A computational framework for modelling infectious disease policy based on age and household structure with applications to the COVID-19 pandemic.

The widespread, and in many countries unprecedented, use of non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic has highlighted the need for mathematical models which can estimate the impact of these measures while accounting for the highly heterogeneous risk profile of COVID-19. Models accounting either for age structure or the household structure necessary to explicitly model many NPIs are commonly used in infectious disease modelling, but models incorporating both levels of structure present substantial computational and mathematical challenges due to their high dimensionality. Here we present a modelling framework for the spread of an epidemic that includes explicit representation of age structure and household structure. Our model is formulated in terms of tractable systems of ordinary differential equations for which we provide an open-source Python implementation. Such tractability leads to significant benefits for model calibration, exhaustive evaluation of possible parameter values, and interpretability of results. We demonstrate the flexibility of our model through four policy case studies, where we quantify the likely benefits of the following measures which were either considered or implemented in the UK during the current COVID-19 pandemic: control of within- and between-household mixing through NPIs; formation of support bubbles during lockdown periods; out-of-household isolation (OOHI); and temporary relaxation of NPIs during holiday periods. Our ordinary differential equation formulation and associated analysis demonstrate that multiple dimensions of risk stratification and social structure can be incorporated into infectious disease models without sacrificing mathematical tractability. This model and its software implementation expand the range of tools available to infectious disease policy analysts.

Novel methods for estimating the instantaneous and overall COVID-19 case fatality risk among care home residents in England.

The COVID-19 pandemic has had high mortality rates in the elderly and frail worldwide, particularly in care homes. This is driven by the difficulty of isolating care homes from the wider community, the large population sizes within care facilities (relative to typical households), and the age/frailty of the residents. To quantify the mortality risk posed by disease, the case fatality risk (CFR) is an important tool. This quantifies the proportion of cases that result in death. Throughout the pandemic, CFR amongst care home residents in England has been monitored closely. To estimate CFR, we apply both novel and existing methods to data on deaths in care homes, collected by Public Health England and the Care Quality Commission. We compare these different methods, evaluating their relative strengths and weaknesses. Using these methods, we estimate temporal trends in the instantaneous CFR (at both daily and weekly resolutions) and the overall CFR across the whole of England, and dis-aggregated at regional level. We also investigate how the CFR varies based on age and on the type of care required, dis-aggregating by whether care homes include nursing staff and by age of residents. This work has contributed to the summary of measures used for monitoring the UK epidemic.

Frequency of Potentially Avoidable Surgical Referrals for Asymptomatic Umbilical Hernias in Children.

INTRODUCTION: The American Association of Pediatrics released guidelines in 2019 recommending delay of surgical referral in children with asymptomatic umbilical hernias until 4-5 y of age. The purpose of this study was to assess contemporary rates of potentially avoidable referrals in this cohort of children, and to assess whether rates have decreased following guideline release. METHODS: Retrospective analysis of umbilical hernias referrals evaluated at a single pediatric surgery clinic from October 2014 to August 2021. Potentially avoidable referrals (PAR) were defined as asymptomatic, non-enlarging umbilical hernia referrals in a child 3 y of age or younger without a history of incarceration. Referral indication, disposition following clinic visit, and rates of PAR were compared before and after guideline release. RESULTS: A total of 803 umbilical hernia referrals were evaluated, of which 48% were in children 3 y of age or younger at time of evaluation ("early" referrals). 33% of all referrals and 68% of early referrals were categorized as a PAR, and rates were similar before and after guideline release (all referrals: 32% versus 33%, P = 0.94; early referrals: 68% versus 67%, P = 0.94). Of the 333 early referrals who were managed expectantly per guideline recommendations, 2 (0.6%) developed incarceration which was managed with successful reduction and interval repair. CONCLUSIONS: One-third of all referrals for umbilical hernia evaluation are potentially avoidable, and this rate did not change following release of American Academy of Pediatrics guidelines. Aligning expectations between surgeons and referring providers through improved education and guideline dissemination may reduce avoidable visits, lost caregiver productivity, and exposure to potentially avoidable surgery.

Antibiotic Therapy for Culture-Proven Bacterial Overgrowth in Children With Intestinal Failure Results in Improved Symptoms and Growth.

OBJECTIVES: To evaluate symptoms, enteral tolerance, growth, and antibiotic regimens in pediatric intestinal failure (IF) patients after treated with antibiotic therapy for small bowel bacterial overgrowth (SBBO). METHODS: Single-center retrospective review of children 0-18 years with IF with endoscopic cultures demonstrating >10 5 CFU/mL from 2010 to 2017. Symptoms, enteral tolerance, growth, and antibiotic regimens were evaluated at the time of endoscopy and 6 months later. RESULTS: Of 505 patients followed in our intestinal rehabilitation program, 104 underwent upper gastrointestinal endoscopy and 78 had positive duodenal cultures. Clinical data pre- and post-endoscopy were available for 56 patients. Compared to baseline, in the 6 months following targeted antibiotic treatment, children showed significant improvement in emesis or feeding intolerance (58.9% vs 23.2%, P < 0.001), abdominal pain (16.1% vs 7.1%, P = 0.02), high stool output (42.9% vs 19.6%, P = 0.002), and gross GI bleeding (19.6% vs 3.6%, P = 0.003). Mean BMI-for-age z scores increased significantly (-0.03 ± 0.94 vs 0.27 ± 0.82, P = 0.03); however, height-for-age z scores, weight-for-age z scores, and percent of calories from enteral intake were not significantly different after therapy. Antibiotic regimens remained highly variable. CONCLUSIONS: Children with IF and culture-positive SBBO showed significant improvement in symptoms and BMI-for-age z scores after duodenal culture with subsequent targeted antibiotic therapy. Longer follow-up may be needed to detect improvements in linear growth and percent of calories from enteral feeds. Antibiotic regimens remain highly variable. Long-term consequences of chronic antimicrobial therapy, including antimicrobial resistance, remain unknown. Prospective studies focused on standardizing duodenal sampling technique, correlating culture and pathology data, and evaluating antibiotic resistance patterns are needed.

Hand2 ensures an appropriate environment for cardiac fusion by limiting Fibronectin function.

Heart formation requires the fusion of bilateral cardiomyocyte populations as they move towards the embryonic midline. The bHLH transcription factor Hand2 is essential for cardiac fusion; however, the effector genes that execute this function of Hand2 are unknown. Here, we provide in zebrafish the first evidence for a downstream component of the Hand2 pathway that mediates cardiac morphogenesis. Although hand2 is expressed in cardiomyocytes, mosaic analysis demonstrates that it plays a non-autonomous role in regulating cardiomyocyte movement. Gene expression profiles reveal heightened expression of fibronectin 1 (fn1) in hand2 mutant embryos. Reciprocally, overexpression of hand2 leads to decreased Fibronectin levels. Furthermore, reduction of fn1 function enables rescue of cardiac fusion in hand2 mutants: bilateral cardiomyocyte populations merge and exhibit improved tissue architecture, albeit without major changes in apicobasal polarity. Together, our data provide a novel example of a tissue creating a favorable environment for its morphogenesis: the Hand2 pathway establishes an appropriate environment for cardiac fusion through negative modulation of Fn1 levels.

Inferring risks of coronavirus transmission from community household data.

The response of many governments to the COVID-19 pandemic has involved measures to control within- and between-household transmission, providing motivation to improve understanding of the absolute and relative risks in these contexts. Here, we perform exploratory, residual-based, and transmission-dynamic household analysis of the Office for National Statistics COVID-19 Infection Survey data from 26 April 2020 to 15 July 2021 in England. This provides evidence for: (i) temporally varying rates of introduction of infection into households broadly following the trajectory of the overall epidemic and vaccination programme; (ii) susceptible-Infectious transmission probabilities of within-household transmission in the 15-35% range; (iii) the emergence of the Alpha and Delta variants, with the former being around 50% more infectious than wildtype and 35% less infectious than Delta within households; (iv) significantly (in the range of 25-300%) more risk of bringing infection into the household for workers in patient-facing roles pre-vaccine; (v) increased risk for secondary school-age children of bringing the infection into the household when schools are open; (vi) increased risk for primary school-age children of bringing the infection into the household when schools were open since the emergence of new variants.

Functional modulation of cardiac form through regionally confined cell shape changes.

Developing organs acquire a specific three-dimensional form that ensures their normal function. Cardiac function, for example, depends upon properly shaped chambers that emerge from a primitive heart tube. The cellular mechanisms that control chamber shape are not yet understood. Here, we demonstrate that chamber morphology develops via changes in cell morphology, and we determine key regulatory influences on this process. Focusing on the development of the ventricular chamber in zebrafish, we show that cardiomyocyte cell shape changes underlie the formation of characteristic chamber curvatures. In particular, cardiomyocyte elongation occurs within a confined area that forms the ventricular outer curvature. Because cardiac contractility and blood flow begin before chambers emerge, cardiac function has the potential to influence chamber curvature formation. Employing zebrafish mutants with functional deficiencies, we find that blood flow and contractility independently regulate cell shape changes in the emerging ventricle. Reduction of circulation limits the extent of cardiomyocyte elongation; in contrast, disruption of sarcomere formation releases limitations on cardiomyocyte dimensions. Thus, the acquisition of normal cardiomyocyte morphology requires a balance between extrinsic and intrinsic physical forces. Together, these data establish regionally confined cell shape change as a cellular mechanism for chamber emergence and as a link in the relationship between form and function during organ morphogenesis.

Long-term outcomes of severe surgical necrotizing enterocolitis.

PURPOSE: We sought to describe long-term outcomes of infants with severe surgical necrotizing enterocolitis (NEC). METHODS: Data were collected on infants with surgical NEC (2009-2018). Severe surgical NEC was defined by extensive bowel loss with residual bowel length <30 cm, and "NEC totalis" was identified per operative report. Post-operative management and long-term outcomes were assessed, including enteral autonomy, severe neurodevelopmental disability, and educational attainment. RESULTS: Of 268 infants with surgical NEC, 41 (15%) had severe surgical NEC, and 14/41 were identified as "NEC totalis". Zero severe NEC vs. 8 (57%) "NEC totalis" patients were placed on comfort measures following initial surgery (p < 0.001). Twenty-five patients (93%) with severe NEC survived vs 3/6 with "NEC totalis" (p < 0.001). The 28 survivors (68%) were followed for a median (IQR) duration of 8(4,10) years. Nine (32%) with severe NEC were weaned from parenteral nutrition. Eight (29%) had ≥1 marker for severe neurodevelopmental disability, and 11/16(69%) (7-16 years) were attending school at last follow-up. CONCLUSION: Long-term survival is excellent following initial discharge, and achievement of enteral autonomy is feasible in patients with severe surgical NEC. The majority of patients who survive do not have severe neurodevelopmental disability and participate in school. Given current survivals and outcomes, focus on measured residual bowel length may be more appropriate than the subjective term "NEC-totalis." TYPE OF STUDY: Prognosis Study. LEVEL OF EVIDENCE: Level II.

Integrating Non-monotonic Logical Reasoning and Inductive Learning With Deep Learning for Explainable Visual Question Answering.

State of the art algorithms for many pattern recognition problems rely on data-driven deep network models. Training these models requires a large labeled dataset and considerable computational resources. Also, it is difficult to understand the working of these learned models, limiting their use in some critical applications. Toward addressing these limitations, our architecture draws inspiration from research in cognitive systems, and integrates the principles of commonsense logical reasoning, inductive learning, and deep learning. As a motivating example of a task that requires explainable reasoning and learning, we consider Visual Question Answering in which, given an image of a scene, the objective is to answer explanatory questions about objects in the scene, their relationships, or the outcome of executing actions on these objects. In this context, our architecture uses deep networks for extracting features from images and for generating answers to queries. Between these deep networks, it embeds components for non-monotonic logical reasoning with incomplete commonsense domain knowledge, and for decision tree induction. It also incrementally learns and reasons with previously unknown constraints governing the domain's states. We evaluated the architecture in the context of datasets of simulated and real-world images, and a simulated robot computing, executing, and providing explanatory descriptions of plans and experiences during plan execution. Experimental results indicate that in comparison with an "end to end" architecture of deep networks, our architecture provides better accuracy on classification problems when the training dataset is small, comparable accuracy with larger datasets, and more accurate answers to explanatory questions. Furthermore, incremental acquisition of previously unknown constraints improves the ability to answer explanatory questions, and extending non-monotonic logical reasoning to support planning and diagnostics improves the reliability and efficiency of computing and executing plans on a simulated robot.

Does hypoxia play a role in the development of sarcopenia in humans? Mechanistic insights from the Caudwell Xtreme Everest Expedition.

OBJECTIVES: Sarcopenia refers to the involuntary loss of skeletal muscle and is a predictor of physical disability/mortality. Its pathogenesis is poorly understood, although roles for altered hypoxic signaling, oxidative stress, adipokines and inflammatory mediators have been suggested. Sarcopenia also occurs upon exposure to the hypoxia of high altitude. Using data from the Caudwell Xtreme Everest expedition we therefore sought to analyze the extent of hypoxia-induced body composition changes and identify putative pathways associated with fat-free mass (FFM) and fat mass (FM) loss. METHODS: After baseline testing in London (75m), 24 investigators ascended from Kathmandu (1300m) to Everest base camp (EBC 5300m) over 13 days. Fourteen investigators climbed above EBC, eight of whom reached the summit (8848m). Assessments were conducted at baseline, during ascent and after one, six and eight week(s) of arrival at EBC. Changes in body composition (FM, FFM, total body water, intra- and extra-cellular water) were measured by bioelectrical impedance. Biomarkers of nitric oxide and oxidative stress were measured together with adipokines, inflammatory, metabolic and vascular markers. RESULTS: Participants lost a substantial, but variable, amount of body weight (7.3±4.9kg by expedition end; p<0.001). A progressive loss of both FM and FFM was observed, and after eight weeks, the proportion of FFM loss was 48% greater than FM loss (p<0.008). Changes in protein carbonyls (p<0.001) were associated with a decline in FM whereas 4-hydroxynonenal (p<0.001) and IL-6 (p<0.001) correlated with FFM loss. GLP-1 (r=-0.45, p<0.001) and nitrite (r=-0.29, p<0.001) concentration changes were associated with FFM loss. In a multivariate model, GLP-1, insulin and nitrite were significant predictors of FFM loss while protein carbonyls were predicted FM loss. CONCLUSIONS: The putative role of GLP-1 and nitrite as mediators of the effects of hypoxia on FFM is an intriguing finding. If confirmed, nutritional and pharmacological interventions targeting these pathways may offer new avenues for prevention and treatment of sarcopenia.

Effects of prolonged exposure to hypobaric hypoxia on oxidative stress, inflammation and gluco-insular regulation: the not-so-sweet price for good regulation.

OBJECTIVES: The mechanisms by which low oxygen availability are associated with the development of insulin resistance remain obscure. We thus investigated the relationship between such gluco-insular derangements in response to sustained (hypobaric) hypoxemia, and changes in biomarkers of oxidative stress, inflammation and counter-regulatory hormone responses. METHODS: After baseline testing in London (75 m), 24 subjects ascended from Kathmandu (1,300 m) to Everest Base Camp (EBC;5,300 m) over 13 days. Of these, 14 ascended higher, with 8 reaching the summit (8,848 m). Assessments were conducted at baseline, during ascent to EBC, and 1, 6 and 8 week(s) thereafter. Changes in body weight and indices of gluco-insular control were measured (glucose, insulin, C-Peptide, homeostasis model assessment of insulin resistance [HOMA-IR]) along with biomarkers of oxidative stress (4-hydroxy-2-nonenal-HNE), inflammation (Interleukin-6 [IL-6]) and counter-regulatory hormones (glucagon, adrenalin, noradrenalin). In addition, peripheral oxygen saturation (SpO2) and venous blood lactate concentrations were determined. RESULTS: SpO2 fell significantly from 98.0% at sea level to 82.0% on arrival at 5,300 m. Whilst glucose levels remained stable, insulin and C-Peptide concentrations increased by >200% during the last 2 weeks. Increases in fasting insulin, HOMA-IR and glucagon correlated with increases in markers of oxidative stress (4-HNE) and inflammation (IL-6). Lactate levels progressively increased during ascent and remained significantly elevated until week 8. Subjects lost on average 7.3 kg in body weight. CONCLUSIONS: Sustained hypoxemia is associated with insulin resistance, whose magnitude correlates with the degree of oxidative stress and inflammation. The role of 4-HNE and IL-6 as key players in modifying the association between sustained hypoxia and insulin resistance merits further investigation.

The role of nitrogen oxides in human adaptation to hypoxia.

Lowland residents adapt to the reduced oxygen availability at high altitude through a process known as acclimatisation, but the molecular changes underpinning these functional alterations are not well understood. Using an integrated biochemical/whole-body physiology approach we here show that plasma biomarkers of NO production (nitrite, nitrate) and activity (cGMP) are elevated on acclimatisation to high altitude while S-nitrosothiols are initially consumed, suggesting multiple nitrogen oxides contribute to improve hypoxia tolerance by enhancing NO availability. Unexpectedly, oxygen cost of exercise and mechanical efficiency remain unchanged with ascent while microvascular blood flow correlates inversely with nitrite. Our results suggest that NO is an integral part of the human physiological response to hypoxia. These findings may be of relevance not only to healthy subjects exposed to high altitude but also to patients in whom oxygen availability is limited through disease affecting the heart, lung or vasculature, and to the field of developmental biology.