Search results for: Leah Howard

Authors: Atbin Mahabbati, Jason Beringer, Matthias Leopold

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To address the global challenges of climate and environmental changes, there is a need for quantifying and reducing uncertainties in environmental data, including observations of carbon, water, and energy. Global eddy covariance flux tower networks (FLUXNET), and their regional counterparts (i.e., OzFlux, AmeriFlux, China Flux, etc.) were established in the late 1990s and early 2000s to address the demand. Despite the capability of eddy covariance in validating process modelling analyses, field surveys and remote sensing assessments, there are some serious concerns regarding the challenges associated with the technique, e.g. data gaps and uncertainties. To address these concerns, this research has developed an ensemble model to fill the data gaps of CO₂ flux to avoid the limitations of using a single algorithm, and therefore, provide less error and decline the uncertainties associated with the gap-filling process. In this study, the data of five towers in the OzFlux Network (Alice Springs Mulga, Calperum, Gingin, Howard Springs and Tumbarumba) during 2013 were used to develop an ensemble machine learning model, using five feedforward neural networks (FFNN) with different structures combined with an eXtreme Gradient Boosting (XGB) algorithm. The former methods, FFNN, provided the primary estimations in the first layer, while the later, XGB, used the outputs of the first layer as its input to provide the final estimations of CO₂ flux. The introduced model showed slight superiority over each single FFNN and the XGB, while each of these two methods was used individually, overall RMSE: 2.64, 2.91, and 3.54 g C m⁻² yr⁻¹ respectively (3.54 provided by the best FFNN). The most significant improvement happened to the estimation of the extreme diurnal values (during midday and sunrise), as well as nocturnal estimations, which is generally considered as one of the most challenging parts of CO₂ flux gap-filling. The towers, as well as seasonality, showed different levels of sensitivity to improvements provided by the ensemble model. For instance, Tumbarumba showed more sensitivity compared to Calperum, where the differences between the Ensemble model on the one hand and the FFNNs and XGB, on the other hand, were the least of all 5 sites. Besides, the performance difference between the ensemble model and its components individually were more significant during the warm season (Jan, Feb, Mar, Oct, Nov, and Dec) compared to the cold season (Apr, May, Jun, Jul, Aug, and Sep) due to the higher amount of photosynthesis of plants, which led to a larger range of CO₂ exchange. In conclusion, the introduced ensemble model slightly improved the accuracy of CO₂ flux gap-filling and robustness of the model. Therefore, using ensemble machine learning models is potentially capable of improving data estimation and regression outcome when it seems to be no more room for improvement while using a single algorithm.

Keywords: carbon flux, Eddy covariance, extreme gradient boosting, gap-filling comparison, hybrid model, OzFlux network

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Authors: Leah Li Echiverri, Haoyu Shang, Yue Li

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Wenzhou-Kean University (WKU) is a Sino-US Cooperative University in China. It practices the English Immersion Program (EIP), where all the courses are taught in English. Class discussions and presentations are pervasively interwoven in designing students’ learning experiences. This WKU model has brought positive influences on students and is in some way ahead of traditional college English majors. However, literature to support the perceptions on the positive outcomes of this teaching and learning model remain scarce. The distinctive profile of Chinese-ESL students in an English Medium of Instruction (EMI) environment contributes further to the scarcity of literature compared to existing studies conducted among ESL learners in Western educational settings. Hence, the study investigated the students’ perceptions towards the English Immersion Program and determine how it influences Chinese-ESL students’ academic performance (AP). This research can provide empirical data that would be helpful to educators, teaching practitioners, university administrators, and other researchers in making informed decisions when developing curricular reforms, instructional and pedagogical methods, and university-wide support programs using this educational model. The purpose of the study was to establish the relationship between the English Immersion Program and Academic Performance among Chinese-ESL students enrolled at WKU for the academic year 2020-2021. Course length, immersion location, course type, and instructional design were the constructs of the English immersion program. English language learning, learning efficiency, and class participation were used to measure academic performance. Descriptive-correlational design was used in this cross-sectional research project. A quantitative approach for data analysis was applied to determine the relationship between the English immersion program and Chinese-ESL students’ academic performance. The research was conducted at WKU; a Chinese-American jointly established higher educational institution located in Wenzhou, Zhejiang province. Convenience, random, and snowball sampling of 283 students, a response rate of 10.5%, were applied to represent the WKU student population. The questionnaire was posted through the survey website named Wenjuanxing and shared to QQ or WeChat. Cronbach’s alpha was used to test the reliability of the research instrument. Findings revealed that when professors integrate technology (PowerPoint, videos, and audios) in teaching, students pay more attention. This contributes to the acquisition of more professional knowledge in their major courses. As to course immersion, students perceive WKU as a good place to study, providing them a high degree of confidence to talk with their professors in English. This also contributes to their English fluency and better pronunciation in their communication. In the construct of designing instruction, the use of pictures, video clips, and professors’ non-verbal communication, and demonstration of concern for students encouraged students to be more active in-class participation. Findings on course length and academic performance indicated that students’ perception regarding taking courses during fall and spring terms can moderately contribute to their academic performance. In conclusion, the findings revealed a significantly strong positive relationship between course type, immersion location, instructional design, and academic performance.

Keywords: class participation, English immersion program, English language learning, learning efficiency

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Authors: Soumava Boral, Sanjay K. Chaturvedi, Ian Howard, Kristoffer McKee, V. N. A. Naikan

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Due to strict regulations from government to enhance the possibilities of sustainability practices in industries, and noting the advances in sustainable manufacturing practices, it is necessary that the associated processes are also sustainable. Maintenance of large scale and complex machines is a pivotal task to maintain the uninterrupted flow of manufacturing processes. Appropriate maintenance practices can prolong the lifetime of machines, and prevent associated breakdowns, which subsequently reduces different cost heads. Selection of the best maintenance strategies for such machines are considered as a burdensome task, as they require the consideration of multiple technical criteria, complex mathematical calculations, previous fault data, maintenance records, etc. In the era of the fourth industrial revolution, organizations are rapidly changing their way of business, and they are giving their utmost importance to sensor technologies, artificial intelligence, data analytics, automations, etc. In this work, the effectiveness of several maintenance strategies (e.g., preventive, failure-based, reliability centered, condition based, total productive maintenance, etc.) related to a large scale and complex gearbox, operating in a steel processing plant is evaluated in terms of economic, social, environmental and technical criteria. As it is not possible to obtain/describe some criteria by exact numerical values, these criteria are evaluated linguistically by cross-functional experts. Fuzzy sets are potential soft-computing technique, which has been useful to deal with linguistic data and to provide inferences in many complex situations. To prioritize different maintenance practices based on the identified sustainable criteria, multi-criteria decision making (MCDM) approaches can be considered as potential tools. Multi-Attributive Ideal Real Comparative Analysis (MAIRCA) is a recent addition in the MCDM family and has proven its superiority over some well-known MCDM approaches, like TOPSIS (Technique for Order Preference by Similarity to Ideal Solution) and ELECTRE (ELimination Et Choix Traduisant la REalité). It has a simple but robust mathematical approach, which is easy to comprehend. On the other side, due to some inherent drawbacks of Intuitionistic Fuzzy Sets (IFS) and Pythagorean Fuzzy Sets (PFS), recently, the use of Fermatean Fuzzy Sets (FFSs) has been proposed. In this work, we propose the novel concept of FF-MAIRCA. We obtain the weights of the criteria by experts’ evaluation and use them to prioritize the different maintenance practices according to their suitability by FF-MAIRCA approach. Finally, a sensitivity analysis is carried out to highlight the robustness of the approach.

Keywords: Fermatean fuzzy sets, Fermatean fuzzy MAIRCA, maintenance strategy selection, sustainable manufacturing, MCDM

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Authors: Anna Demian, Levi Howard, L. Ng, Leslie Simon, Mark Dragon, A. Desai, Timothy Devlantes, W. David Freeman

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Introduction: Out-of-hospital cardiac arrest (OHCA) can carry a high mortality. For survivors, the most common complication is hypoxic-ischemic brain injury (HIBI). Rarely, lumbosacral spinal cord and/or other spinal cord artery ischemia can occur due to anatomic variation and variable mean arterial pressure after the return of spontaneous circulation. We present a case of an OHCA survivor who later woke up with bilateral leg weakness with preserved sensation (ASIA grade B, L2 level). Methods: We describe a clinical, radiographic, and laboratory presentation, as well as a National Library of Medicine (NLM) search engine methodology, characterizing incidence/prevalence of this entity is discussed. A 70-year-old male, a longtime smoker, and alcohol user, suddenly collapsed at a bar surrounded by friends. He had complained of chest pain before collapsing. 911 was called. EMS arrived, and the patient was in pulseless electrical activity (PEA), cardiopulmonary resuscitation (CPR) was initiated, and the patient was intubated, and a LUCAS device was applied for continuous, high-quality CPR in the field by EMS. In the ED, central lines were placed, and thrombolysis was administered for a suspected Pulmonary Embolism (PE). It was a prolonged code that lasted 90 minutes. The code continued with the eventual return of spontaneous circulation. The patient was placed on an epinephrine and norepinephrine drip to maintain blood pressure. ECHO was performed and showed a “D-shaped” ventricle worrisome for PE as well as an ejection fraction around 30%. A CT with PE protocol was performed and confirmed bilateral PE. Results: The patient woke up 24 hours later, following commands, and was extubated. He was found paraplegic below L2 with preserved sensation, with hypotonia and areflexia consistent with “spinal shock” or anterior spinal cord syndrome. MRI thoracic and lumbar spine showed a conus medullaris level spinal cord infarction. The patient was given IV steroids upon initial discovery of cord infarct. NLM search using “cardiac arrest” and “spinal cord infarction” revealed 57 results, with only 8 review articles. Risk factors include age, atherosclerotic disease, and intraaortic balloon pump placement. AoA (Artery of Adamkiewicz) anatomic variation along with existing atherosclerotic factors and low perfusion were also known risk factors. Conclusion: Acute paraplegia from anterior spinal cord infarction of the AoA territory after cardiac arrest is rare. Larger prospective, multicenter trials are needed to examine potential interventions of hypothermia, lumbar drains, which are sometimes used in aortic surgery to reduce ischemia and/or other neuroprotectants.

Keywords: cardiac arrest, spinal cord infarction, artery of Adamkiewicz, paraplegia

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Authors: Niamh Higgins, Dawn Howard

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The Irish agri-food sector is of major importance to Ireland’s manufacturing sector and to the Irish economy through employment and the exporting of animal products worldwide. Infectious diseases and parasites have an impact on farm animal health causing profitability and productivity to be affected. For the sustainability of Irish dairy farming, there must be the highest standard of animal health. There can be a lack of information in accounting for > 1% of complete microbial diversity in an environment. There is the tendency of culture-based methods of microbial identification to overestimate the prevalence of species which grow easily on an agar surface. There is a need for new technologies to address these issues to assist with animal health. Metagenomic approaches provide information on both the whole genome and transcriptome present through DNA sequencing of total DNA from environmental samples producing high determination of functional and taxonomic information. Nanopore Next Generation Technologies have the ability to be powerful sequencing technologies. They provide high throughput, low material requirements and produce ultra-long reads, simplifying the experimental process. The aim of this study is to use a metagenomics approach to analyze dairy cattle faecal samples using the Oxford Nanopore MinION Next Generation Sequencer and to establish an in-house pipeline for metagenomic characterization of complex samples. Faecal samples will be obtained from Irish dairy farms, DNA extracted and the MinION will be used for sequencing, followed by bioinformatics analysis. Of particular interest, will be the parasite Buxtonella sulcata, which there has been little research on and which there is no research on its presence on Irish dairy farms. Preliminary results have shown the ability of the MinION to produce hundreds of reads in a relatively short time frame of eight hours. The faecal samples were obtained from 90 dairy cows on a Galway farm. The results from Oxford Nanopore ‘What’s in my pot’ (WIMP) using the Epi2me workflow, show that from a total of 926 classified reads, 87% were from the Kingdom Bacteria, 10% were from the Kingdom Eukaryota, 3% were from the Kingdom Archaea and < 1% were from the Kingdom Viruses. The most prevalent bacteria were those from the Genus Acholeplasma (71 reads), Bacteroides (35 reads), Clostridium (33 reads), Acinetobacter (20 reads). The most prevalent species present were those from the Genus Acholeplasma and included Acholeplasma laidlawii (39 reads) and Acholeplasma brassicae (26 reads). The preliminary results show the ability of the MinION for the identification of microorganisms to species level coming from a complex sample. With ongoing optimization of the pipe-line, the number of classified reads are likely to increase. Metagenomics has the potential in animal health for diagnostics of microorganisms present on farms. This would support wprevention rather than a cure approach as is outlined in the DAFMs National Farmed Animal Health Strategy 2017-2022.

Keywords: animal health, buxtonella sulcata, infectious disease, irish dairy cattle, metagenomics, minION, next generation sequencing

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Authors: Iman Farasat, Howard M. Salis

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Engineered genetic circuits reprogram cellular behavior to act as living computers with applications in detecting cancer, creating self-controlling artificial tissues, and dynamically regulating metabolic pathways. Phenemenological models are often used to simulate and design genetic circuit behavior towards a desired behavior. While such models assume that each circuit component’s function is modular and independent, even small changes in a circuit (e.g. a new promoter, a change in transcription factor expression level, or even a new media) can have significant effects on the circuit’s function. Here, we use statistical thermodynamics to account for the several factors that control transcriptional regulation in bacteria, and experimentally demonstrate the model’s accuracy across 825 measurements in several genetic contexts and hosts. We then employ our first principles model to design, experimentally construct, and characterize a family of signal amplifying genetic circuits (genetic OpAmps) that expand the dynamic range of cell sensors. To develop these models, we needed a new approach to measuring the in vivo binding free energies of transcription factors (TFs), a key ingredient of statistical thermodynamic models of gene regulation. We developed a new high-throughput assay to measure RNA polymerase and TF binding free energies, requiring the construction and characterization of only a few constructs and data analysis (Figure 1A). We experimentally verified the assay on 6 TetR-homolog repressors and a CRISPR/dCas9 guide RNA. We found that our binding free energy measurements quantitatively explains why changing TF expression levels alters circuit function. Altogether, by combining these measurements with our biophysical model of translation (the RBS Calculator) as well as other measurements (Figure 1B), our model can account for changes in TF binding sites, TF expression levels, circuit copy number, host genome size, and host growth rate (Figure 1C). Model predictions correctly accounted for how these 8 factors control a promoter’s transcription rate (Figure 1D). Using the model, we developed a design framework for engineering multi-promoter genetic circuits that greatly reduces the number of degrees of freedom (8 factors per promoter) to a single dimensionless unit. We propose the Ptashne (Pt) number to encapsulate the 8 co-dependent factors that control transcriptional regulation into a single number. Therefore, a single number controls a promoter’s output rather than these 8 co-dependent factors, and designing a genetic circuit with N promoters requires specification of only N Pt numbers. We demonstrate how to design genetic circuits in Pt number space by constructing and characterizing 15 2-repressor OpAmp circuits that act as signal amplifiers when within an optimal Pt region. We experimentally show that OpAmp circuits using different TFs and TF expression levels will only amplify the dynamic range of input signals when their corresponding Pt numbers are within the optimal region. Thus, the use of the Pt number greatly simplifies the genetic circuit design, particularly important as circuits employ more TFs to perform increasingly complex functions.

Keywords: transcription factor, synthetic biology, genetic circuit, biophysical model, binding energy measurement

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Authors: V. Howard, R. Maguire, S. Corrigan

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Background: Type 1 Diabetes (T1D) is a chronic autoimmune disease, typically diagnosed in childhood. T1D puts an enormous strain on families; controlling blood-glucose in children is difficult and the consequences of poor control for patient health are significant. Successful illness management and better health outcomes can be dependent on quality of caregiving. On diagnosis, parent-caregivers face a steep learning curve as T1D care requires a significant level of knowledge to inform complex decision making throughout the day. The majority of illness management is carried out in the home setting, independent of clinical health providers. Parent-caregivers vary in their level of knowledge and their level of engagement in applying this knowledge in the practice of illness management. Enabling researchers to quantify these aspects of the caregiver experience is key to identifying targets for psychosocial support interventions, which are desirable for reducing stress and anxiety in this highly burdened cohort, and supporting better health outcomes in children. Currently, there are limited tools available that are designed to capture this information. Where tools do exist, they are not comprehensive and do not adequately capture the lived experience. Objectives: Development of quantitative tools, informed by lived experience, to enable researchers gather data on parent-caregiver knowledge and engagement, which accurately represents the experience/cohort and enables exploration of questions that are of real-world value to the cohort themselves. Methods: This research employed an engaged approach to address the problem of quantifying two key aspects of caregiver diabetes management: Knowledge and engagement. The research process was multi-staged and iterative. Stage 1: Working from a constructivist standpoint, literature was reviewed to identify relevant questionnaires, scales and single-item measures of T1D caregiver knowledge and engagement, and harvest candidate questionnaire items. Stage 2: Aggregated findings from the review were circulated among a PPI (patient and public involvement) expert panel of caregivers (n=6), for discussion and feedback. Stage 3: In collaboration with the expert panel, data were interpreted through the lens of lived experience to create a long-list of candidate items for novel questionnaires. Items were categorized as either ‘knowledge’ or ‘engagement’. Stage 4: A Delphi-method process (iterative surveys) was used to prioritize question items and generate novel questions that further captured the lived experience. Stage 5: Both questionnaires were piloted to refine wording of text to increase accessibility and limit socially desirable responding. Stage 6: Tools were piloted using an online survey that was deployed using an online peer-support group for caregivers for Juveniles with T1D. Ongoing Research: 123 parent-caregivers completed the survey. Data analysis is ongoing to establish face and content validity qualitatively and through exploratory factor analysis. Reliability will be established using an alternative-form method and Cronbach’s alpha will assess internal consistency. Work will be completed by early 2024. Conclusion: These tools will enable researchers to gain deeper insights into caregiving practices among parents of juveniles with T1D. Development was driven by lived experience, illustrating the value of engaged research at all levels of the research process.

Keywords: caregiving, engaged research, juvenile type 1 diabetes, quantified engagement and knowledge

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Authors: Tim Crocker-Buque, Sandra Mounier-Jack, Natasha Howard

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Background: Due to both the increasing scale and speed of urbanisation, urban areas in low and middle-income countries (LMICs) host increasingly large populations of under-immunized children, with the additional associated risks of rapid disease transmission in high-density living environments. Multiple interdependent factors are associated with these coverage disparities in urban areas and most evidence comes from relatively few countries, e.g., predominantly India, Kenya, Nigeria, and some from Pakistan, Iran, and Brazil. This study aimed to identify, describe, and assess the main tools used to measure or improve coverage of immunisation services in poor urban areas. Methods: Authors used a qualitative review design, including academic and non-academic literature, to identify tools used to improve coverage of public health interventions in urban areas. Authors selected and extracted sources that provided good examples of specific tools, or categories of tools, used in a context relevant to urban immunization. Diagnostic (e.g., for data collection, analysis, and insight generation) and programme tools (e.g., for investigating or improving ongoing programmes) and interventions (e.g., multi-component or stand-alone with evidence) were selected for inclusion to provide a range of type and availability of relevant tools. These were then prioritised using a decision-analysis framework and a tool selection guide for programme managers developed. Results: Authors reviewed tools used in urban immunisation contexts and tools designed for (i) non-immunization and/or non-health interventions in urban areas, and (ii) immunisation in rural contexts that had relevance for urban areas (e.g., Reaching every District/Child/ Zone). Many approaches combined several tools and methods, which authors categorised as diagnostic, programme, and intervention. The most common diagnostic tools were cross-sectional surveys, key informant interviews, focus group discussions, secondary analysis of routine data, and geographical mapping of outcomes, resources, and services. Programme tools involved multiple stages of data collection, analysis, insight generation, and intervention planning and included guidance documents from WHO (World Health Organisation), UNICEF (United Nations Children's Fund), USAID (United States Agency for International Development), and governments, and articles reporting on diagnostics, interventions, and/or evaluations to improve urban immunisation. Interventions involved service improvement, education, reminder/recall, incentives, outreach, mass-media, or were multi-component. The main gaps in existing tools were an assessment of macro/policy-level factors, exploration of effective immunization communication channels, and measuring in/out-migration. The proposed framework uses a problem tree approach to suggest tools to address five common challenges (i.e. identifying populations, understanding communities, issues with service access and use, improving services, improving coverage) based on context and available data. Conclusion: This study identified many tools relevant to evaluating urban LMIC immunisation programmes, including significant crossover between tools. This was encouraging in terms of supporting the identification of common areas, but problematic as data volumes, instructions, and activities could overwhelm managers and tools are not always suitably applied to suitable contexts. Further research is needed on how best to combine tools and methods to suit local contexts. Authors’ initial framework can be tested and developed further.

Keywords: health equity, immunisation, low and middle-income countries, poverty, urban health

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