Development of a prediction score (ThyroCOVID) for identifying abnormal thyroid function in COVID-19 patients.

PURPOSE: Thyroid dysfunction in COVID-19 carries clinical and prognostic implications. In this study, we developed a prediction score (ThyroCOVID) for abnormal thyroid function (TFT) on admission amongst COVID-19 patients. METHODS: Consecutive COVID-19 patients admitted to Queen Mary Hospital were prospectively recruited during July 2020-May 2021. Thyroid-stimulating hormone (TSH), free thyroxine (fT4) and free triiodothyronine (fT3) were measured on admission. Multivariable logistic regression analysis was performed to identify independent determinants of abnormal TFTs. ThyroCOVID was developed based on a clinical model with the lowest Akaike information criteria. RESULTS: Five hundred and forty six COVID-19 patients were recruited (median age 50 years, 45.4% men, 72.9% mild disease on admission). 84 patients (15.4%) had abnormal TFTs on admission. Patients with abnormal TFTs were more likely to be older, have more comorbidities, symptomatic, have worse COVID-19 severity, higher SARS-CoV-2 viral loads and more adverse profile of acute-phase reactants, haematological and biochemical parameters. ThyroCOVID consisted of five parameters: symptoms (malaise), comorbidities (ischaemic heart disease/congestive heart failure) and laboratory parameters (lymphocyte count, C-reactive protein, and SARS-CoV-2 cycle threshold values). It was able to identify abnormal TFT on admission with an AUROC of 0.73 (95% CI 0.67-0.79). The optimal cut-off of 0.15 had a sensitivity of 75.0%, specificity of 65.2%, negative predictive value of 93.5% and positive predictive value of 28.1% in identifying abnormal TFTs on admission amongst COVID-19 patients. CONCLUSION: ThyroCOVID, a prediction score to identify COVID-19 patients at risk of having abnormal TFT on admission, was developed based on a cohort of predominantly non-severe COVID-19 patients.

A multiphase flux balance model reveals flexibility of central carbon metabolism in guard cells of C3 plants.

Experimental research into guard cell metabolism has revealed the roles of the accumulation of various metabolites in guard cell function, but a comprehensive understanding of their metabolism over the diel cycle is still incomplete due to the limitations of current experimental methods. In this study we constructed a four-phase flux balance model of guard cell metabolism to investigate the changes in guard cell metabolism over the diel cycle, including the day and night and stomatal opening and closing. Our model predicted metabolic flexibility in guard cells of C3 plants, showing that multiple metabolic processes can contribute to the synthesis and metabolism of malate and sucrose as osmolytes during stomatal opening and closing. Our model showed the possibility of guard cells adapting to varying light availability and sucrose uptake from the apoplast during the day by operating in a mixotrophic mode with a switch between sucrose synthesis via the Calvin-Benson cycle and sucrose degradation via the oxidative pentose phosphate pathway. During stomatal opening, our model predicted an alternative flux mode of the Calvin-Benson cycle with all dephosphorylating steps diverted to diphosphate-fructose-6-phosphate 1-phosphotransferase to produce inorganic pyrophosphate, which is used to pump protons across the tonoplast for the accumulation of osmolytes. An analysis of the energetics of the use of different osmolytes in guard cells showed that malate and Cl- are similarly efficient as the counterion of K+ during stomatal opening.

Multi-tissue to whole plant metabolic modelling.

Genome-scale metabolic models have been successfully applied to study the metabolism of multiple plant species in the past decade. While most existing genome-scale modelling studies have focussed on studying the metabolic behaviour of individual plant metabolic systems, there is an increasing focus on combining models of multiple tissues or organs to produce multi-tissue models that allow the investigation of metabolic interactions between tissues and organs. Multi-tissue metabolic models were constructed for multiple plants including Arabidopsis, barley, soybean and Setaria. These models were applied to study various aspects of plant physiology including the division of labour between organs, source and sink tissue relationship, growth of different tissues and organs and charge and proton balancing. In this review, we outline the process of constructing multi-tissue genome-scale metabolic models, discuss the strengths and challenges in using multi-tissue models, review the current status of plant multi-tissue and whole plant metabolic models and explore the approaches for integrating genome-scale metabolic models into multi-scale plant models.

A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants.

BACKGROUND: C4 photosynthesis is a key domain of plant research with outcomes ranging from crop quality improvement, biofuel production and efficient use of water and nutrients. A metabolic network model of C4 "lab organism" Setaria viridis with extensive gene-reaction associations can accelerate target identification for desired metabolic manipulations and thereafter in vivo validation. Moreover, metabolic reconstructions have also been shown to be a significant tool to investigate fundamental metabolic traits. RESULTS: A mass and charge balance genome-scale metabolic model of Setaria viridis was constructed, which was tested to be able to produce all major biomass components in phototrophic and heterotrophic conditions. Our model predicted an important role of the utilization of NH[Formula: see text] and NO[Formula: see text] ratio in balancing charges in plants. A multi-tissue extension of the model representing C4 photosynthesis was able to utilize NADP-ME subtype of C4 carbon fixation for the production of lignocellulosic biomass in stem, providing a tool for identifying gene associations for cellulose, hemi-cellulose and lignin biosynthesis that could be potential target for improved lignocellulosic biomass production. Besides metabolic engineering, our modeling results uncovered a previously unrecognized role of the 3-PGA/triosephosphate shuttle in proton balancing. CONCLUSIONS: A mass and charge balance model of Setaria viridis, a model C4 plant, provides the possibility of system-level investigation to identify metabolic characteristics based on stoichiometric constraints. This study demonstrated the use of metabolic modeling in identifying genes associated with the synthesis of particular biomass components, and elucidating new role of previously known metabolic processes.

A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism.

Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome-scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome-scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses.

A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf.

Flux balance analysis of plant metabolism is an established method for predicting metabolic flux phenotypes and for exploring the way in which the plant metabolic network delivers specific outcomes in different cell types, tissues, and temporal phases. A recurring theme is the need to explore the flexibility of the network in meeting its objectives and, in particular, to establish the extent to which alternative pathways can contribute to achieving specific outcomes. Unfortunately, predictions from conventional flux balance analysis minimize the simultaneous operation of alternative pathways, but by introducing flux-weighting factors to allow for the variable intrinsic cost of supporting each flux, it is possible to activate different pathways in individual simulations and, thus, to explore alternative pathways by averaging thousands of simulations. This new method has been applied to a diel genome-scale model of Arabidopsis (Arabidopsis thaliana) leaf metabolism to explore the flexibility of the network in meeting the metabolic requirements of the leaf in the light. This identified alternative flux modes in the Calvin-Benson cycle revealed the potential for alternative transitory carbon stores in leaves and led to predictions about the light-dependent contribution of alternative electron flow pathways and futile cycles in energy rebalancing. Notable features of the analysis include the light-dependent tradeoff between the use of carbohydrates and four-carbon organic acids as transitory storage forms and the way in which multiple pathways for the consumption of ATP and NADPH can contribute to the balancing of the requirements of photosynthetic metabolism with the energy available from photon capture.

Intrarenal abscess caused by community-associated methicillin-resistant Staphylococcus aureus in a transplanted kidney.

Emergence of multidrug-resistant bacteria is important in solid organ transplant recipients, because it can jeopardize patient and graft survival. Methicillin-resistant Staphylococcus aureus (MRSA) infections are not rare in kidney transplant recipients. On the other hand, infections related to community-associated MRSA (CA-MRSA) strains are seldom reported in the literature. Herein, we report the first patient, to our knowledge, with CA-MRSA renal graft abscess who was successfully treated with drainage and parenteral antibiotics.

Factors affecting the deceased organ donation rate in the Chinese community: an audit of hospital medical records in Hong Kong.

INTRODUCTION: The number of actual donors per million population is the most commonly used metric to measure organ donation rates worldwide. It is deemed inadequate, however, because it does not take into account the potential donor pool. The aim of this study was to determine the true potential for solid organ donation from deceased brain-dead donors and the reasons for non-donation from potential donors in the Chinese community. METHODS: Medical records of all hospital deaths between 1 January and 31 December 2014 at a large regional hospital in Hong Kong were reviewed. Those who were on mechanical ventilation with documented brain injury and aged ≤75 years were classified as possible organ donors. The reasons why some potential organ donors did not become utilised organ donors were recorded and evaluated. RESULTS: Among 3659 patient deaths, 121 were classified as possible organ donors. The mean age of the possible organ donors was 59.4 years and 72.7% of them were male. The majority (88%) were from non-intensive care units. Of the 121 possible organ donors, 108 were classified as potential organ donors after excluding 13 unlikely to fulfil brain death criteria. Finally 11 patients became actual organ donors with an overall conversion rate of 10%. Reasons for non-donation included medical contra-indication (46%), failure to identify and inform organ donation coordinators (14%), failure of donor maintenance (11%), brain death diagnosis not established (18%), and refusal by relatives (11%). CONCLUSIONS: It is possible to increase the organ donation rate considerably by action at different stages of the donation process. Ongoing accurate audit of current practice is necessary.

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves.

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis.

Genetics of Apparently Sporadic Pheochromocytoma and Paraganglioma in a Chinese Population.

Identification of germline mutation in patients with apparently sporadic pheochromocytomas and paragangliomas is crucial. Clinical indicators, which include young age, bilateral or multifocal, extra-adrenal, malignant, or recurrent tumors, predict the likelihood of harboring germline mutation in Caucasian subjects. However, data on the prevalence of germline mutation, as well as the applicability of these clinical indicators in Chinese, are lacking. We conducted a cross-sectional study at a single endocrine tertiary referral center in Hong Kong. Subjects with pheochromocytomas and paragangliomas were evaluated for the presence of germline mutations involving 10 susceptibility genes, which included NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, TMEM 127, MAX, and FH genes. Clinical indicators were assessed for their association with the presence of germline mutations. Germline mutations, 2 being novel, were found in 24.4% of the 41 Chinese subjects recruited and 11.4% among those with apparently sporadic presentation. The increasing number of the afore-mentioned clinical indicators significantly correlated with the likelihood of harboring germline mutation in one of the 10 susceptibility genes. (r=0.757, p=0.026). The presence of 2 or more clinical indicators should prompt genetic testing for germline mutations in Chinese subjects. In conclusion, our study confirmed that a significant proportion of Chinese subjects with apparently sporadic pheochromocytoma and paraganglioma harbored germline mutations and these clinical indicators identified from Caucasians series were also applicable in Chinese subjects. This information will be of clinical relevance in the design of appropriate genetic screening strategies in Chinese populations.

Clozapine-induced acute interstitial nephritis.

Acute interstitial nephritis is a common cause of acute kidney injury. Acute interstitial nephritis is most commonly induced by drug although the cause may also be infective, autoimmune, or idiopathic. Although eosinophilia and eosinophiluria may help identify this disease entity, the gold standard for diagnosis remains renal biopsy. Prompt diagnosis is important because discontinuation of the culprit drugs can reduce further kidney injury. We present a patient with an underlying psychiatric disorder who was subsequently diagnosed with clozapine-induced acute interstitial nephritis. Monitoring of renal function during clozapine therapy is recommended for early recognition of this rare side-effect.

A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions.

Flux balance models of metabolism generally utilize synthesis of biomass as the main determinant of intracellular fluxes. However, the biomass constraint alone is not sufficient to predict realistic fluxes in central heterotrophic metabolism of plant cells because of the major demand on the energy budget due to transport costs and cell maintenance. This major limitation can be addressed by incorporating transport steps into the metabolic model and by implementing a procedure that uses Pareto optimality analysis to explore the trade-off between ATP and NADPH production for maintenance. This leads to a method for predicting cell maintenance costs on the basis of the measured flux ratio between the oxidative steps of the oxidative pentose phosphate pathway and glycolysis. We show that accounting for transport and maintenance costs substantially improves the accuracy of fluxes predicted from a flux balance model of heterotrophic Arabidopsis cells in culture, irrespective of the objective function used in the analysis. Moreover, when the new method was applied to cells under control, elevated temperature and hyper-osmotic conditions, only elevated temperature led to a substantial increase in cell maintenance costs. It is concluded that the hyper-osmotic conditions tested did not impose a metabolic stress, in as much as the metabolic network is not forced to devote more resources to cell maintenance.

Tropism of avian influenza A (H5N1) in the upper and lower respiratory tract.

Poor human-to-human transmission of influenza A H5N1 virus has been attributed to the paucity of putative sialic acid alpha2-3 virus receptors in the epithelium of the human upper respiratory tract, and thus to the presumed inability of the virus to replicate efficiently at this site. We now demonstrate that ex vivo cultures of human nasopharyngeal, adenoid and tonsillar tissues can be infected with H5N1 viruses in spite of an apparent lack of these receptors.

Modelling metabolic CO2 evolution--a fresh perspective on respiration.

Respiration is a major contributor to net exchange of CO2 between plants and the atmosphere and thus an important aspect of the vegetation component of global climate change models. However, a mechanistic model of respiration is lacking, and so here we explore the potential for flux balance analysis (FBA) to predict cellular CO2 evolution rates. Metabolic flux analysis reveals that respiration is not always the dominant source of CO2, and that metabolic processes such as the oxidative pentose phosphate pathway (OPPP) and lipid synthesis can be quantitatively important. Moreover, there is considerable variation in the metabolic origin of evolved CO2 between tissues, species and conditions. Comparison of FBA-predicted CO2 evolution profiles with those determined from flux measurements reveals that FBA is able to predict the metabolic origin of evolved CO2 in different tissues/species and under different conditions. However, FBA is poor at predicting flux through certain metabolic processes such as the OPPP and we identify the way in which maintenance costs are accounted for as a major area of improvement for future FBA studies. We conclude that FBA, in its standard form, can be used to predict CO2 evolution in a range of plant tissues and in response to environment.

Identification of rare variants from exome sequence in a large pedigree with autism.

We carried out analyses with the goal of identifying rare variants in exome sequence data that contribute to disease risk for a complex trait. We analyzed a large, 47-member, multigenerational pedigree with 11 cases of autism spectrum disorder, using genotypes from 3 technologies representing increasing resolution: a multiallelic linkage marker panel, a dense diallelic marker panel, and variants from exome sequencing. Genome-scan marker genotypes were available on most subjects, and exome sequence data was available on 5 subjects. We used genome-scan linkage analysis to identify and prioritize the chromosome 22 region of interest, and to select subjects for exome sequencing. Inheritance vectors (IVs) generated by Markov chain Monte Carlo analysis of multilocus marker data were the foundation of most analyses. Genotype imputation used IVs to determine which sequence variants reside on the haplotype that co-segregates with the autism diagnosis. Together with a rare-allele frequency filter, we identified only one rare variant on the risk haplotype, illustrating the potential of this approach to prioritize variants. The associated gene, MYH9, is biologically unlikely, and we speculate that for this complex trait, the key variants may lie outside the exome.

Role of cyclooxygenase-2 in H5N1 viral pathogenesis and the potential use of its inhibitors.

1. Cyclooxygenase-2 (COX-2), along with TNF-α and other proinflammatory cytokines, was hyperinduced in H5N1- infected macrophages in vitro and in epithelial cells of autopsied lung tissues of infected patients. 2. The COX-2 mediated amplification of the proinflammatory response is rapid, and the effects elicited by the H5N1-triggered proinflammatory cascade are broader than those arising from direct viral infection. 3. Selective COX-2 inhibitors suppress the H5N1- hyperinduced cytokines in the proinflammatory cascade.

Aspirin desensitisation for Chinese patients with coronary artery disease.

OBJECTIVE. To assess the efficacy and safety of aspirin desensitisation in Chinese patients with coronary artery disease. DESIGN. Case series. SETTING. A regional hospital in Hong Kong. PATIENTS. Chinese patients with coronary artery disease and a history of a hypersensitivity reaction to aspirin or non-steroidal anti-inflammatory drug, who underwent aspirin desensitisation between February 2008 and July 2012. RESULTS. There were 24 Chinese patients with coronary artery disease who were admitted to our unit for aspirin desensitisation during this period. The majority (79%) were clinical admissions for desensitisation; eight (33%) of them developed a hypersensitivity reaction during desensitisation. Half of the latter had only limited cutaneous reactions and were able to complete the desensitisation protocol and developed aspirin tolerance. Overall, 20 (83%) of the patients were successfully desensitised at the initial attempt. No serious adverse reactions occurred in the cohort. Twelve of the patients had significant coronary artery disease revealed by coronary angiography and received a percutaneous coronary intervention, nine of whom received drug-eluting stents while three received bare metal stents due to financial constraints. All 11 successfully desensitised patients received aspirin and clopidogrel as double antiplatelet therapy after percutaneous coronary intervention. The remaining patient had a bare metal stent implant due to failed aspirin desensitisation. CONCLUSION. Given the potentially different genetic basis of aspirin hypersensitivity in different ethnicities, recourse to desensitisation in the Chinese population has not previously been addressed. This study demonstrated that aspirin desensitisation using a rapid protocol can be performed effectively and safely in Chinese patients. Our results were comparable to those in other reported studies involving other ethnicities. Successful aspirin desensitisation permits patients to pursue long-term double antiplatelet therapy that includes aspirin after percutaneous coronary intervention, and thus allows the use of drug-eluting stents as a feasible option.

Metabolic modelling revealed source-sink interactions between four segments of Setaria viridis leaves.

As in most plants, during their growth from immature to mature stages, the leaves of Setaria viridis, a model C4 bioenergy plant, have differential growth rates from the base (immature or growing) to the tip (most mature). In this study, we constructed a multi-segment C4 leaf metabolic model of S. viridis with two cell types (bundle sheath and mesophyll cells) across four leaf segments (base to tip). We incorporated differential growth rates for each leaf segment as constraints and integrated transcriptomic data as the objective function for our model simulation using flux balance analysis. The model was able to predict the exchanges of metabolites between immature and mature segments of the leaf and the distribution of the activities of biomass synthesis across those segments. Our model demonstrated the use of a modelling approach in studying the source-sink relationship within an organ and provided insights into the metabolic interactions across different parts of a leaf.