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Article ; Online: Comorbidities in the UK Primary Sjögren’s Syndrome Registry

Jessica Tarn / Dennis Lendrem / Michael Barnes / John Casement / Wan-Fai Ng

Frontiers in Immunology, Vol

2022 Volume 13

Abstract: IntroductionPrimary Sjögren’s Syndrome (PSS) is a chronic disease characterised by symptoms of oral and ocular dryness, pain, fatigue, anxiety and depression. PSS patients can be subclassified by the pattern of severity of these five key symptoms using ... ...

Abstract	IntroductionPrimary Sjögren’s Syndrome (PSS) is a chronic disease characterised by symptoms of oral and ocular dryness, pain, fatigue, anxiety and depression. PSS patients can be subclassified by the pattern of severity of these five key symptoms using the Newcastle Sjögren’s Stratification Tool (NSST). Although PSS is often associated with one or more comorbidities, the relationship between comorbidities, polypharmacy, and PSS symptom burden is unclear. Using data from the UK Primary Sjögren’s Syndrome Registry (UKPSSR) we describe the landscape of polypharmacy and comorbidities in PSS.MethodsThe UKPSSR is research biobank of clinically well-defined PSS patients where clinical, demographic, comorbidities and concomitant medications data are recorded. Patients were subclassified into the four NSST subgroups: Low Symptom Burden (LSB), High Symptom Burden (HSB), Dryness Dominated Fatigue (DDF) and Pain Dominated Fatigue (PDF). Group analyses of comorbid conditions and polypharmacy scores were performed. Comorbidity and Polypharmacy Scores (CPS) were modelled as a function of age, sex, symptom duration, body mass index (BMI), current immunosuppressant and hydroxychloroquine prescriptions and NSST subgroup.ResultsThere were marked differences in the number and the nature of comorbidities associated with the NSST subgroups. LSB and DDF patients were characterized by fewer comorbidities and medications. In contrast, HSB and PDF patients were associated with more comorbidities and were more likely to be prescribed multiple medications. Group analysis shows that HSB patients are more closely associated with peripheral vascular disease and infection whereas the PDF patients were associated with cardiovascular disease and gastrointestinal comorbidities. Comorbidity and polypharmacy scores increase with age and BMI regardless of symptom subgroup and symptom duration. In addition, the longer the reported symptom duration the higher the associated comorbidities and polypharmacy scores.ConclusionComorbid conditions are more ...
Keywords	Sjogren’s syndrome ; comorbidity ; crossectional analysis ; polypharmacy ; stratified medicine ; Immunologic diseases. Allergy ; RC581-607
Subject code	610
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ferrocenophanium Stability and Catalysis

Sai Anvesh Bezawada / Neira Ušto / Chloe Wilke / Michael Barnes-Flaspoler / Rajamoni Jagan / Eike B. Bauer

Molecules, Vol 28, Iss 2729, p

2023 Volume 2729

Abstract: Ferrocenium catalysis is a vibrant research area, and an increasing number of ferrocenium-catalyzed processes have been reported in the recent years. However, the ferrocenium cation is not very stable in solution, which may potentially hamper catalytic ... ...

Abstract	Ferrocenium catalysis is a vibrant research area, and an increasing number of ferrocenium-catalyzed processes have been reported in the recent years. However, the ferrocenium cation is not very stable in solution, which may potentially hamper catalytic applications. In an effort to stabilize ferrocenium-type architectures by inserting a bridge between the cyclopentadienyl rings, we investigated two ferrocenophanium (or ansa -ferrocenium) cations with respect to their stability and catalytic activity in propargylic substitution reactions. One of the ferrocenophanium complexes was characterized by single crystal X-ray diffraction. Cyclic voltammetry experiments of the ferrocenophane parent compounds were performed in the absence and presence of alcohol nucleophiles, and the stability of the cations in solution was judged based on the reversibility of the electron transfer. The experiments revealed a moderate stabilizing effect of the bridge, albeit the effect is not very pronounced or straightforward. Catalytic propargylic substitution test reactions revealed decreased activity of the ferrocenophanium cations compared to the ferrocenium cation. It appears that the somewhat stabilized ferrocenophanium cations show decreased catalytic activity.
Keywords	ferrocenophanium cations ; catalyst stability ; propargylic substitution reactions ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Predicting suicidal thoughts and behavior among adolescents using the risk and protective factor framework

Orion Weller / Luke Sagers / Carl Hanson / Michael Barnes / Quinn Snell / E. Shannon Tass

PLoS ONE, Vol 16, Iss

A large-scale machine learning approach

2021 Volume 11

Abstract: Introduction Addressing the problem of suicidal thoughts and behavior (STB) in adolescents requires understanding the associated risk factors. While previous research has identified individual risk and protective factors associated with many adolescent ... ...

Abstract	Introduction Addressing the problem of suicidal thoughts and behavior (STB) in adolescents requires understanding the associated risk factors. While previous research has identified individual risk and protective factors associated with many adolescent social morbidities, modern machine learning approaches can help identify risk and protective factors that interact (group) to provide predictive power for STB. This study aims to develop a prediction algorithm for STB among adolescents using the risk and protective factor framework and social determinants of health. Methods The sample population consisted of more than 179,000 high school students living in Utah and participating in the Communities That Care (CTC) Youth Survey from 2011-2017. The dataset includes responses to 300+ questions from the CTC and 8000+ demographic factors from the American Census Survey for a total of 1.2 billion values. Machine learning techniques were employed to extract the survey questions that were best able to predict answers indicative of STB, using recent work in interpretable machine learning. Results Analysis showed strong predictive power, with the ability to predict individuals with STB with 91% accuracy. After extracting the top ten questions that most affected model predictions, questions fell into four main categories: familial life, drug consumption, demographics, and peer acceptance at school. Conclusions Modern machine learning approaches provide new methods for understanding the interaction between root causes and outcomes, such as STB. The model developed in this study showed significant improvement in predictive accuracy compared to previous research. Results indicate that certain risk and protective factors, such as adolescents being threatened or harassed through digital media or bullied at school, and exposure or involvement in serious arguments and yelling at home are the leading predictors of STB and can help narrow and reaffirm priority prevention programming and areas of focused policymaking.
Keywords	Medicine ; R ; Science ; Q
Subject code	370
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Predicting suicidal thoughts and behavior among adolescents using the risk and protective factor framework

Orion Weller / Luke Sagers / Carl Hanson / Michael Barnes / Quinn Snell / E Shannon Tass

PLoS ONE, Vol 16, Iss 11, p e

A large-scale machine learning approach.

2021 Volume 0258535

Abstract	Introduction Addressing the problem of suicidal thoughts and behavior (STB) in adolescents requires understanding the associated risk factors. While previous research has identified individual risk and protective factors associated with many adolescent social morbidities, modern machine learning approaches can help identify risk and protective factors that interact (group) to provide predictive power for STB. This study aims to develop a prediction algorithm for STB among adolescents using the risk and protective factor framework and social determinants of health. Methods The sample population consisted of more than 179,000 high school students living in Utah and participating in the Communities That Care (CTC) Youth Survey from 2011-2017. The dataset includes responses to 300+ questions from the CTC and 8000+ demographic factors from the American Census Survey for a total of 1.2 billion values. Machine learning techniques were employed to extract the survey questions that were best able to predict answers indicative of STB, using recent work in interpretable machine learning. Results Analysis showed strong predictive power, with the ability to predict individuals with STB with 91% accuracy. After extracting the top ten questions that most affected model predictions, questions fell into four main categories: familial life, drug consumption, demographics, and peer acceptance at school. Conclusions Modern machine learning approaches provide new methods for understanding the interaction between root causes and outcomes, such as STB. The model developed in this study showed significant improvement in predictive accuracy compared to previous research. Results indicate that certain risk and protective factors, such as adolescents being threatened or harassed through digital media or bullied at school, and exposure or involvement in serious arguments and yelling at home are the leading predictors of STB and can help narrow and reaffirm priority prevention programming and areas of focused policymaking.
Keywords	Medicine ; R ; Science ; Q
Subject code	370
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Influence of Heat Treatment and Tannin Impregnation on Boron Depletion and Wood Durability

Dercilio Junior Verly Lopes / H. Michael Barnes / Gabrielly dos Santos Bobadilha

Forests, Vol 11, Iss 2, p

2020 Volume 201

Abstract: Heat treatment (HT) of a mixture of tannins and inorganic boron compounds showed effective results against wood decay organisms. Boron compounds play a critical role in the preservation of wood against wood decay organisms. The use of tannins and HT ... ...

Abstract	Heat treatment (HT) of a mixture of tannins and inorganic boron compounds showed effective results against wood decay organisms. Boron compounds play a critical role in the preservation of wood against wood decay organisms. The use of tannins and HT represents a relatively new environmentally friendly approach to the wood preservation industry. The aim of this study was to investigate the effect of tannin impregnation and HT on boron depletion, and termite and fungi resistance. Southern yellow pine (SYP) and yellow-poplar (YP) cube samples were used for this study. A mixture of condensed tannins from the Quebracho tree and disodium octaborate tetrahydrate (DOT) was injected into the specimens using a vacuum/pressure cycle, and the specimens were then heat-treated under N 2 atmosphere for four hours at 190 °C to investigate both the tannin’s fixative ability to reduce boron leaching and the performance of the mixture against brown and white-rot fungi and termites. Tannins restricted boron leaching in 46% and 34% for SYP and YP, respectively, and also significantly increased the resistance against white-rot fungi for YP. Tannins and HT showed unpredictably good performance against termites. Tannins may be acting to denature proteins; in that case, fungal enzymes would be inhibited. This study revealed the importance of HT on a mixture of boron and tannins to decrease boron leaching and increase the durability of preservative systems.
Keywords	heat treatment ; dot ; tannins ; leaching ; termites ; fungi ; Plant ecology ; QK900-989
Subject code	580
Language	English
Publishing date	2020-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The clinical potential of optogenetic interrogation of pathogenesis

Tianyu Terry Gao / Teak‐Jung Oh / Kritika Mehta / Yu‐En Andrew Huang / Tyler Camp / Huaxun Fan / Jeong Won Han / Collin Michael Barnes / Kai Zhang

Clinical and Translational Medicine, Vol 13, Iss 5, Pp n/a-n/a (2023)

2023

Abstract: Abstract Background Opsin‐based optogenetics has emerged as a powerful biomedical tool using light to control protein conformation. Such capacity has been initially demonstrated to control ion flow across the cell membrane, enabling precise control of ... ...

Abstract	Abstract Background Opsin‐based optogenetics has emerged as a powerful biomedical tool using light to control protein conformation. Such capacity has been initially demonstrated to control ion flow across the cell membrane, enabling precise control of action potential in excitable cells such as neurons or muscle cells. Further advancement in optogenetics incorporates a greater variety of photoactivatable proteins and results in flexible control of biological processes, such as gene expression and signal transduction, with commonly employed light sources such as LEDs or lasers in optical microscopy. Blessed by the precise genetic targeting specificity and superior spatiotemporal resolution, optogenetics offers new biological insights into physiological and pathological mechanisms underlying health and diseases. Recently, its clinical potential has started to be capitalized, particularly for blindness treatment, due to the convenient light delivery into the eye. Aims and methods This work summarizes the progress of current clinical trials and provides a brief overview of basic structures and photophysics of commonly used photoactivable proteins. We highlight recent achievements such as optogenetic control of the chimeric antigen receptor, CRISPR‐Cas system, gene expression, and organelle dynamics. We discuss conceptual innovation and technical challenges faced by current optogenetic research. Conclusion In doing so, we provide a framework that showcases ever‐growing applications of optogenetics in biomedical research and may inform novel precise medicine strategies based on this enabling technology.
Keywords	channelrhodopsin ; non‐opsin‐based ; opsin‐based ; optogenetics ; photoactivatable proteins ; protein‐protein interaction ; Medicine (General) ; R5-920
Subject code	612
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Breeding and genetics key to stemming Pierce's disease

Michael Barnes

California Agriculture, Vol 57, Iss 3, Pp 69-

2003 Volume 70

Keywords	Agriculture ; S ; Agriculture (General) ; S1-972
Language	English
Publishing date	2003-07-01T00:00:00Z
Publisher	University of California Agriculture and Natural Resources
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using technology to reduce critical deterioration (the DETECT study)

Eduardo Costa / Céu Mateus / Bernie Carter / Holly Saron / Chin-Kien Eyton-Chong / Fulya Mehta / Steven Lane / Sarah Siner / Jason Dean / Michael Barnes / Chris McNally / Caroline Lambert / Bruce Hollingsworth / Enitan D. Carrol / Gerri Sefton

BMC Health Services Research, Vol 23, Iss 1, Pp 1-

a cost analysis of care costs at a tertiary children's hospital in the United Kingdom

2023 Volume 10

Abstract: Abstract Background Electronic early warning systems have been used in adults for many years to prevent critical deterioration events (CDEs). However, implementation of similar technologies for monitoring children across the entire hospital poses ... ...

Abstract	Abstract Background Electronic early warning systems have been used in adults for many years to prevent critical deterioration events (CDEs). However, implementation of similar technologies for monitoring children across the entire hospital poses additional challenges. While the concept of such technologies is promising, their cost-effectiveness is not established for use in children. In this study we investigate the potential for direct cost savings arising from the implementation of the DETECT surveillance system. Methods Data were collected at a tertiary children’s hospital in the United Kingdom. We rely on the comparison between patients in the baseline period (March 2018 to February 2019) and patients in the post-intervention period (March 2020 to July 2021). These provided a matched cohort of 19,562 hospital admissions for each group. From these admissions, 324 and 286 CDEs were observed in the baseline and post-intervention period, respectively. Hospital reported costs and Health Related Group (HRG) National Costs were used to estimate overall expenditure associated with CDEs for both groups of patients. Results Comparing post-intervention with baseline data we found a reduction in the total number of critical care days, driven by an overall reduction in the number of CDEs, however without statistical significance. Using hospital reported costs adjusted for the Covid-19 impact, we estimate a non-significant reduction of total expenditure from £16.0 million to £14.3 million (corresponding to £1.7 million of savings – 11%). Additionally, using HRG average costs, we estimated a non-significant reduction of total expenditure from £8.2 million to £ 7.2 million (corresponding to £1.1 million of savings – 13%). Discussion and conclusion Unplanned critical care admissions for children not only impose a substantial burden on patients and families but are also costly for hospitals. Interventions aimed at reducing emergency critical care admissions can be crucial to contribute to the reduction of these episodes’ ...
Keywords	Children’s critical care ; Cost analysis ; Critical deterioration events ; Paediatric ; Paediatric early warning system score ; Paediatric early warning system ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigation of the Utility of Features in a Clinical De-identification Model

Tanmoy Paul / Md Kamruz Zaman Rana / Preethi Aishwarya Tautam / Teja Venkat Pavan Kotapati / Yaswitha Jampani / Nitesh Singh / Humayera Islam / Vasanthi Mandhadi / Vishakha Sharma / Michael Barnes / Richard D. Hammer / Abu Saleh Mohammad Mosa

Frontiers in Digital Health, Vol

A Demonstration Using EHR Pathology Reports for Advanced NSCLC Patients

2022 Volume 4

Abstract: BackgroundElectronic health record (EHR) systems contain a large volume of texts, including visit notes, discharge summaries, and various reports. To protect the confidentiality of patients, these records often need to be fully de-identified before ... ...

Abstract	BackgroundElectronic health record (EHR) systems contain a large volume of texts, including visit notes, discharge summaries, and various reports. To protect the confidentiality of patients, these records often need to be fully de-identified before circulating for secondary use. Machine learning (ML) based named entity recognition (NER) model has emerged as a popular technique of automatic de-identification.ObjectiveThe performance of a machine learning model highly depends on the selection of appropriate features. The objective of this study was to investigate the usability of multiple features in building a conditional random field (CRF) based clinical de-identification NER model.MethodsUsing open-source natural language processing (NLP) toolkits, we annotated protected health information (PHI) in 1,500 pathology reports and built supervised NER models using multiple features and their combinations. We further investigated the dependency of a model's performance on the size of training data.ResultsAmong the 10 feature extractors explored in this study, n-gram, prefix–suffix, word embedding, and word shape performed the best. A model using combination of these four feature sets yielded precision, recall, and F1-score for each PHI as follows: NAME (0.80; 0.79; 0.80), LOCATION (0.85; 0.83; 0.84), DATE (0.86; 0.79; 0.82), HOSPITAL (0.96; 0.93; 0.95), ID (0.99; 0.82; 0.90), and INITIALS (0.97; 0.49; 0.65). We also found that the model's performance becomes saturated when the training data size is beyond 200.ConclusionManual de-identification of large-scale data is an impractical procedure since it is time-consuming and subject to human errors. Analysis of the NER model's performance in this study sheds light on a semi-automatic clinical de-identification pipeline for enterprise-wide data warehousing.
Keywords	clinical text de-identification ; protected health information ; NLP ; named entity recognition ; de-identification ; conditional random field ; Medicine ; R ; Public aspects of medicine ; RA1-1270 ; Electronic computers. Computer science ; QA75.5-76.95
Subject code	006
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Clinical practice guidelines in the diagnosis and management of acute pancreatitis

Hiroyuki Kinoshita / Jianhua Zhang / Aroon Ponthisarn / Manoj Sharma / Nguyen Binh / Alex Siam / Chandika Samaranayake / Arnold Darnindro / Michael Barnes

Studia Medyczne, Vol 35, Iss 4, Pp 304-

2019 Volume 311

Abstract: Acute pancreatitis (AP) continues to be a cause of significant morbidity and mortality and requires more research to identify the best clinical management practices. Many guidelines have been proposed for the initial management of AP. Although these ... ...

Abstract	Acute pancreatitis (AP) continues to be a cause of significant morbidity and mortality and requires more research to identify the best clinical management practices. Many guidelines have been proposed for the initial management of AP. Although these guidelines have a significant overlap in the recommendations provided for diagnosing and managing AP, there is still some disagreement in aspects of the types and timing of interventions that should be used for the diagnosis and management of both mild and severe AP. A working group consisting of physicians, especially gastroenterologists from various hospitals and universities from the Asia-Pacific region, has led to the development of these evidence-based guidelines and recommendations. Early enteral feedings, performing a cholecystectomy in the case of gallstones if indicated during the initial hospitalisation, treatment of hypertriglyceridaemia-induced acute pancreatitis using intravenous regular insulin or plasmapheresis if severe, and providing counselling for alcohol avoidance are recommended.
Keywords	diagnosis ; management ; acute pancreatitis ; evidence-based recommendations ; clinical practice guidelines ; Medicine ; R
Language	English
Publishing date	2019-12-01T00:00:00Z
Publisher	Termedia Publishing House
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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