) Project has been designed to respond to the nuanced needs of SMEs in this locale, whilst promoting the adoption of research and innovation. CUSP utilizes a funnel method to support rural businesses with access to university innovation intervention. CUSP has been built on a three-tier model: Communicate, Collaborate and Create. The paper describes this project in detail and presents results in terms of output indicators achieved, a beneficiary telephone survey and wider economic forecasts. From a pragmatic point-of-view, the paper provides experiences and reflections of those people who are delivering and evaluating knowledge exchange. The authors discuss some of the benefits, challenges and implications for both policy makers and practitioners. Finally, the paper aims to serve as an invitation to others who may consider adopting a similar method of university-industry collaboration in their own region.

Keywords: regional business support, rural business support, university-industry collaboration, collaborative R&D, SMEs, knowledge exchange

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Authors: Alexandros Lioulemes, Michail Theofanidis, Varun Kanal, Konstantinos Tsiakas, Maher Abujelala, Chris Collander, William B. Townsend, Angie Boisselle, Fillia Makedon

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This paper presents a home-based robot-rehabilitation instrument, called ”MAGNI Dynamics”, that utilized a vision-based kinematic/dynamic module and an adaptive haptic feedback controller. The system is expected to provide personalized rehabilitation by adjusting its resistive and supportive behavior according to a fuzzy intelligence controller that acts as an inference system, which correlates the user’s performance to different stiffness factors. The vision module uses the Kinect’s skeletal tracking to monitor the user’s effort in an unobtrusive and safe way, by estimating the torque that affects the user’s arm. The system’s torque estimations are justified by capturing electromyographic data from primitive hand motions (Shoulder Abduction and Shoulder Forward Flexion). Moreover, we present and analyze how the Barrett WAM generates a force-field with a haptic controller to support or challenge the users. Experiments show that by shifting the proportional value, that corresponds to different stiffness factors of the haptic path, can potentially help the user to improve his/her motor skills. Finally, potential areas for future research are discussed, that address how a rehabilitation robotic framework may include multisensing data, to improve the user’s recovery process.

Keywords: human-robot interaction, kinect, kinematics, dynamics, haptic control, rehabilitation robotics, artificial intelligence

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Authors: Manjula Weerasekera, Chris Sissons, Lisa Wong, Sally Anderson, Ann Holmes, Richard Cannon

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The aim of this study was to characterize bacterial population and yeasts in saliva by Polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) and measure yeast levels by culture. PCR-DGGE was performed to identify oral bacteria and yeasts in 24 saliva samples. DNA was extracted and used to generate DNA amplicons of the V2–V3 hypervariable region of the bacterial 16S rDNA gene using PCR. Further universal primers targeting the large subunit rDNA gene (25S-28S) of fungi were used to amplify yeasts present in human saliva. Resulting PCR products were subjected to denaturing gradient gel electrophoresis using Universal mutation detection system. DGGE bands were extracted and sequenced using Sanger method. A potential relationship was evaluated between groups of bacteria identified by cluster analysis of DGGE fingerprints with the yeast levels and with their diversity. Significant interpersonal variation of salivary microbiome was observed. Cluster and principal component analysis of the bacterial DGGE patterns yielded three significant major clusters, and outliers. Seventeen of the 24 (71%) saliva samples were yeast positive going up to 10³ cfu/mL. Predominately, C. albicans, and six other species of yeast were detected. The presence, amount and species of yeast showed no clear relationship to the bacterial clusters. Microbial community in saliva showed a significant variation between individuals. A lack of association between yeasts and the bacterial fingerprints in saliva suggests the significant ecological person-specific independence in highly complex oral biofilm systems under normal oral conditions.

Keywords: bacteria, denaturing gradient gel electrophoresis, oral biofilm, yeasts

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Authors: Hajar Hajmohammadi, Paul Pfeffer, Anna De Simoni, Jim Cole, Chris Griffiths, Sally Hull, Benjamin Heydecker

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Background: There is strong interest in the relationship between short-term air pollution exposure and human health. Most studies in this field focus on serious health effects such as death or hospital admission, but air pollution exposure affects many people with less severe impacts, such as exacerbations of respiratory conditions. A lack of quantitative analysis and inconsistent findings suggest improved methodology is needed to understand these effectsmore fully. Method: We developed a time series regression model to quantify the relationship between daily NOₓ concentration and Asthma exacerbations requiring oral steroids from primary care settings. Explanatory variables include daily NOₓ concentration measurements extracted from 8 available background and roadside monitoring stations in east London and daily ambient temperature extracted for London City Airport, located in east London. Lags of NOx concentrations up to 21 days (3 weeks) were used in the model. The dependent variable was the daily number of oral steroid courses prescribed for GP registered patients with asthma in east London. A mixed distribution model was then fitted to the significant lags of the regression model. Result: Results of the time series modelling showed a significant relationship between NOₓconcentrations on each day and the number of oral steroid courses prescribed in the following three weeks. In addition, the model using only roadside stations performs better than the model with a mixture of roadside and background stations.

Keywords: air pollution, time series modeling, public health, road transport

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Authors: Daniel Martin, Roberto Rodriguez, Derek Woller, Chris Reuter, Lonnie Black, Mohamed Latheef

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The grasshoppers comprised of heterogeneous assemblages of Acrididae (Family: Orthoptera) species periodically reach outbreak levels by their gregarious behavior and voracious feeding habits, devouring stems and leaves of food crops and rangeland pasture. Cattle consume about 1.5-2.5% of their body weight in forage per day, so pound for pound, a grasshopper will eat 12-20 times as much plant material as a steer and cause serious economic damage to the cattle industry, especially during a drought when forage is already scarce. Grasshoppers annually consume more than 20% of rangeland forages in the western United States at an estimated loss of $1.25 billion per year in forage. A remotely piloted aerial application system with both a spreader and spray application system was used to apply granular insect bait and a liquid formulation of Carbaryl for control of grasshopper infestations on rangeland in New Mexico, United States. Pattern testing and calibration of both the granular and liquid application systems were conducted to determine proper application rate set up and distribution pattern. From these tests, an effective swath was calculated. Results showed that 14 days after application, granular baits were only effective on those grasshopper species that accepted the baits. The liquid formulation at 16 ounces per acre was highly successful at controlling all grasshopper species. Results of this study indicated that a remotely piloted aerial application system can be used to effectively deliver grasshopper control products in both granular and liquid form. However, the spray application treatment proved to be most effective and efficient for all grasshopper species present.

Keywords: Carbaryl, Grasshopper, Insecticidal Efficacy, Remotely Piloted Aerial Application System

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Authors: Abdulsalam A. Al-Tamimi, Chris Peach, Paulo Rui Fernandes, Paulo J. Bartolo

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Bone fixation implants currently used to treat traumatic fractured bones and to promote fracture healing are built with biocompatible metallic materials such as stainless steel, cobalt chromium and titanium and its alloys (e.g., CoCrMo and Ti6Al4V). The noticeable stiffness mismatch between current metallic implants and host bone associates with negative outcomes such as stress shielding which causes bone loss and implant loosening leading to deficient fracture treatment. This paper, part of a major research program to design the next generation of bone fixation implants, describes the combined use of three-dimensional (3D) topology optimization (TO) and additive manufacturing powder bed technology (Electron Beam Melting) to redesign and fabricate the plates based on the current standard one (i.e., locking compression plate). Topology optimization is applied with an objective function to maximize the stiffness and constraint by volume reductions (i.e., 25-75%) in order to obtain optimized implant designs with reduced stress shielding phenomenon, under different boundary conditions (i.e., tension, bending, torsion and combined loads). The stiffness of the original and optimised plates are assessed through a finite-element study. The TO results showed actual reduction in the stiffness for most of the plates due to the critical values of volume reduction. Additionally, the optimized plates fabricated using powder bed techniques proved that the integration between the TO and additive manufacturing presents the capability of producing stiff reduced plates with acceptable tolerances.

Keywords: additive manufacturing, locking compression plate, finite element, topology optimization

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Authors: Shruti Malviya, Chris Bowler

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Analysis of microbial eukaryotic diversity is fundamental to understanding ecosystems’ structure, biology, and ecology. Diatoms (Stramenopiles, Bacillariophyceae) are one of the most diverse and ecologically prominent groups of phytoplankton. This study was performed to enhance the understanding of global biodiversity patterns and structure of planktonic diatom communities across the world's oceans. We used the metabarcoding data set generated from the biological samples and associated environmental data collected during the Tara Oceans (2009-2013) global circumnavigation covering all major oceanic provinces. A total of ~18 million diatom V9-18S rDNA tags from 126 sampling stations, constituting 631 size-fractionated plankton communities were generated. Using ~250,000 unique diatom metabarcodes, the global diatom distribution and diversity across size classes, genus and ecological niches was assessed. Notably, our analysis revealed: (i) a new estimate of the total number of planktonic diatom species, (ii) a considerable unknown diversity and exceptionally high diversity in the open ocean, and (iii) complex diversity patterns across oceanic provinces. Also, co-occurrence of several ribotypes in locations separated by great geographic distances (equatorial stations) demonstrated a widespread but not ubiquitous distribution. This work provides a comprehensive perspective on diatom distribution and diversity in the world’s oceans and elaborates interconnections between associated theories and underlying drivers. It shows how meta-barcoding approaches can provide a framework to investigate environmental diversity at a global scale, which is deemed as an essential step in answering various ecological research questions. Consequently, this work also provides a reference point to explore how microbial communities will respond to environmental conditions.

Keywords: diatoms, Tara Oceans, biodiversity, metabarcoding

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Authors: Modi Alsubaie, Willem Kuyken, Rebecca Abbott, Barnaby Dunn, Chris Dickens, Tina Keil, William Henley

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Background: Recently, there has been an increased interest in studying the effects of mindfulness-based interventions for people with psychological and physical problems. However, the mechanisms of action in these interventions that lead to beneficial physical and psychological outcomes have yet to be clearly identified. Purpose: The aim of this paper is to review, systematically, the evidence to date on the mechanisms of action in mindfulness interventions in populations with physical and/or psychological conditions. Method: Searches of seven databases (PsycINFO, Medline (Ovid), Cochrane Central Register of Controlled Trials, EMBASE, CINAHL, AMED, ClinicalTrials.gov) were undertaken in June 2014 and July 2015. We evaluated to what extent the studies we identified met the criteria suggested by Kazdin for establishing mechanisms of action within a psychological treatment (2007, 2009). Results: We identified four trials examining mechanisms of mindfulness interventions in those with comorbid psychological and physical health problems and 14 in those with psychological conditions. These studies examined a diverse range of potential mechanisms, including mindfulness and rumination. Of these candidate mechanisms, the most consistent finding was that greater self-reported change in mindfulness mediated superior clinical outcomes. However, very few studies fully met the Kazdin criteria for examining treatment mechanisms. Conclusion: There was evidence that global changes in mindfulness are linked to better outcomes. This evidence pertained more to interventions targeting psychological rather than physical health conditions. While there is promising evidence that MBCT/MBSR intervention effects are mediated by hypothesised mechanisms, there is a lack of methodological rigour in the field of testing mechanisms of action for both MBCT and MBSR, which precludes definitive conclusions.

Keywords: MBCT, MBSR, mechanisms, physical conditions, psychological conditions, systematic review

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Authors: Chris Phan, Yong Seok Park

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The Toyota Camry is one of the best-selling cars in America. It is economical, reliable, and most importantly, safe. These attributes allowed the Camry to be the trustworthy choice when choosing dependable vehicle. However, a new finding brought question to the Camry’s safety. Since 1997, the Camry received a “good” rating on its moderate overlap front crash test through the Insurance Institute of Highway Safety. In 2012, the Insurance Institute of Highway Safety introduced a frontal small overlap crash test into the overall evaluation of vehicle occupant safety test. The 2012 Camry received a “poor” rating on this new test, while the 2015 Camry redeemed itself with a “good” rating once again. This study aims to find a possible solution that Toyota implemented to reduce the severity of a frontal small overlap crash in the Camry during a mid-cycle update. The purpose of this study is to analyze and evaluate the performance of various A-pillar shapes as energy absorbing structures in improving passenger safety in a frontal crash. First, A-pillar structures of the 2012 and 2015 Camry were modeled using CAD software, namely SolidWorks. Then, a crash test simulation using ANSYS software, was applied to the A-pillars to analyze the behavior of the structures in similar conditions. Finally, the results were compared to safety values of cabin intrusion to determine the crashworthy behaviors of both A-pillar structures by measuring total deformation. This study highlights that it is possible that Toyota improved the shape of the A-pillar in the 2015 Camry in order to receive a “good” rating from the IIHS safety evaluation once again. These findings can possibly be used to increase safety performance in future vehicles to decrease passenger injury or fatality.

Keywords: A-pillar, Crashworthiness, Design Synthesis, Finite Element Analysis

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Authors: Ileen Van den Berg, Reinier J. Daals, Chris E. M. Heuberger, Sven P. Hildering, Bob E. Van Maris, Carla M. Smulders, Rafael Aránguiz

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Chile is located along the subduction zone of the Nazca plate beneath the South American plate, where large earthquakes and tsunamis have taken place throughout history. The last significant earthquake (Mw 8.2) occurred in September 2015 and generated a destructive tsunami, which mainly affected the city of Coquimbo (71.33°W, 29.96°S). The inundation area consisted of a beach, damaged seawall, damaged railway, wetland and old neighborhood; therefore, local authorities started a reconstruction process immediately after the event. Moreover, a seismic gap has been identified in the same area, and another large event could take place in the near future. The present work proposed an integrated tsunami reconstruction plan for the city of Coquimbo that considered several variables such as safety, nature & recreation, neighborhood welfare, visual obstruction, infrastructure, construction process, and durability & maintenance. Possible future tsunami scenarios are simulated by means of the Non-hydrostatic Evolution of Ocean WAVEs (NEOWAVE) model with 5 nested grids and a higher grid resolution of ~10 m. Based on the score from a multi-criteria analysis, the costs of the alternatives and a preference for a multifunctional solution, the alternative that includes an elevated coastal road with floodgates to reduce tsunami overtopping and control the return flow of a tsunami was selected as the best solution. It was also observed that the wetlands are significantly restored to their former configuration; moreover, the dynamic behavior of the wetlands is stimulated. The numerical simulation showed that the new coastal protection decreases damage and the probability of loss of life by delaying tsunami arrival time. In addition, new evacuation routes and a smaller inundation zone in the city increase safety for the area.

Keywords: tsunami, Coquimbo, Chile, reconstruction, numerical simulation

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Authors: Ahmed Elbeltagy, Francesca Bertolini, Damarius Fleming, Angelica Van Goor, Chris Ashwell, Carl Schmidt, Donald Kugonza, Susan Lamont, Max Rothschild

Abstract:

The major factor in shaping genomic variation of the African indigenous rural chicken is likely natural selection drives the development genetic footprints in the chicken genomes. To investigate such a hypothesis of a selection footprint, a total of 292 birds were randomly sampled from three indigenous ecotypes from East Africa (Uganda, Rwanda) and North Africa (Egypt) and two registered Egyptian breeds (Fayoumi and Dandarawi), and from the synthetic Kuroiler breed. Samples were genotyped using the Affymetrix 600K Axiom® Array. A total of 526,652 SNPs were utilized in the downstream analysis after quality control measures. The intra-population runs of homozygosity (ROH) that were consensuses in > 50% of individuals of an ecotype or > 75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East- African populations in addition to population-pairwise combinations for overlapping windows (500Kb with an overlap of 250Kb). A total of 28,563 ROH were determined and were classified into three length categories. ROH and Fst detected sweeps were identified on several autosomes. Several genes in these regions are likely to be related to adaptation to local environmental stresses that include high altitude, diseases resistance, poor nutrition, oxidative and heat stresses and were linked to gene ontology terms (GO) related to immune response, oxygen consumption and heme binding, carbohydrate metabolism, oxidation-reduction, and behavior. Results indicated a possible effect of natural selection forces on shaping genomic structure for adaptation to local environmental stresses.

Keywords: African Chicken, runs of homozygosity, FST, selection footprints

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Authors: Muhammed Ordu, Eren Demir, Chris Tofallis

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The number of inpatient admissions in the UK has been significantly increasing over the past decade. These increases cause bed occupancy rates to exceed the target level (85%) set by the Department of Health in England. Therefore, hospital service managers are struggling to better manage key resource such as beds. On the other hand, this severe demand pressure might lead to confusion in wards. For example, patients can be admitted to the ward of another inpatient specialty due to lack of resources (i.e., bed). This study aims to develop a simulation-optimization model to reallocate the available number of beds in a mid-sized hospital in the UK. A hospital simulation model was developed to capture the stochastic behaviours of the hospital by taking into account the accident and emergency department, all outpatient and inpatient services, and the interactions between each other. A couple of outputs of the simulation model (e.g., average length of stay and revenue) were generated as inputs to be used in the optimization model. An integer linear programming was developed under a number of constraints (financial, demand, target level of bed occupancy rate and staffing level) with the aims of maximizing number of admitted patients. In addition, a sensitivity analysis was carried out by taking into account unexpected increases on inpatient demand over the next 12 months. As a result, the major findings of the approach proposed in this study optimally reallocate the available number of beds for each inpatient speciality and reveal that 74 beds are idle. In addition, the findings of the study indicate that the hospital wards will be able to cope with 14% demand increase at most in the projected year. In conclusion, this paper sheds a new light on how best to reallocate beds in order to cope with current and future demand for healthcare services.

Keywords: bed occupancy rate, bed reallocation, discrete event simulation, inpatient admissions, integer linear programming, projected usage

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Authors: Zhuanfang Fred Zhang, Tim C. Johnson, Yilin Fang, Chris E. Strickland

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A variety of geophysical techniques are available to image the opaque subsurface with little or no contact with the soil. It is common to conduct time-lapse surveys of different types for a given site for improved results of subsurface imaging. Regardless of the chosen survey methods, it is often a challenge to process the massive amount of survey data. The currently available software applications are generally based on the one-dimensional assumption for a desktop personal computer. Hence, they are usually incapable of imaging the three-dimensional (3D) processes/variables in the subsurface of reasonable spatial scales; the maximum amount of data that can be inverted simultaneously is often very small due to the capability limitation of personal computers. Presently, high-performance or integrating software that enables real-time integration of multi-process geophysical methods is needed. E4D-MP enables the integration and inversion of time-lapsed large-scale data surveys from geophysical methods. Using the supercomputing capability and parallel computation algorithm, E4D-MP is capable of processing data across vast spatiotemporal scales and in near real time. The main code and the modules of E4D-MP for inverting individual or combined data sets of time-lapse 3D electrical resistivity, spectral induced polarization, and gravity surveys have been developed and demonstrated for sub-surface imaging. E4D-MP provides capability of imaging the processes (e.g., liquid or gas flow, solute transport, cavity development) and subsurface properties (e.g., rock/soil density, conductivity) critical for successful control of environmental engineering related efforts such as environmental remediation, carbon sequestration, geothermal exploration, and mine land reclamation, among others.

Keywords: gravity survey, high-performance computing, sub-surface monitoring, electrical resistivity tomography

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Authors: Saoussen Dhib, Chris M. Mannaerts, Zoubeida Bargaoui, Ben H. P. Maathuis, Petra Budde

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In this study, a new method to delineate rain areas in northern Tunisia is presented. The proposed approach is based on the blending of the geostationary Meteosat Second Generation (MSG) infrared channel (IR) with the low-earth orbiting passive Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI). To blend this two products, we need to apply two main steps. Firstly, we have to identify the rainy pixels. This step is achieved based on a classification using MSG channel IR 10.8 and the water vapor WV 0.62, applying a threshold on the temperature difference of less than 11 Kelvin which is an approximation of the clouds that have a high likelihood of precipitation. The second step consists on fitting the relation between IR cloud top temperature with the TMI rain rates. The correlation coefficient of these two variables has a negative tendency, meaning that with decreasing temperature there is an increase in rainfall intensity. The fitting equation will be applied for the whole day of MSG 15 minutes interval images which will be summed. To validate this combined product, daily extreme rainfall events occurred during the period 2007-2009 were selected, using a threshold criterion for large rainfall depth (> 50 mm/day) occurring at least at one rainfall station. Inverse distance interpolation method was applied to generate rainfall maps for the drier summer season (from May to October) and the wet winter season (from November to April). The evaluation results of the estimated rainfall combining MSG and TMI was very encouraging where all the events were detected rainy and the correlation coefficients were much better than previous evaluated products over the study area such as MSGMPE and PERSIANN products. The combined product showed a better performance during wet season. We notice also an overestimation of the maximal estimated rain for many events.

Keywords: combination, extreme, rainfall, TMI-MSG, Tunisia

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Authors: Lucia Steenkamp, Chris V. D. Westhuyzen, Kgama Mathiba

Abstract:

Ambergris, and more specifically its oxidation product (–)-ambrafuran, is a scarce, valuable, and sought-after perfumery ingredient. The material is used as a fixative agent to stabilise perfumes in formulations by reducing the evaporation rate of volatile substances. Ambergris is a metabolic product of the sperm whale (Physeter macrocephatus L.), resulting from intestinal irritation. Chemically, (–)-ambrafuran is produced from the natural product sclareol in eight synthetic steps – in the process using harsh and often toxic chemicals to do so. An overall yield of no more than 76% can be achieved in some routes, but generally, this is lower. A new 'green' route has been developed in our laboratory in which sclareol, extracted from the Clary sage plant, is converted to (–)-ambrafuran in two steps with an overall yield in excess of 80%. The first step uses a microorganism, Hyphozyma roseoniger, to bioconvert sclareol to an intermediate diol using substrate concentrations up to 50g/L. The yield varies between 90 and 67% depending on the substrate concentration used. The purity of the diol product is 95%, and the diol is used without further purification in the next step. The intermediate diol is then cyclodehydrated to the final product (–)-ambrafuran using a zeolite, which is not harmful to the environment and is readily recycled. The yield of the product is 96%, and following a single recrystallization, the purity of the product is > 99.5%. A preliminary LC-MS study of the bioconversion identified several intermediates produced in the fermentation broth under oxygen-restricted conditions. Initially, a short-lived ketone is produced in equilibrium with a more stable pyranol, a key intermediate in the process. The latter is oxidised under Norrish type I cleavage conditions to yield an acetate, which is hydrolysed either chemically or under lipase action to afford the primary fermentation product, an intermediate diol. All the intermediates identified point to the likely CYP450 action as the key enzyme(s) in the mechanism. This invention is an exceptional example of how the power of biocatalysis, combined with a mild, benign chemical step, can be deployed to replace a total chemical synthesis of a specific chiral antipode of a commercially relevant material.

Keywords: ambrafuran, biocatalysis, fragrance, microorganism

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Authors: Kayode O. Afolabi, Benson C. Iweriebor, Anthony I. Okoh, Larry C. Obi

Abstract:

Porcine circovirus type 2 (PCV2) is the major etiological viral agent of porcine multisystemic wasting syndrome (PWMS) and other porcine circovirus-associated diseases (PCVAD) of great economic importance in pig industry globally. In an effort to determine the status of swine herds in the Province as regarding the ‘small but powerful’ viral pathogen; a total of 375 blood, faecal and nasal swab samples were obtained from seven pig farms (commercial and communal) in Amathole, O.R. Tambo and Chris-Hani District Municipalities of Eastern Cape Province between the year 2015 and 2016. Three hundred and thirty nine (339) samples out of the total sample were subjected to molecular screening using PCV2 specific primers by conventional polymerase chain reaction (PCR). Selected sequences were further analyzed and confirmed through genome sequencing and phylogenetic analyses. The data obtained revealed that 15.93% of the screened samples (54/339) from the swine herds of the studied areas were positive for PCV2; while the severity of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6% to 60% in the studied farms. The Majority, precisely 15 out of 17 (88%) analyzed sequences were found clustering with other PCV2b reference strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genogroup, which is presently another fast-spreading genotype with observable higher virulence in global swine herds. This finding confirmed the presence of this all-important viral pathogen in pigs of the region; which could result in a serious outbreak of PCVAD and huge economic loss at the instances of triggering factors if no appropriate measures are taken to curb its spread effectively.

Keywords: pigs, polymerase chain reaction, porcine circovirus type 2, South Africa

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