A digital twin of the infant microbiome to predict neurodevelopmental deficits

Despite the recognized gut-brain axis link, natural variations in microbial profiles between patients hinder definition of normal abundance ranges, confounding the impact of dysbiosis on infant neurodevelopment. We infer a digital twin of the infant microbiome, forecasting ecosystem trajectories from a few initial observations. Using 16S ribosomal RNA profiles from 88 preterm infants (398 fecal samples and 32,942 abundance estimates for 91 microbial classes), the model (Q-net) predicts abundance dynamics with R2 = 0.69. Contrasting the fit to Q-nets of typical versus suboptimal development, we can reliably estimate individual deficit risk (Mδ) and identify infants achieving poor future head circumference growth with ≈76% area under the receiver operator characteristic curve, 95% ± 1.8% positive predictive value at 98% specificity at 30 weeks postmenstrual age. We find that early transplantation might mitigate risk for ≈45.2% of the cohort, with potentially negative effects from incorrect supplementation. Q-nets are generative artificial intelligence models for ecosystem dynamics, with broad potential applications.

Pulmonary Fibrosis Stakeholder Summit: A Joint NHLBI, Three Lakes Foundation, and Pulmonary Fibrosis Foundation Workshop Report

Despite progress in elucidation of disease mechanisms, identification of risk factors, biomarker discovery, and the approval of two medications to slow lung function decline in idiopathic pulmonary fibrosis and one medication to slow lung function decline in progressive pulmonary fibrosis, pulmonary fibrosis remains a disease with a high morbidity and mortality. In recognition of the need to catalyze ongoing advances and collaboration in the field of pulmonary fibrosis, the NHLBI, the Three Lakes Foundation, and the Pulmonary Fibrosis Foundation hosted the Pulmonary Fibrosis Stakeholder Summit on November 8-9, 2022. This workshop was held virtually and was organized into three topic areas: 1) novel models and research tools to better study pulmonary fibrosis and uncover new therapies, 2) early disease risk factors and methods to improve diagnosis, and 3) innovative approaches toward clinical trial design for pulmonary fibrosis. In this workshop report, we summarize the content of the presentations and discussions, enumerating research opportunities for advancing our understanding of the pathogenesis, treatment, and outcomes of pulmonary fibrosis.

Clinical characterization and differentiation of B-SNIP psychosis Biotypes: Algorithmic Diagnostics for Efficient Prescription of Treatments (ADEPT)-1

Clinically defined psychosis diagnoses are neurobiologically heterogeneous. The B-SNIP consortium identified and validated more neurobiologically homogeneous psychosis Biotypes using an extensive battery of neurocognitive and psychophysiological laboratory measures. However, typically the first step in any diagnostic evaluation is the clinical interview. In this project, we evaluated if psychosis Biotypes have clinical characteristics that can support their differentiation in addition to obtaining laboratory testing. Clinical interview data from 1907 individuals with a psychosis Biotype were used to create a diagnostic algorithm. The features were 58 ratings from standard clinical scales. Extremely randomized tree algorithms were used to evaluate sensitivity, specificity, and overall classification success. Biotype classification accuracy peaked at 91 % with the use of 57 items on average. A reduced feature set of 28 items, though, also showed 81 % classification accuracy. Using this reduced item set, we found that only 10-11 items achieved a one-vs-all (Biotype-1 or not, Biotype-2 or not, Biotype-3 or not) area under the sensitivity-specificity curve of .78 to .81. The top clinical characteristics for differentiating psychosis Biotypes, in order of importance, were (i) difficulty in abstract thinking, (ii) multiple indicators of social functioning, (iii) conceptual disorganization, (iv) severity of hallucinations, (v) stereotyped thinking, (vi) suspiciousness, (vii) unusual thought content, (viii) lack of spontaneous speech, and (ix) severity of delusions. These features were remarkably different from those that differentiated DSM psychosis diagnoses. This low-burden adaptive algorithm achieved reasonable classification accuracy and will support Biotype-specific etiological and treatment investigations even in under-resourced clinical and research environments.

Predicting Malignant Ventricular Arrhythmias Using Real-Time Remote Monitoring

BACKGROUND

Although implantable cardioverter-defibrillator (ICD) therapies are associated with increased morbidity and mortality, the prediction of malignant ventricular arrhythmias has remained elusive.

OBJECTIVES

The purpose of this study was to evaluate whether daily remote-monitoring data may predict appropriate ICD therapies for ventricular tachycardia or ventricular fibrillation.

METHODS

This was a post hoc analysis of IMPACT (Randomized trial of atrial arrhythmia monitoring to guide anticoagulation in patients with implanted defibrillator and cardiac resynchronization devices), a multicenter, randomized, controlled trial of 2,718 patients evaluating atrial tachyarrhythmias and anticoagulation for patients with heart failure and ICD or cardiac resynchronization therapy with defibrillator devices. All device therapies were adjudicated as either appropriate (to treat ventricular tachycardia or ventricular fibrillation) or inappropriate (all others). Remote monitoring data in the 30 days before device therapy were utilized to develop separate multivariable logistic regression and neural network models to predict appropriate device therapies.

RESULTS

A total of 59,807 device transmissions were available for 2,413 patients (age 64 ± 11 years, 26% women, 64% ICD). Appropriate device therapies (141 shocks, 10 antitachycardia pacing) were delivered to 151 patients. Logistic regression identified shock lead impedance and ventricular ectopy as significantly associated with increased risk of appropriate device therapy (sensitivity 39%, specificity 91%, AUC: 0.72). Neural network modeling yielded significantly better (P < 0.01 for comparison) predictive performance (sensitivity 54%, specificity 96%, AUC: 0.90), and also identified patterns of change in atrial lead impedance, mean heart rate, and patient activity as predictors of appropriate therapies.

CONCLUSIONS

Daily remote monitoring data may be utilized to predict malignant ventricular arrhythmias in the 30 days before device therapies. Neural networks complement and enhance conventional approaches to risk stratification.

Cardiac Comorbidity Risk Score: Zero-Burden Machine Learning to Improve Prediction of Postoperative Major Adverse Cardiac Events in Hip and Knee Arthroplasty

Background In this retrospective, observational study we introduce the Cardiac Comorbidity Risk Score, predicting perioperative major adverse cardiac events (MACE) after elective hip and knee arthroplasty. MACE is a rare but important driver of mortality, and existing tools, eg, the Revised Cardiac Risk Index demonstrate only modest accuracy. We demonstrate an artificial intelligence-based approach to identify patients at high risk of MACE within 4 weeks (primary outcome) of arthroplasty, that imposes zero additional burden of cost/resources. Methods and Results Cardiac Comorbidity Risk Score calculation uses novel machine learning to estimate MACE risk from patient electronic health records, without requiring blood work or access to any demographic data beyond that of sex and age, and accounts for variable/missing/incomplete information across patient records. Validated on a deidentified cohort (age >45 years, n=445 391), performance was evaluated using the area under the receiver operator characteristics curve (AUROC), sensitivity/specificity, positive predictive value, and positive/negative likelihood ratios. In our cohort (age 63.5±10.5 years, 58.2% women, 34.2%/65.8% hip/knee procedures), 0.19% (882) experienced the primary outcome. Cardiac Comorbidity Risk Score achieved area under the receiver operator characteristics curve=80.0±0.4% (95% CI) for women and 80.1±0.5% (95% CI) for males, with 36.4% and 35.1% sensitivities, respectively, at 95% specificity, significantly outperforming Revised Cardiac Risk Index across all studied age-, sex-, risk-, and comorbidity-based subgroups. Conclusions Cardiac Comorbidity Risk Score, a novel artificial intelligence-based screening tool using known and unknown comorbidity patterns, outperforms state-of-the-art in predicting MACE within 4 weeks postarthroplasty, and can identify patients at high risk that do not demonstrate traditional risk factors.

Development of a computerized adaptive diagnostic screening tool for psychosis

We develop a two-stage diagnostic classification system for psychotic disorders using an extremely randomized trees machine learning algorithm. Item bank was developed from clinician-rated items drawn from an inpatient and outpatient sample. In stage 1, we differentiate schizophrenia and schizoaffective disorder from depression and bipolar disorder (with psychosis). In stage 2 we differentiate schizophrenia from schizoaffective disorder. Out of sample classification accuracy, determined by area under the receiver operator characteristic (ROC) curve, was outstanding for stage 1 (Area under the ROC curve (AUC) = 0.93, 95% confidence interval (CI) = 0.89, 0.94), and excellent for stage 2 (AUC = 0.86, 95% CI = 0.83, 0.88). This is achieved based on an average of 5 items for stage 1 and an average of 6 items for stage 2, out of a bank of 73 previously validated items.

Event-level prediction of urban crime reveals a signature of enforcement bias in US cities

Policing efforts to thwart crime typically rely on criminal infraction reports, which implicitly manifest a complex relationship between crime, policing and society. As a result, crime prediction and predictive policing have stirred controversy, with the latest artificial intelligence-based algorithms producing limited insight into the social system of crime. Here we show that, while predictive models may enhance state power through criminal surveillance, they also enable surveillance of the state by tracing systemic biases in crime enforcement. We introduce a stochastic inference algorithm that forecasts crime by learning spatio-temporal dependencies from event reports, with a mean area under the receiver operating characteristic curve of ~90% in Chicago for crimes predicted per week within ~1,000 ft. Such predictions enable us to study perturbations of crime patterns that suggest that the response to increased crime is biased by neighbourhood socio-economic status, draining policy resources from socio-economically disadvantaged areas, as demonstrated in eight major US cities.

Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts

The spread of a communicable disease is a complex spatio-temporal process shaped by the specific transmission mechanism, and diverse factors including the behavior, socio-economic and demographic properties of the host population. While the key factors shaping transmission of influenza and COVID-19 are beginning to be broadly understood, making precise forecasts on case count and mortality is still difficult. In this study we introduce the concept of a universal geospatial risk phenotype of individual US counties facilitating flu-like transmission mechanisms. We call this the Universal Influenza-like Transmission (UnIT) score, which is computed as an information-theoretic divergence of the local incidence time series from an high-risk process of epidemic initiation, inferred from almost a decade of flu season incidence data gleaned from the diagnostic history of nearly a third of the US population. Despite being computed from the past seasonal flu incidence records, the UnIT score emerges as the dominant factor explaining incidence trends for the COVID-19 pandemic over putative demographic and socio-economic factors. The predictive ability of the UnIT score is further demonstrated via county-specific weekly case count forecasts which consistently outperform the state of the art models throughout the time-line of the COVID-19 pandemic. This study demonstrates that knowledge of past epidemics may be used to chart the course of future ones, if transmission mechanisms are broadly similar, despite distinct disease processes and causative pathogens.

Accurate case count forecasts in an epidemic is non-trivial, with the spread of infectious diseases being modulated by diverse hard-to-model factors. This study introduces the concept of a universal risk phenotype for US counties that predictably increases the risk of person-to-person transmission of influenza-like illnesses; universal in the sense that it is pathogen-agnostic provided the transmission mechanism is similar to that of seasonal influenza. We call this the Universal Influenza-like Transmission (UnIT) score, which accounts for unmodeled effects by automatically leveraging subtle geospatial patterns underlying the flu epidemics of the past. It is a phenotype of the counties themselves, as it characterizes how the transmission process is differentially impacted in different geospatial contexts. Grounded in information-theory and machine learning, the UnIT score reduces the need to manually identify every factor that impacts the case counts. Applying to the COVID-19 pandemic, we show that incidence patterns from a past epidemic caused by an appropriately-chosen distinct pathogen can substantially inform future projections. Our forecasts consistently outperform the state of the art models throughout the time-line of the COVID-19 pandemic, and thus is an important step to inform policy decisions in current and future pandemics.

Reduced false positives in autism screening via digital biomarkers inferred from deep comorbidity patterns

Here, we develop digital biomarkers for autism spectrum disorder (ASD), computed from patterns of past medical encounters, identifying children at high risk with an area under the receiver operating characteristic exceeding 80% from shortly after 2 years of age for either sex, and across two independent patient databases. We leverage uncharted ASD comorbidities, with no requirement of additional blood work, or procedures, to estimate the autism comorbid risk score (ACoR), during the earliest years when interventions are the most effective. ACoR has superior predictive performance to common questionnaire-based screenings and can reduce their current socioeconomic, ethnic, and demographic biases. In addition, we can condition on current screening scores to either halve the state-of-the-art false-positive rate or boost sensitivity to over 60%, while maintaining specificity above 95%. Thus, ACoR can significantly reduce the median diagnostic age, reducing diagnostic delays and accelerating access to evidence-based interventions.

Postnatal immune activation causes social deficits in a mouse model of tuberous sclerosis: Role of microglia and clinical implications

There is growing evidence that prenatal immune activation contributes to neuropsychiatric disorders. Here, we show that early postnatal immune activation resulted in profound impairments in social behavior, including in social memory in adult male mice heterozygous for a gene responsible for tuberous sclerosis complex (Tsc2+/−), a genetic disorder with high prevalence of autism. Early postnatal immune activation did not affect either wild-type or female Tsc2+/− mice. We demonstrate that these memory deficits are caused by abnormal mammalian target of rapamycin–dependent interferon signaling and impairments in microglia function. By mining the medical records of more than 3 million children followed from birth, we show that the prevalence of hospitalizations due to infections in males (but not in females) is associated with future development of autism spectrum disorders (ASD). Together, our results suggest the importance of synergistic interactions between strong early postnatal immune activation and mutations associated with ASD.

Development and Validation of Computerized Adaptive Assessment Tools for the Measurement of Posttraumatic Stress Disorder Among US Military Veterans

IMPORTANCE

Veterans from recent and past conflicts have high rates of posttraumatic stress disorder (PTSD). Adaptive testing strategies can increase accuracy of diagnostic screening and symptom severity measurement while decreasing patient and clinician burden.

OBJECTIVE

To develop and validate a computerized adaptive diagnostic (CAD) screener and computerized adaptive test (CAT) for PTSD symptom severity.

DESIGN, SETTING, AND PARTICIPANTS

A diagnostic study of measure development and validation was conducted at a Veterans Health Administration facility. A total of 713 US military veterans were included. The study was conducted from April 25, 2017, to November 10, 2019.

MAIN OUTCOMES AND MEASURES

The participants completed a PTSD-symptom questionnaire from the item bank and provided responses on the PTSD Checklist for Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) (PCL-5). A subsample of 304 participants were interviewed using the Clinician-Administered Scale for PTSD for DSM-5.

RESULTS

Of the 713 participants, 585 were men; mean (SD) age was 52.8 (15.0) years. The CAD-PTSD reproduced the Clinician-Administered Scale for PTSD for DSM-5 PTSD diagnosis with high sensitivity and specificity as evidenced by an area under the curve of 0.91 (95% CI, 0.87-0.95). The CAT-PTSD demonstrated convergent validity with the PCL-5 (r = 0.88) and also tracked PTSD diagnosis (area under the curve = 0.85; 95% CI, 0.79-0.89). The CAT-PTSD reproduced the final 203-item bank score with a correlation of r = 0.95 with a mean of only 10 adaptively administered items, a 95% reduction in patient burden.

CONCLUSIONS AND RELEVANCE

Using a maximum of only 6 items, the CAD-PTSD developed in this study was shown to have excellent diagnostic screening accuracy. Similarly, using a mean of 10 items, the CAT-PTSD provided valid severity ratings with excellent convergent validity with an extant scale containing twice the number of items. The 10-item CAT-PTSD also outperformed the 20-item PCL-5 in terms of diagnostic accuracy. The results suggest that scalable, valid, and rapid PTSD diagnostic screening and severity measurement are possible.

Conjunction of factors triggering waves of seasonal influenza

Using several longitudinal datasets describing putative factors affecting influenza incidence and clinical data on the disease and health status of over 150 million human subjects observed over a decade, we investigated the source and the mechanistic triggers of influenza epidemics. We conclude that the initiation of a pan-continental influenza wave emerges from the simultaneous realization of a complex set of conditions. The strongest predictor groups are as follows, ranked by importance: (1) the host population's socio- and ethno-demographic properties; (2) weather variables pertaining to specific humidity, temperature, and solar radiation; (3) the virus' antigenic drift over time; (4) the host population'€™s land-based travel habits, and; (5) recent spatio-temporal dynamics, as reflected in the influenza wave auto-correlation. The models we infer are demonstrably predictive (area under the Receiver Operating Characteristic curve 80%) when tested with out-of-sample data, opening the door to the potential formulation of new population-level intervention and mitigation policies.

Increasing incidence of chronic subdural haematoma in the elderly

BACKGROUND

Chronic subdural haematoma (CSDH) is a condition predominantly affecting the elderly. We reported an incidence of 8.2 per 100 000 per year in people above the age of 65 in 2002.

AIM

Since recent studies have demonstrated a higher incidence, we repeated our study to estimate the current incidence of CSDH amongst people above the age of 65 in North Wales.

DESIGN

We used radiological reports to identify patients with CSDH over a 1-year period.

METHODS

We collected data on demographics, clinical presentations, indications for brain imaging, drug history and 30-day outcome from the case notes and electronic records.

RESULTS

The population of North Wales was 687 937 of which 138 325 (20%) were above 65. There were 66 cases of CSDH giving an incidence of 48 per 100 000 per year. Mean age was 81 and there were 32 males and 34 females. Falls and confusion were the commonest indications to request a CT scan (90%). Other indications were drowsiness (9%) and focal neurological deficit (4%). 17 were on antiplatelets and 20 were on warfarin. Ten underwent surgical intervention. At 30 days 28 were discharged, 22 were still in hospital and 16 died.

CONCLUSION

The incidence of CSDH is much higher than previously reported. Reasons include a low threshold for imaging patients with recurrent falls and confusion, increasing use of anti-thrombotics and ageing population. In many older patients CSDH is a marker of underlying co-morbidities rather than a primary event.

Data smashing: uncovering lurking order in data

From automatic speech recognition to discovering unusual stars, underlying almost all automated discovery tasks is the ability to compare and contrast data streams with each other, to identify connections and spot outliers. Despite the prevalence of data, however, automated methods are not keeping pace. A key bottleneck is that most data comparison algorithms today rely on a human expert to specify what 'features' of the data are relevant for comparison. Here, we propose a new principle for estimating the similarity between the sources of arbitrary data streams, using neither domain knowledge nor learning. We demonstrate the application of this principle to the analysis of data from a number of real-world challenging problems, including the disambiguation of electro-encephalograph patterns pertaining to epileptic seizures, detection of anomalous cardiac activity from heart sound recordings and classification of astronomical objects from raw photometry. In all these cases and without access to any domain knowledge, we demonstrate performance on a par with the accuracy achieved by specialized algorithms and heuristics devised by domain experts. We suggest that data smashing principles may open the door to understanding increasingly complex observations, especially when experts do not know what to look for.

Abductive learning of quantized stochastic processes with probabilistic finite automata

We present an unsupervised learning algorithm (GenESeSS) to infer the causal structure of quantized stochastic processes, defined as stochastic dynamical systems evolving over discrete time, and producing quantized observations. Assuming ergodicity and stationarity, GenESeSS infers probabilistic finite state automata models from a sufficiently long observed trace. Our approach is abductive; attempting to infer a simple hypothesis, consistent with observations and modelling framework that essentially fixes the hypothesis class. The probabilistic automata we infer have no initial and terminal states, have no structural restrictions and are shown to be probably approximately correct-learnable. Additionally, we establish rigorous performance guarantees and data requirements, and show that GenESeSS correctly infers long-range dependencies. Modelling and prediction examples on simulated and real data establish relevance to automated inference of causal stochastic structures underlying complex physical phenomena.

Contribution of germ line BRCA2 sequence alterations to risk of familial esophageal cancer in a high-risk area of India

The incidence of esophageal squamous cell carcinoma (ESCC) is very high in the northeast region of India. An earlier study from China and Iran suggested that mutations in BRCA2 gene may play a role in the etiology of familial ESCC. However, the frequency of BRCA2 gene germ line mutations and its contribution to risk of familial aggregation of ESCC in high-risk region of India are not known. In the current study of 317 cases of esophageal cancer, 92 (29%) cases had a family history of esophageal and/or other cancers. Of these 92 patients, 45 (49%) patients had a family history of esophageal cancer. The risk of developing esophageal cancer was higher in cases where family history showed occurrence of cancers in first-degree relatives (odds ratio [OR]: 3.1; confidence interval [CI]: 1.9-5.3) than in second-degree relatives (OR: 1.3; CI: 0.25-3.2). Moreover, the risk of developing esophageal cancer was higher in subjects whose predegree suffered from esophageal cancer (OR: 2.4; CI: 1.1-4.1) than from any other cancers (OR: 1.1; CI: 0.32-3.3). The subjects with family history of cancer were more likely to develop ESCC if they were tobacco chewers (OR: 4.2; CI: 2.1-5.8) and betel quid users (OR: 3.6; CI: 1.8-4.6). Screening for mutations of the BRCA2 gene in the germ line DNA was carried out for 20 familial and 80 nonfamilial ESCC patients. One hundred unrelated healthy controls from the same population were included in this study. Nonsynonymous variants in exon 18 (K2729N) and exon 27 (I3412V) of BRCA2 gene were found in 3 of 20 patients with familial ESCC. No sequence alterations were found in 80 nonfamilial ESCC cases (P=0.01) and 100 healthy controls (P=0.0037), suggesting that germ line BRCA2 gene mutation may play a role in familial aggregation of ESCC in high-risk region of India.

Supervised self-organization of homogeneous swarms using ergodic projections of Markov chains

This paper formulates a self-organization algorithm to address the problem of global behavior supervision in engineered swarms of arbitrarily large population sizes. The swarms considered in this paper are assumed to be homogeneous collections of independent identical finite-state agents, each of which is modeled by an irreducible finite Markov chain. The proposed algorithm computes the necessary perturbations in the local agents' behavior, which guarantees convergence to the desired observed state of the swarm. The ergodicity property of the swarm, which is induced as a result of the irreducibility of the agent models, implies that while the local behavior of the agents converges to the desired behavior only in the time average, the overall swarm behavior converges to the specification and stays there at all times. A simulation example illustrates the underlying concept.

Subcortical white matter abnormalities related to drug resistance in Wilson disease

Wilson disease (WD) produces typical lesions in the brain, which can aid in diagnosis and therapy. The authors present a drug-resistant WD case with atypical cerebral lesions with marked involvement of white matter as visualized on MRI scans. The diagnosis was confirmed by identification of mutations in the ATP7B gene. The case demonstrates an uncommon pathology-related cerebral copper accumulation and emphasizes the importance of genetic screening in the diagnosis of WD.

Non diethylstilbesterol induced vaginal adenosis--a case series and review of literature

Non diethylstilbestrol induced vaginal adenosis has a reported incidence of about 10% in adult women. Although in some, it may be an insignificant coincidental finding, it is probably under-diagnosed even in symptomatic women. Little is known about the aetiology, pathogenesis, symptomatology and management of this poorly understood condition. Our experience with the four cases of vaginal adenosis unrelated to diethylstilbestrol (DES) exposure and a review of the literature will probably shed some light on this, as it still remains an enigma in gynaecological oncology.

Colchicine induced rhabdomyolysis

A case of colchicine induced rhabdomyolysis is reported. A 73 year old man with ischaemic heart disease, atrial fibrillation, chronic congestive cardiac failure, and chronic gout presented with diffuse muscle pain. He had been taking an increased dose of colchicine (1.5 mg daily) for an exacerbation of gout for six weeks before the presentation. Investigations confirmed the diagnosis of rhabdomyolysis and discontinuation of colchicine resulted in resolution of clinical and biochemical features of rhabdomyolysis. Although neuromuscular adverse effects of colchicine are well recognised, rhabdomyolysis is rare and this is only the fourth reported case of colchicine induced rhabdomyolysis in the literature.