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1.
Article in English | MEDLINE | ID: mdl-38640067

ABSTRACT

We critically evaluate the current status of portable mass spectrometry (pMS), particularly where this aligns with ambient ionization. Assessing the field of pMS can be quite subjective, especially in relation to the portable aspects of design, deployment, and operation. In this review, we discuss what it means to be portable and introduce a set of criteria by which pMS and ambient ionization sources can be assessed. Moreover, we consider the recent literature in terms of the most popular and significant advances in portable instrumentation for ambient ionization and miniature mass spectrometers. Finally, emerging trends and exciting future prospects are discussed and some recommendations are offered.

2.
Article in English | MEDLINE | ID: mdl-38369906

ABSTRACT

There is high demand for specialist mental health services for children and young people in the UK. Non-mental health nurses are well-placed to assess the mental health needs and risks of children and young people to maximise opportunities for early intervention and relieve the pressure on child and adolescent mental health services. This article provides an overview of a service development project to develop a web-based application (app) to support non-mental health nurses when assessing the mental health needs and risks of children and young people. The article describes the development, testing and evaluation process, which involved consultation with children and young people as well as interviews, focus groups and an online survey with a range of professionals working with children and young people. Overall, the findings suggest that the app is appropriate for use by non-mental health nurses in terms of quality, functionality and acceptability.

3.
PLoS One ; 19(1): e0285093, 2024.
Article in English | MEDLINE | ID: mdl-38236918

ABSTRACT

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.


Subject(s)
Biological Ontologies , COVID-19 , Communicable Diseases , Virus Diseases , Humans , Pandemics , Vocabulary, Controlled , COVID-19/epidemiology
4.
Standards (Basel) ; 3(3): 316-340, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37873508

ABSTRACT

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors' rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs.

5.
Analyst ; 148(21): 5366-5379, 2023 Oct 23.
Article in English | MEDLINE | ID: mdl-37702052

ABSTRACT

Paracetamol overdose is a leading cause of acute liver failure that can prove fatal. Establishing paracetamol concentration accurately and quickly is critical. Current detection methods are invasive, time-consuming and/or expensive. Non-invasive, rapid and cost-effective techniques are urgently required. To address this challenge, a novel approach, called Paper-Arrow Mass Spectrometry (PA-MS) has been developed. This technique combines sample collection, extraction, enrichment, separation and ionisation onto a single paper strip, and the entire analysis process, from sample to result, can be carried out in less than 10 min requiring only 2 µL of raw human saliva. PA-MS achieved a LOQ of 185 ng mL-1, mean recovery of 107 ± 7%, mean accuracy of 11 ± 8% and precision ≤5% using four concentrations, and had excellent linearity (r2 = 0.9988) in the range of 0.2-200 µg mL-1 covering the treatment concentration range, surpassing the best-in-class methods currently available for paracetamol analysis. Furthermore, from a panel of human saliva samples, inter-individual variability was found to be <10% using this approach. This technique represents a promising tool for rapid and accurate emergency diagnosis.

6.
Analyst ; 148(19): 4677-4687, 2023 Sep 25.
Article in English | MEDLINE | ID: mdl-37697928

ABSTRACT

Surface-enhanced Raman scattering (SERS) is a powerful technique for detecting trace amounts of analytes. However, the performance of SERS substrates depends on many variables including the enhancement factor, morphology, consistency, and interaction with target analytes. In this study, we investigated, for the first time, the use of electrospray deposition (ESD) combined with a novel ambient focusing DC ion funnel to deposit a high density of gold nanoparticles (AuNPs) to generate large-area, uniform substrates for highly sensitive SERS analysis. We found that the combination of ambient ion focusing with ESD facilitated high-density and intact deposition of non-spherical NPs. This also allowed us to take advantage of a polydisperse colloidal solution of AuNPs (consisting of nanospheres and nanorods), as confirmed by finite-difference time domain (FDTD) simulations. Our SERS substrate exhibited excellent capture capacity for model analyte molecules, namely 4-aminothiophenol (4-ATP) and Rhodamine 6G (R6G), with detection limits in the region of 10-11 M and a relative standard deviation of <6% over a large area (∼500 × 500 µm2). Additionally, we assessed the quantitative performance of our SERS substrate using the R6G probe molecule. The results demonstrated excellent linearity (R2 > 0.99) over a wide concentration range (10-4 M to 10-10 M) with a detection limit of 80 pM.

7.
Mikrochim Acta ; 190(6): 215, 2023 05 12.
Article in English | MEDLINE | ID: mdl-37171648

ABSTRACT

The detection of biogenic amines released from degraded meats is an effective method for evaluating meat freshness. However, existing traditional methods like titration are deemed tedious, while the use of sophisticated analytical instruments is not amenable to field testing. Herein, a cyanostilbene-based fluorescent array was rapidly fabricated using macroarray synthesis on a cellulose paper surface to detect amines liberated from spoiled beef, fish, and chicken. The fluorescence changes of immobilized molecules from the interaction with gaseous amines were used to monitor changes in freshness levels. Thanks to the high-throughput nature of macroarray synthesis, a set of highly responsive molecules such as pyridinium and dicyanovinyl moieties were quickly revealed. Importantly, this method offers flexibility in sensing applications including (1) sensing by individual sensor molecules, where the fluorescence response correlated well with established titration methods, and (2) collective sensing whereby chemometric analysis was used to provide a cutoff of freshness with 73-100% accuracy depending on meat types. Overall, this study paves the way for a robust and cost-effective tool for monitoring meat freshness.


Subject(s)
Biogenic Amines , Meat , Animals , Cattle , Meat/analysis , Biogenic Amines/analysis , Coloring Agents , Fishes , Chickens
8.
Int J Infect Dis ; 127: 63-68, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36436752

ABSTRACT

OBJECTIVES: We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection. METHODS: We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection. RESULTS: Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective. CONCLUSION: Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , COVID-19/epidemiology , SARS-CoV-2 , South Africa/epidemiology , Hospitalization , Laboratories
9.
J Biomed Semantics ; 13(1): 25, 2022 10 21.
Article in English | MEDLINE | ID: mdl-36271389

ABSTRACT

BACKGROUND: The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO) in early 2020. RESULTS: As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. CONCLUSION: CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications.


Subject(s)
COVID-19 , Communicable Diseases , Coronavirus , Vaccines , Humans , SARS-CoV-2 , Pandemics , Amino Acids , COVID-19 Drug Treatment
10.
medRxiv ; 2022 Jul 01.
Article in English | MEDLINE | ID: mdl-35794899

ABSTRACT

Objective: We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection. Methods: We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination and prior infection. Results: Among 3,793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had lower risk of severe outcomes than previous waves. Prior infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for boosted vs. no vaccine) were protective. Conclusion: Disease severity was similar amongst diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to prior infection and vaccination, both of which were strongly protective.

11.
Foods ; 11(12)2022 Jun 08.
Article in English | MEDLINE | ID: mdl-35741884

ABSTRACT

Olfactory dysfunction often has severe consequences on patients' quality of life. The most common complaint in these patients is their reduced enjoyment of food in both patients with olfactory loss and parosmia. How the different types of olfactory dysfunction differ in relation to food and cooking habits, sensory awareness, and food-related quality of life has not yet received much attention. By applying questionnaires on cooking, food, olfactory function, weight changes, sensory awareness, and food-related quality of life, we investigated how various aspects of eating differ between participants with olfactory loss (n = 271), parosmia (n = 251), and normosmic controls (n = 166). Cooking habits in olfactory dysfunction revealed pronounced differences as compared with normosmic controls. Cooking with olfactory dysfunction was associated with, e.g., a lack of comfort and inspiration for cooking and an inability to make new foods successfully. Significant differences in cooking were also found between olfactory loss and parosmia. Food items were less familiar in participants with olfactory loss and parosmia, while the ratings of liking food items differed between olfactory loss and parosmia, indicating the importance of adapting ingredients in meals separately for olfactory loss and parosmia. Parosmia was associated with a higher incidence of weight loss, but we found no difference in food-related quality of life between participants with olfactory loss and parosmia. While olfactory loss and parosmia have wide-ranging consequences on patients' cooking and food habits, adapting meals to include 'safer food items' and integrating multisensory stimulation may be a possible avenue for improving the enjoyment of food.

12.
Surg Endosc ; 36(11): 8255-8260, 2022 11.
Article in English | MEDLINE | ID: mdl-35474390

ABSTRACT

BACKGROUND: The use of the magnetic sphincter augmentation (MSA) in patients with de novo or persistent gastroesophageal reflux disease (GERD) after sleeve gastrectomy has not been thoroughly investigated. OBJECTIVE: The aim of this study is to evaluate the efficacy of MSA device placement in improving GERD symptoms and reducing anti-reflux medication usage in patients with persistent or de novo GERD after sleeve gastrectomy. METHODS: This is a retrospective analysis of patients who underwent laparoscopic MSA device placement between January 2018 and July 2020 after sleeve gastrectomy. RESULTS: A total of twenty-two patients met inclusion criteria. Twenty patients were female (91%) and two patients were male (9%). All patients were taking anti-reflux medications daily to control GERD symptoms prior to MSA device placement. There was a significant improvement in the mean GERD-HRQL survey scores when comparing scores prior to (43.8) and after (16.7) MSA device placement (p < 0.0001). Majority of the patients did well without any post-operative complications (77%). Nearly 82% of patients were no longer taking any anti-acid medications after MSA device placement (p < 0.0485). There were no patients that required MSA device removals. There were no adverse events such as MSA device erosions or device-related mortalities. CONCLUSIONS: MSA device placement in patients with medically refractory GERD after sleeve gastrectomy is a safe and viable alternative to Roux-en-Y gastric bypass without conferring additional risks. We show an improvement in reflux symptoms after MSA device placement as evidenced by decreased post-operative GERD-HRQL scores, decreased anti-acid medication usage, and overall patient satisfaction with the procedure. Further prospective and comparative studies with longer term follow-up are needed to validate the use of MSA in patients who have undergone sleeve gastrectomy.


Subject(s)
Gastroesophageal Reflux , Laparoscopy , Obesity, Morbid , Male , Female , Humans , Retrospective Studies , Quality of Life , Gastroesophageal Reflux/etiology , Gastroesophageal Reflux/surgery , Gastrectomy/adverse effects , Gastrectomy/methods , Laparoscopy/adverse effects , Magnetic Phenomena , Treatment Outcome , Obesity, Morbid/surgery
13.
Foods ; 11(7)2022 Mar 27.
Article in English | MEDLINE | ID: mdl-35407054

ABSTRACT

Olfactory dysfunction is amongst the many symptoms of Long COVID. Whilst most people that experience smell loss post COVID-19 recover their sense of smell and taste within a few weeks, about 10% of cases experience long-term problems, and their smell recovery journey often begins a few months later when everyday items start to smell distorted. This is known as parosmia. The aim of this study was to identify the key food triggers of parosmic distortions and investigate the relationship between distortion and disgust in order to establish the impact of parosmia on diet and quality of life. In this cross-sectional study (n = 727), respondents experiencing smell distortions completed a questionnaire covering aspects of smell loss, parosmia and the associated change in valence of everyday items. There was a significant correlation between strength and disgust (p < 0.0001), and when the selected items were reported as distorted, they were described as either unpleasant or gag-inducing 84% of the time. This change in valence associated with loss of expected pleasure and the presence of strange tastes and burning sensations must certainly lead to changes in eating behaviours and serious longer-term consequences for mental health and quality of life.

14.
Trop Med Int Health ; 27(6): 564-573, 2022 06.
Article in English | MEDLINE | ID: mdl-35411997

ABSTRACT

OBJECTIVES: The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained. METHODS: In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection. RESULTS: We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58). CONCLUSIONS: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.


Subject(s)
COVID-19 , Clinical Laboratory Techniques , SARS-CoV-2 , Adult , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , COVID-19 Testing , COVID-19 Vaccines/administration & dosage , Cohort Studies , Female , Humans , Male , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Seroepidemiologic Studies , South Africa/epidemiology , Young Adult
16.
Xenotransplantation ; 29(3): e12747, 2022 05.
Article in English | MEDLINE | ID: mdl-35384085

ABSTRACT

Although human islet transplantation has proven to provide clinical benefits, especially the near complete amelioration of hypoglycemia, the supply of human islets is limited and insufficient to meet the needs of all people that could benefit from islet transplantation. Porcine islets, secreting insulin nearly identical to that of human insulin, have been proposed as a viable supply of unlimited islets. Further, encapsulation of the porcine islets has been shown to reduce or eliminate the use of immunosuppressive therapy that would be required to prevent rejection of the foreign islet tissue. The goal of the current study was to determine the long-term safety and efficacy of agarose encapsulated porcine islets (macrobeads) in diabetic cynomolgus macaques, in a study emulating a proposed IND trial in which daily exogenous insulin therapy would be reduced by 50% with no loss of glucose regulation. Four of six animals implanted with macrobeads demonstrated ≥ 30% reduction in insulin requirements in year 1 of follow-up. Animals were followed for 2, 3.5, and 7.4 years with no serious adverse events, mortality or evidence of pathogen transmission. This study supports the continued pursuit of encapsulated porcine islet therapy as a promising treatment option for diabetes mellitus.


Subject(s)
Diabetes Mellitus, Experimental , Islets of Langerhans Transplantation , Animals , Diabetes Mellitus, Experimental/therapy , Humans , Insulin/therapeutic use , Macaca , Swine , Transplantation, Heterologous
17.
medRxiv ; 2022 Jan 12.
Article in English | MEDLINE | ID: mdl-35043121

ABSTRACT

OBJECTIVES: We aimed to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection, and whether protection against severe disease conferred by prior infection and/or vaccination was maintained. METHODS: In this cohort study, we included public sector patients aged ≥20 years with a laboratory confirmed COVID-19 diagnosis between 14 November-11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalization or death and any hospitalization or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection. RESULTS: We included 5,144 patients from wave four and 11,609 from prior waves. Risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted Hazard Ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR:0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58). CONCLUSIONS: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25% reduced risk of severe hospitalization or death compared to Delta.

18.
Chronic Illn ; 18(2): 286-294, 2022 06.
Article in English | MEDLINE | ID: mdl-32972238

ABSTRACT

OBJECTIVES: This qualitative study explored factors that may influence decisions regarding kidney transplantation among African-American and Latino adults on dialysis. METHODS: Qualitative interviews were audio-recorded and transcribed. Open-coding techniques were used to identify concepts, categories, and themes. The Social Ecological Model (SEM) was used to organize themes and identify potential solutions across multiple levels (individual, interpersonal, community, and policy/health system). RESULTS: Thirty-six patients were interviewed. Their mean age was 53 SD 12 years; 50% were female; and their duration on dialysis was 4.9 SD 6 years. Five themes emerged and were organized according to the levels of the SEM: 1) Fear about the outcomes of transplantation and 2) faith in God (individual level); 3) Family dynamics and reluctance to involve family in the decision making process (interpersonal level); 4) The experiences of friends and social networks (community level); and 5) Concerns about the social and economic impact of transplantation (policy and health system). DISCUSSION: The application of a Social Ecological model in this study helped to illuminate the complex and multilevel factors that may influence the decisions for kidney transplantation. Future studies are needed to further explore how family members, social networks, faith communities, and policies/health systems influence the decision making process.


Subject(s)
Kidney Transplantation , Renal Dialysis , Decision Making , Female , Hispanic or Latino , Humans , Male , Middle Aged , Qualitative Research
19.
Front Immunol ; 13: 1066733, 2022.
Article in English | MEDLINE | ID: mdl-36591248

ABSTRACT

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed.


Subject(s)
COVID-19 , Humans , Host-Pathogen Interactions
20.
JMIR Form Res ; 5(12): e29086, 2021 Dec 14.
Article in English | MEDLINE | ID: mdl-34904953

ABSTRACT

BACKGROUND: The impact of qualitative olfactory disorders is underestimated. Parosmia, the distorted perception of familiar odors, and phantosmia, the experience of odors in the absence of a stimulus, can arise following postinfectious anosmia, and the incidences of both have increased substantially since the outbreak of COVID-19. OBJECTIVE: The aims of this study are to explore the symptoms and sequalae of postinfectious olfactory dysfunction syndrome using unstructured and unsolicited threads from social media, and to articulate the perspectives and concerns of patients affected by these debilitating olfactory disorders. METHODS: A thematic analysis and content analysis of posts in the AbScent Parosmia and Phantosmia Support group on Facebook was conducted between June and December 2020. RESULTS: In this paper, we identify a novel symptom, olfactory perseveration, which is a triggered, identifiable, and usually unpleasant olfactory percept that persists in the absence of an ongoing stimulus. We also observe fluctuations in the intensity and duration of symptoms of parosmia, phantosmia, and olfactory perseveration. In addition, we identify a group of the most common items (coffee, meat, onion, and toothpaste) that trigger distortions; however, people have difficulty describing these distortions, using words associated with disgust and revulsion. The emotional aspect of living with qualitative olfactory dysfunction was evident and highlighted the detrimental impact on mental health. CONCLUSIONS: Qualitative and unsolicited data acquired from social media has provided useful insights into the patient experience of parosmia and phantosmia, which can inform rehabilitation strategies and ongoing research into understanding the molecular triggers associated with parosmic distortions and research into patient benefit.

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