Real-world implementation of the National Early Warning Score-2 in an acute respiratory unit.

INTRODUCTION: The National Early Warning Score-2 (NEWS-2) is used to detect deteriorating patients in hospital settings. We aimed to understand how NEWS-2 functions in the real-life setting of an acute respiratory unit. METHODS: Clinical observations data were extracted for adult patients (age ≥18 years), admitted under the care of respiratory medicine services from July to December 2019, who had at least one recorded task relating to clinical deterioration. The timing and nature of urgent out-of-hours medical reviews (escalations) were extracted through manual review of the case notes. RESULTS: The data set comprised 765 admission episodes (48.9% women) with a mean (SD) age of 69.3 (14.8). 8971 out of 35 991 out-of-hours observation sets (24.9%) had a NEWS-2 ≥5, and 586 of these (6.5%) led to an escalation. Out of 687 escalations, 101 (14.7%) were associated with observation sets with NEWS-2<5. Rising oxygen requirement and extreme values of individual observations were associated with an increased risk of escalation. 57.6% of escalations resulted in a change in treatment. Inpatient mortality was higher in patients who were escalated at least once, compared with those who were not escalated. CONCLUSIONS: Most observation sets with NEWS-2 scores ≥5 did not lead to a medical escalation in an acute respiratory setting out-of-hours, but more than half of escalations resulted in a change in treatment. Rising oxygen requirement is a key indicator of respiratory patient acuity which appears to influence the decision to request urgent out-of-hours medical reviews.

Respiratory rate responses to both hypercapnia and acidaemia are modified by age in patients with acidosis.

OBJECTIVE: To explore the associations between arterial pO2, pCO2 and pH and how these are modified by age. METHODS: An analysis of 2598 patients admitted with a diagnosis of Covid-19 infection to a large UK teaching hospital. RESULTS: There were inverse associations for arterial pO2, pCO2 and pH with respiratory rate. The effects of pCO2 and pH on respiratory rate were modified by age; older patients had higher respiratory rates at higher pCO2 (p = 0.004) and lower pH (p = 0.007) values. CONCLUSIONS: This suggests that ageing is associated with complex changes in the physiological feedback loops that control respiratory rate. As well as having clinical relevance, this may also impact on the use of respiratory rate in early warning scores across the age range.

Anaemia of acute inflammation: a higher acute systemic inflammatory response is associated with a larger decrease in blood haemoglobin levels in patients with COVID-19 infection.

AIMS: The study tests the hypothesis that a higher acute systemic inflammatory response was associated with a larger decrease in blood hemoglobin levels in patients with Coronavirus 2019 (COVID-19) infection. METHODS: All patients with either suspected or confirmed COVID-19 infection admitted to a busy UK hospital from February 2020 to December 2021 provided data for analysis. The exposure of interest was maximal serum C-reactive protein (CRP) level after COVID-19 during the same admission. RESULTS: A maximal serum CRP >175mg/L was associated with a decrease in blood haemoglobin (-5.0 g/L, 95% confidence interval: -5.9 to -4.2) after adjustment for covariates, including the number of times blood was drawn for analysis.Clinically, for a 55-year-old male patient with a maximum haemoglobin of 150 g/L who was admitted for a 28-day admission, a peak CRP >175 mg/L would be associated with an 11 g/L decrease in blood haemoglobin, compared with only 6 g/L if the maximal CRP was <4 mg/L. CONCLUSIONS: A higher acute systemic inflammatory response is associated with larger decreases in blood haemoglobin levels in patients with COVID-19. This represents an example of anaemia of acute inflammation, and a potential mechanism by which severe disease can increase morbidity and mortality.

Inverse association between blood pressure and pulse oximetry accuracy: an observational study in patients with suspected or confirmed COVID-19 infection.

BACKGROUND: Pulse oximeters are a standard non-invasive tool to measure blood oxygen levels, and are used in multiple healthcare settings. It is important to understand the factors affecting their accuracy to be able to use them optimally and safely. This analysis aimed to explore the association of the measurement error of pulse oximeters with systolic BP, diastolic BP and heart rate (HR) within ranges of values commonly observed in clinical practice. METHODS: The study design was a retrospective observational study of all patients admitted to a large teaching hospital with suspected or confirmed COVID-19 infection from February 2020 to December 2021. Data on systolic and diastolic BPs and HR levels were available from the same time period as the pulse oximetry measurements. RESULTS: Data were available for 3420 patients with 5927 observations of blood oxygen saturations as measured by pulse oximetry and ABG sampling within 30 min. The difference in oxygen saturation using the paired pulse oximetry and arterial oxygen saturation difference measurements was inversely associated with systolic BP, increasing by 0.02% with each mm Hg decrease in systolic BP (95% CI 0.00% to 0.03%) over a range of 80-180 mm Hg. Inverse associations were also observed between the error for oxygen saturation as measured by pulse oximetry and with both diastolic BP (+0.03%; 95% CI 0.00% to 0.05%) and HR (+0.04%; 95% CI 0.02% to 0.06% for each unit decrease in the HR). CONCLUSIONS: Care needs to be taken in interpreting pulse oximetry measurements in patients with lower systolic and diastolic BPs, and HRs, as oxygen saturation is overestimated as BP and HR decrease. Confirmation of the oxygen saturation with an ABG may be appropriate in some clinical scenarios.

Predicting Need for Escalation of Care or Death From Repeated Daily Clinical Observations and Laboratory Results in Patients With Severe Acute Respiratory Syndrome Coronavirus 2.

We compared the performance of prognostic tools for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using parameters fitted either at the time of hospital admission or across all time points of an admission. This cohort study used clinical data to model the dynamic change in prognosis of SARS-CoV-2 at a single hospital center in the United Kingdom, including all patients admitted from February 1, 2020, to December 31, 2020, and then followed up for 60 days for intensive care unit (ICU) admission, death, or discharge from the hospital. We incorporated clinical observations and blood tests into 2 time-varying Cox proportional hazards models predicting daily 24- to 48-hour risk of admission to the ICU for those eligible for escalation of care or death for those ineligible for escalation. In developing the model, 491 patients were eligible for ICU escalation and 769 were ineligible for escalation. Our model had good discrimination of daily risk of ICU admission in the validation cohort (n = 1,141; C statistic: C = 0.91, 95% confidence interval: 0.89, 0.94) and our score performed better than other scores (National Early Warning Score 2, International Severe Acute Respiratory and Emerging Infection Comprehensive Clinical Characterisation Collaboration score) calculated using only parameters measured on admission, but it overestimated the risk of escalation (calibration slope = 0.7). A bespoke daily SARS-CoV-2 escalation risk prediction score can predict the need for clinical escalation better than a generic early warning score or a single estimation of risk calculated at admission.

Age modifies both the maximal temperature and inflammatory response in patients with SARS-CoV-2 infection.

OBJECTIVE: To determine the maximal response of the temperature and inflammatory response to SARS-CoV-2 infection and how these are modified by age. METHODS: Participants were patients admitted to hospital with SARS-CoV-2 infection. For each participant, the maximal temperature and serum C-reactive protein (CRP) were identified and stratified by age. In a secondary analysis, these were compared in patients treated before and after dexamethasone. RESULTS: Mean maximal temperature varied by age (p<0.001; ANOVA) with the highest mean maximal temperature of 37.3°C observed in patients aged 30-49 years and decreasing maximal mean temperatures in the older age groups, with the lowest measure of 36.8°C observed in individuals aged 90-99 years. The mean maximal serum CRP also varied across age groups (p<0.001; ANOVA) and increased with age across all age categories from 34.5 mg/dL (95% confidence interval (CI) 22.0-47.0) for individuals aged 20-29 years to 77.6 mg/dL (95% CI 72.0-83.2) in those aged 80-89 years. After dexamethasone became standard treatment for COVID-19 pneumonia, mean maximal CRP decreased by 17 mg/dL (95% CI -22 to -11). CONCLUSION: Age modifies both maximal temperature and systemic inflammatory response in patients with SARS-CoV-2 infection.

Chest Radiograph Scoring Alone or Combined with Other Risk Scores for Predicting Outcomes in COVID-19.

Background Radiographic severity may help predict patient deterioration and outcomes from COVID-19 pneumonia. Purpose To assess the reliability and reproducibility of three chest radiograph reporting systems (radiographic assessment of lung edema [RALE], Brixia, and percentage opacification) in patients with proven SARS-CoV-2 infection and examine the ability of these scores to predict adverse outcomes both alone and in conjunction with two clinical scoring systems, National Early Warning Score 2 (NEWS2) and International Severe Acute Respiratory and Emerging Infection Consortium: Coronavirus Clinical Characterization Consortium (ISARIC-4C) mortality. Materials and Methods This retrospective cohort study used routinely collected clinical data of patients with polymerase chain reaction-positive SARS-CoV-2 infection admitted to a single center from February 2020 through July 2020. Initial chest radiographs were scored for RALE, Brixia, and percentage opacification by one of three radiologists. Intra- and interreader agreement were assessed with intraclass correlation coefficients. The rate of admission to the intensive care unit (ICU) or death up to 60 days after scored chest radiograph was estimated. NEWS2 and ISARIC-4C mortality at hospital admission were calculated. Daily risk for admission to ICU or death was modeled with Cox proportional hazards models that incorporated the chest radiograph scores adjusted for NEWS2 or ISARIC-4C mortality. Results Admission chest radiographs of 50 patients (mean age, 74 years ± 16 [standard deviation]; 28 men) were scored by all three radiologists, with good interreader reliability for all scores, as follows: intraclass correlation coefficients were 0.87 for RALE (95% CI: 0.80, 0.92), 0.86 for Brixia (95% CI: 0.76, 0.92), and 0.72 for percentage opacification (95% CI: 0.48, 0.85). Of 751 patients with a chest radiograph, those with greater than 75% opacification had a median time to ICU admission or death of just 1-2 days. Among 628 patients for whom data were available (median age, 76 years [interquartile range, 61-84 years]; 344 men), opacification of 51%-75% increased risk for ICU admission or death by twofold (hazard ratio, 2.2; 95% CI: 1.6, 2.8), and opacification greater than 75% increased ICU risk by fourfold (hazard ratio, 4.0; 95% CI: 3.4, 4.7) compared with opacification of 0%-25%, when adjusted for NEWS2 score. Conclusion Brixia, radiographic assessment of lung edema, and percentage opacification scores all reliably helped predict adverse outcomes in SARS-CoV-2 infection. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Little in this issue.

Impact of COVID-19 pandemic on prevalence of Clostridioides difficile infection in a UK tertiary centre.

Serious concerns have been raised about a possible increase in cases of Clostridioides difficile infection (CDI) during the COVID-19 pandemic. We conducted a retrospective observational single centre study which revealed that total combined community and hospital-based quarterly rates of CDI decreased during the pandemic compared to the pre-pandemic period.

The Second Site Modifier, Sympathy for the ligule, Encodes a Homolog of Arabidopsis ENHANCED DISEASE RESISTANCE4 and Rescues the Liguleless narrow Maize Mutant.

Liguleless narrow1 encodes a plasma membrane-localized receptor-like kinase required for normal development of maize (Zea mays) leaves, internodes, and inflorescences. The semidominant Lgn-R mutation lacks kinase activity, and phenotypic severity is dependent on inbred background. We created near isogenic lines and assayed the phenotype in multiple environments. Lgn-R plants that carry the B73 version of Sympathy for the ligule (Sol-B) fail to grow under hot conditions, but those that carry the Mo17 version (Sol-M) survive at hot temperatures and are significantly taller at cool temperatures. To identify Sol, we used recombinant mapping and analyzed the Lgn-R phenotype in additional inbred backgrounds. We identified amino acid sequence variations in GRMZM2G075262 that segregate with severity of the Lgn-R phenotypes. This gene is expressed at high levels in Lgn-R B73, but expression drops to nonmutant levels with one copy of Sol-M An EMS mutation solidified the identity of SOL as a maize homolog of Arabidopsis (Arabidopsis thaliana) ENHANCED DISEASE RESISTANCE4 (EDR4). SOL, like EDR4, is induced in response to pathogen-associated molecular patterns such as flg22. Integrated transcriptomic and phosphoproteomic analyses suggest that Lgn-R plants constitutively activate an immune signaling cascade that induces temperature-sensitive responses in addition to defects in leaf development. We propose that aspects of the severe Lgn-R developmental phenotype result from constitutive defense induction and that SOL potentially functions in repressing this response in Mo17 but not B73. Identification of LGN and its interaction with SOL provides insight into the integration of developmental control and immune responses.

Initiation of ER Body Formation and Indole Glucosinolate Metabolism by the Plastidial Retrograde Signaling Metabolite, MEcPP.

Plants have evolved tightly regulated signaling networks to respond and adapt to environmental perturbations, but the nature of the signaling hub(s) involved have remained an enigma. We have previously established that methylerythritol cyclodiphosphate (MEcPP), a precursor of plastidial isoprenoids and a stress-specific retrograde signaling metabolite, enables cellular readjustments for high-order adaptive functions. Here, we specifically show that MEcPP promotes two Brassicaceae-specific traits, namely endoplasmic reticulum (ER) body formation and induction of indole glucosinolate (IGs) metabolism selectively, via transcriptional regulation of key regulators NAI1 for ER body formation and MYB51/122 for IGs biosynthesis). The specificity of MEcPP is further confirmed by the lack of induction of wound-inducible ER body genes as well as IGs by other altered methylerythritol phosphate pathway enzymes. Genetic analyses revealed MEcPP-mediated COI1-dependent induction of these traits. Moreover, MEcPP signaling integrates the biosynthesis and hydrolysis of IGs through induction of nitrile-specifier protein1 and reduction of the suppressor, ESM1, and production of simple nitriles as the bioactive end product. The findings position the plastidial metabolite, MEcPP, as the initiation hub, transducing signals to adjust the activity of hard-wired gene circuitry to expand phytochemical diversity and alter the associated subcellular structure required for functionality of the secondary metabolites, thereby tailoring plant stress responses.

Proteomics studies of the interactome of RNA polymerase II C-terminal repeated domain.

BACKGROUND: Eukaryotic RNA polymerase II contains a C-terminal repeated domain (CTD) consisting of 52 consensus heptad repeats of Y1S2P3T4S5P6S7 that mediate interactions with many cellular proteins to regulate transcription elongation, RNA processing and chromatin structure. A number of CTD-binding proteins have been identified and the crystal structures of several protein-CTD complexes have demonstrated considerable conformational flexibility of the heptad repeats in those interactions. Furthermore, phosphorylation of the CTD at tyrosine, serine and threonine residues can regulate the CTD-protein interactions. Although the interactions of CTD with specific proteins have been elucidated at the atomic level, the capacity and specificity of the CTD-interactome in mammalian cells is not yet determined. RESULTS: A proteomic study was conducted to examine the mammalian CTD-interactome. We utilized six synthetic peptides each consisting of four consensus CTD-repeats with different combinations of serine and tyrosine phosphorylation as affinity-probes to pull-down nuclear proteins from HeLa cells. The pull-down fractions were then analyzed by MUDPIT mass spectrometry, which identified 100 proteins with the majority from the phospho-CTD pull-downs. Proteins pulled-down by serine-phosphorylated CTD-peptides included those containing the previously defined CTD-interacting domain (CID). Using SILAC mass spectrometry, we showed that the in vivo interaction of RNA polymerase II with the mammalian CID-containing RPRD1B is disrupted by CID mutation. We also showed that the CID from four mammalian proteins interacted with pS2-phosphorylated but not pY1pS2-doubly phosphorylated CTD-peptides. However, we also found proteins that were preferentially pulled-down by pY1pS2- or pY1pS5-doubly phosphorylated CTD-peptides. We prepared an antibody against tyrosine phosphorylated CTD and showed that ionizing radiation (IR) induced a transient increase in CTD tyrosine phosphorylation by immunoblotting. Combining SILAC and IMAC purification of phospho-peptides, we found that IR regulated the phosphorylation at four CTD tyrosine sites in different ways. CONCLUSION: Upon phosphorylation, the 52 repeats of the CTD have the capacity to generate a large number of binding sites for cellular proteins. This study confirms previous findings that serine phosphorylation stimulates whereas tyrosine phosphorylation inhibits the protein-binding activity of the CTD. However, tyrosine phosphorylation of the CTD can also stimulate other CTD-protein interactions. The CTD-peptide affinity pull-down method described here can be adopted to survey the mammalian CTD-interactome in various cell types and under different biological conditions.

The matrix protein Fibulin-5 is at the interface of tissue stiffness and inflammation in fibrosis.

Fibrosis is a pervasive disease in which the excessive deposition of extracellular matrix (ECM) compromises tissue function. Although the underlying mechanisms are mostly unknown, matrix stiffness is increasingly appreciated as a contributor to fibrosis rather than merely a manifestation of the disease. Here we show that the loss of Fibulin-5, an elastic fibre component, not only decreases tissue stiffness, but also diminishes the inflammatory response and abrogates the fibrotic phenotype in a mouse model of cutaneous fibrosis. Increasing matrix stiffness raises the inflammatory response above a threshold level, independent of TGF-ß, to stimulate further ECM secretion from fibroblasts and advance the progression of fibrosis. These results suggest that Fibulin-5 may be a therapeutic target to short-circuit this profibrotic feedback loop.

The need for agriculture phenotyping: "moving from genotype to phenotype".

Increase in the world population has called for the increased demand for agricultural productivity. Traditional methods to augment crop and animal production are facing exacerbating pressures in keeping up with population growth. This challenge has in turn led to the transformational change in the use of biotechnology tools to meet increased productivity for both plant and animal systems. Although many challenges exist, the use of proteomic techniques to understand agricultural problems is steadily increasing. This review discusses the impact of genomics, proteomics, metabolomics and phenotypes on plant, animal and bacterial systems to achieve global food security and safety and we highlight examples of intra and extra mural research work that is currently being done to increase agricultural productivity. BIOLOGICAL SIGNIFICANCE: This review focuses on the global demand for increased agricultural productivity arising from population growth and how we can address this challenge using biotechnology. With a population well above seven billion humans, in a very unbalanced nutritional state (20% overweight, 20% risking starvation) drastic measures have to be taken at the political, infrastructure and scientific levels. While we cannot influence politics, it is our duty as scientists to see what can be done to feed humanity. Hence we highlight the transformational change in the use of biotechnology tools over traditional methods to increase agricultural productivity (plant and animal). Specifically, this review deals at length on how a three-pronged attack, namely combined genomics, proteomics and metabolomics, can help to ensure global food security and safety. This article is part of a Special Issue entitled: Translational Plant Proteomics.

The HUPO initiative on Model Organism Proteomes, iMOP.

The community working on model organisms is growing steadily and the number of model organisms for which proteome data are being generated is continuously increasing. To standardize efforts and to make optimal use of proteomics data acquired from model organisms, a new Human Proteome Organisation (HUPO) initiative on model organism proteomes (iMOP) was approved at the HUPO Ninth Annual World Congress in Sydney, 2010. iMOP will seek to stimulate scientific exchange and disseminate HUPO best practices. The needs of model organism researchers for central databases will be better represented, catalyzing the integration of proteomics and organism-specific databases. Full details of iMOP activities, members, tools and resources can be found at our website http://www.imop.uzh.ch/ and new members are invited to join us.

Regulatory network of microRNAs in RAW 264.7 macrophage cells.

microRNAs (miRNA) play important roles in regulating immunity. Here we utilize the systems biology approach to predict the regulatory network of miRNAs among the most down-regulated genes by the lipopolysaccharides (LPS) treatment in the macrophage RAW267.4 cell line. We combine the proteome and transcriptome data sets to define 200 target genes that are significantly down-regulated by the LPS treatment. We perform the profiling of over 300 miRNAs with the RNA-Seq method. Using the complementary binding rule between the seed sequences of profiled miRNAs and the 3'UTRs of target genes, we predict genes involved in mobility, metabolism, and oxidative phosphorylation as the top targets of miRNA negative regulation.