EHR-Safe: generating high-fidelity and privacy-preserving synthetic electronic health records.

Privacy concerns often arise as the key bottleneck for the sharing of data between consumers and data holders, particularly for sensitive data such as Electronic Health Records (EHR). This impedes the application of data analytics and ML-based innovations with tremendous potential. One promising approach for such privacy concerns is to instead use synthetic data. We propose a generative modeling framework, EHR-Safe, for generating highly realistic and privacy-preserving synthetic EHR data. EHR-Safe is based on a two-stage model that consists of sequential encoder-decoder networks and generative adversarial networks. Our innovations focus on the key challenging aspects of real-world EHR data: heterogeneity, sparsity, coexistence of numerical and categorical features with distinct characteristics, and time-varying features with highly-varying sequence lengths. Under numerous evaluations, we demonstrate that the fidelity of EHR-Safe is almost-identical with real data (<3% accuracy difference for the models trained on them) while yielding almost-ideal performance in practical privacy metrics.

Comparison of technical errors in pediatric bitewing radiographs acquired with round vs rectangular collimation.

OBJECTIVE: To compare technical errors in bitewing radiographs acquired with round vs rectangular collimation in a hospital-based pediatric dentistry training program. STUDY DESIGN: A retrospective chart review was conducted of 176 digital bitewing radiographs exposed with round collimation and 106 exposed with rectangular collimation. The number of re-exposures was calculated, and errors in central ray entry (CRE; "cone cuts"), horizontal and vertical positioning, and angulation were measured. RESULTS: There were no greater re-exposures but significantly more CRE errors with rectangular collimation (21.7%; n = 23; 95% confidence interval [CI], 13.9%-30.0%) than with round collimation (3.4%; n = 6; 95% CI, 0.7%-6.1%). CRE error location, horizontal positioning errors, and size of horizontal overlapped contacts were statistically different but not clinically important. CONCLUSIONS: Use of rectangular collimation resulted in increased CRE errors but no other clinically significant problems. This technique should be used to reduce radiation exposure to patients.

Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor.

SARS-CoV-2 is a unique event, having emerged suddenly as a highly infectious viral pathogen for human populations. Previous phylogenetic analyses show its closest known evolutionary relative to be a virus detected in bats (RaTG13), with a common assumption that SARS-CoV-2 evolved from a zoonotic ancestor via recent genetic changes (likely in the Spike protein receptor-binding domain or RBD) that enabled it to infect humans. We used detailed phylogenetic analysis, ancestral sequence reconstruction, and in situ molecular dynamics simulations to examine the Spike-RBD's functional evolution, finding that the common ancestral virus with RaTG13, dating to no later than 2013, possessed high binding affinity to the human ACE2 receptor. This suggests that SARS-CoV-2 likely possessed a latent capacity to bind to human cellular targets (though this may not have been sufficient for successful infection) and emphasizes the importance of expanding efforts to catalog and monitor viruses circulating in both human and non-human populations.

Therapeutic vaccine BRII-179 restores HBV-specific immune responses in patients with chronic HBV in a phase Ib/IIa study.

BACKGROUND & AIMS: Functional cure of chronic HBV infection (CHB) without life-long treatment requires the restoration of defective HBV-specific humoral and cellular immunity. Therapeutic vaccines based on the major structural and non-structural proteins have been tested in patients with CHB but have shown scarce immunogenicity. BRII-179, also known as VBI-2601, is a novel formulation comprised of all 3 HBV surface envelope proteins (Pre-S1, Pre-S2, and S). Safety, antiviral activity, and immunogenicity of BRII-179 admixed with co-adjuvant interferon (IFN)-α were assessed in patients with CHB. METHOD: This randomized, open-label, controlled phase Ib/IIa study included 2 dose levels, 20 µg BRII-179 (Part 1, n = 25) and 40 µg BRII-179 (Part 2, n = 24). Patients, virally suppressed under nucleos(t)ide analogue (NA) therapy were randomized 1:2:2 into 3 cohorts in Part 1 and 1:1 into 2 cohorts in Part 2 to receive 4 monthly intramuscular injections of BRII-179 admixed with/without 3 MIU IFN-α. Antibody and cellular responses to HBsAg, as well as evolution of circulating HBsAg were monitored. RESULTS: Both 20 µg and 40 µg BRII-179 with/without IFN-α were well tolerated with no severe adverse events. BRII-179 induced anti-HBs responses in >30% patients in all treatment cohorts, however, moderate anti-Pre-S1 or anti-Pre-S2 antibody responses were only observed in patients receiving BRII-179 with IFN-α. BRII-179 also restored S-, Pre-S1-, Pre-S2-specific IFN-γ-producing T-cells in the majority of treated patients. Overall, no notable reduction of HBsAg was observed after BRII-179 treatment. CONCLUSION: In patients with CHB under NA therapy, BRII-179 with/without IFN-α exhibited a good safety profile and induced HBV-specific B- and T-cell immune responses. These data support further clinical evaluation of BRII-179 in combination with other therapies. CLINICAL TRIAL NUMBER: ACTRN12619001210167. LAY SUMMARY: BRII-179 is a therapeutic vaccine designed to improve the immune response in patients with chronic hepatitis B. In this study, BRII-179 alone or with a low dose of interferon-α was safe, well tolerated, and induced enhanced HBV-specific antibody and T-cell responses in patients with chronic hepatitis B. However, BRII-179 treatment alone had minimal effect on patient's virological status. The potential of BRII-179 to achieve a functional cure in conjunction with other agents is being evaluated in the clinic.

The adaptive landscape of a metallo-enzyme is shaped by environment-dependent epistasis.

Enzymes can evolve new catalytic activity when environmental changes present them with novel substrates. Despite this seemingly straightforward relationship, factors other than the direct catalytic target can also impact adaptation. Here, we characterize the catalytic activity of a recently evolved bacterial methyl-parathion hydrolase for all possible combinations of the five functionally relevant mutations under eight different laboratory conditions (in which an alternative divalent metal is supplemented). The resultant adaptive landscapes across this historical evolutionary transition vary in terms of both the number of "fitness peaks" as well as the genotype(s) at which they are found as a result of genotype-by-environment interactions and environment-dependent epistasis. This suggests that adaptive landscapes may be fluid and molecular adaptation is highly contingent not only on obvious factors (such as catalytic targets), but also on less obvious secondary environmental factors that can direct it towards distinct outcomes.

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease.

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

Statistical analysis of mutational epistasis to reveal intramolecular interaction networks in proteins.

Epistasis occurs when the combined effect of two or more mutations differs from the sum of their individual effects, and reflects molecular interactions that affect the function and fitness of a protein. Epistasis is widely recognized as a key phenomenon that drives the dynamics of evolution. It can profoundly affect our ability to understand sequence-structure-function relationships, and thus has important implications for protein engineering and design. Characterizing higher-order epistasis, i.e., interactions between three or more mutations, can unveil hidden intramolecular interaction networks that underlie essential protein functions and their evolution. For this chapter, we developed an analytical pipeline that can standardize the study of intramolecular epistasis. We describe the generation and characterization of a combinatorial library, the statistical analysis of mutational epistasis, and finally, the depiction of epistatic networks on the 3D structure of a protein. We anticipate that this pipeline will benefit the increasing number of scientists that are interested in the functional characterization of mutational libraries to provide a deeper understanding of the molecular mechanisms of protein evolution.

Author Correction: Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Engaging in building the educational support needed to deliver precision health in Canada.

Canadian healthcare facilities are poised to benefit from the tools of precision health. To do so effectively, however, it is crucial that we align changes in how healthcare professionals are educated in order to ensure they have the skills, knowledge, and training to fully engage with its tools. Here, we propose that the design, development, and delivery of novel educational programs focused on precision health should be prioritized for healthcare professionals, and we suggest some essential curricular considerations to that end. Additionally, it is crucial to see engagement on the part of health leaders, who will ultimately be most responsible for managing the changing needs of frontline staff as the tools of precision health become increasingly available. By engaging directly with educators in establishing new programs for precision health, we can ensure that its promise is fully for healthcare facilities, practitioners, and patients.

Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.

Characterizing the adaptive landscapes that encompass the emergence of novel enzyme functions can provide molecular insights into both enzymatic and evolutionary mechanisms. Here, we combine ancestral protein reconstruction with biochemical, structural and mutational analyses to characterize the functional evolution of methyl-parathion hydrolase (MPH), an organophosphate-degrading enzyme. We identify five mutations that are necessary and sufficient for the evolution of MPH from an ancestral dihydrocoumarin hydrolase. In-depth analyses of the adaptive landscapes encompassing this evolutionary transition revealed that the mutations form a complex interaction network, defined in part by higher-order epistasis, that constrained the adaptive pathways available. By also characterizing the adaptive landscapes in terms of their functional activities towards three additional organophosphate substrates, we reveal that subtle differences in the polarity of the substrate substituents drastically alter the network of epistatic interactions. Our work suggests that the mutations function collectively to enable substrate recognition via subtle structural repositioning.

Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions.

Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions by enabling the observation and investigation of complex sequence-structure-function and evolutionary relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) and phylogenetic reconstructions to map the functional divergence and evolutionary history of protein superfamilies. We exemplify this approach using the nitroreductase (NTR) flavoenzyme superfamily, demonstrating that SSN investigations can provide a rapid and effective means to classify groups of proteins, expose sequence similarity relationships across the global scale of a protein superfamily, and efficiently support detailed phylogenetic analyses. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes, their evolution, and their associated physiological roles.

A non-randomised controlled pilot study of clinical pharmacist collaborative intervention for community dwelling patients with COPD.

UK, home-based patients with COPD receive specialist care from respiratory physicians, nurses, and general practitioners (GPs), but increasing complexity of therapeutic options and a GP/Nurse workforce crisis suggests merit in testing the role of home visits by a clinical pharmacist. We conducted a non-randomised intervention study with a contemporaneous comparator group, in Glasgow (Scotland). A clinical pharmacist (working closely with a consultant respiratory physician) visited patients with COPD living at home, assessing respiratory and other co-morbid conditions, and medicines then, with patient approval, agreed treatment modifications with a consultant physician. Comparator group-patients were drawn from another hospital out-patient clinic. Main outcomes were exacerbations during 4-months of follow-up and respiratory hospitalisations (number and duration) after 1 year. In the intervention group, 86 patients received a median of three home visits; 87 received usual care (UC). At baseline, patients in the intervention group were similar to those in UC in terms of respiratory hospitalisations although slightly younger, more likely to receive specific maintenance antibiotics/Prednisolone and to have had exacerbations. Sixty-two (72.1%) of the intervention group received dose changes; 45 (52.3%) had medicines stopped/started and 21 (24.4%) received an expedited review at the specialist respiratory consultant clinic; 46 (53.5%) were referred to other healthcare services. Over one-third were referred for bone scans and 11% received additional investigations. At follow-up, 54 (63.5%) of intervention group participants had an exacerbation compared with 75 (86.2%) in the UC group (p = 0.001); fewer had respiratory hospitalisations (39 (45.3%) vs. 66 (76.7%); p < 0.001). Hospitalisations were shorter in the intervention group. Pharmacist-consultant care for community dwelling patients with COPD, changed clinical management and improved outcomes. A randomised controlled trial would establish causality.

Design control considerations for biologic-device combination products.

Combination products are therapeutic and diagnostic medical products that combine drugs, devices, and/or biological products with one another. Historically, biologics development involved identifying efficacious doses administered to patients intravenously or perhaps by a syringe. Until fairly recently, there has been limited focus on developing an accompanying medical device, such as a prefilled syringe or auto-injector, to enable easy and more efficient delivery. For the last several years, and looking forward, where there may be little to distinguish biologics medicines with relatively similar efficacy profiles, the biotechnology market is beginning to differentiate products by patient-focused, biologic-device based combination products. As innovative as biologic-device combination products are, they can pose considerable development, regulatory, and commercialization challenges due to unique physicochemical properties and special clinical considerations (e.g., dosing volumes, frequency, co-medications, etc.) of the biologic medicine. A biologic-device combination product is a marriage between two partners with "cultural differences," so to speak. There are clear differences in the development, review, and commercialization processes of the biologic and the device. When these two cultures come together in a combination product, developers and reviewers must find ways to address the design controls and risk management processes of both the biologic and device, and knit them into a single entity with supporting product approval documentation. Moreover, digital medicine and connected health trends are pushing the boundaries of combination product development and regulations even further. Despite an admirable cooperation between industry and FDA in recent years, unique product configurations and design features have resulted in review challenges. These challenges have prompted agency reviewers to modernize consultation processes, while at the same time, promoting development of innovative, safe and effective combination products. It remains the manufacturer's responsibility to comply with the relevant requirements and regulations, and develop good business practices that clearly describe how these practices comply with FDA's final rule (21 CFR Part 4) and aligns with the company's already established quality system.

Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites.

Complexes of specifically interacting molecules, such as transcription factor proteins (TFs) and the DNA response elements (REs) they recognize, control most biological processes, but little is known concerning the functional and evolutionary effects of epistatic interactions across molecular interfaces. We experimentally characterized all combinations of genotypes in the joint protein-DNA sequence space defined by an historical transition in TF-RE specificity that occurred some 500 million years ago in the DNA-binding domain of an ancient steroid hormone receptor. We found that rampant epistasis within and between the two molecules was essential to specific TF-RE recognition and to the evolution of a novel TF-RE complex with unique derived specificity. Permissive and restrictive epistatic mutations across the TF-RE interface opened and closed potential evolutionary paths accessible by the other, making the evolution of each molecule contingent on its partner's history and allowing a molecular complex with novel specificity to evolve.

Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module.

Complex gene regulatory networks require transcription factors (TFs) to bind distinct DNA sequences. To understand how novel TF specificity evolves, we combined phylogenetic, biochemical, and biophysical approaches to interrogate how DNA recognition diversified in the steroid hormone receptor (SR) family. After duplication of the ancestral SR, three mutations in one copy radically weakened binding to the ancestral estrogen response element (ERE) and improved binding to a new set of DNA sequences (steroid response elements, SREs). They did so by establishing unfavorable interactions with ERE and abolishing unfavorable interactions with SRE; also required were numerous permissive substitutions, which nonspecifically improved cooperativity and affinity of DNA binding. Our findings indicate that negative determinants of binding play key roles in TFs' DNA selectivity and-with our prior work on the evolution of SR ligand specificity during the same interval-show how a specific new gene regulatory module evolved without interfering with the integrity of the ancestral module.

Blood pressure after recent stroke: baseline findings from the secondary prevention of small subcortical strokes trial.

BACKGROUND: Hypertension is the most powerful risk factor for stroke. The aim of this study was to characterize baseline blood pressure in participants in the Secondary Prevention of Small Subcortical Strokes trial. METHODS: For this cross-sectional analysis, participants were categorized by baseline systolic blood pressure (SBP) < 120, 120-139, 140-159, 160-179, and ≥ 180 mm Hg and compared on demographic and clinical characteristics. Predictors of SBP < 140 mm Hg were examined. RESULTS: Mean SBP was 143±19 mm Hg while receiving an average of 1.7 antihypertensive medications; SBP ≥ 140 mm Hg for 53% and ≥ 160 mm Hg for 18% of the 3,020 participants. Higher SBP was associated with a history of hypertension and hypertension for longer duration (both P < 0.0001). Higher SBPs were associated with more extensive white matter disease on magnetic resonance imaging (P < 0.0001). There were significant differences in entry-level SBP when participants were categorized by race and region (both P < 0.0001). Black participants were more likely to have SBP ≥ 140 mm Hg. Multivariable logistic regression showed an independent effect for region with those from Canada more likely (odds ratio = 1.7; 95% confidence interval, 1.29, 2.32) to have SBP < 140 mm Hg compared with participants from United States. CONCLUSIONS: In this cohort with symptomatic lacunar stroke, more than half had uncontrolled hypertension at approximately 2.5 months after stroke. Regional, racial, and clinical differences should be considered to improve control and prevent recurrent stroke.

Serum biomarkers reveal long-term cardiac injury in isoproterenol-treated African green monkeys.

The assessment of cardiac toxicity is a major challenge in both drug development and clinical trials, and numerous marketed pharmaceuticals have been removed from the market due to unpredicted cardiac effects. Serum troponins are widely used indicators of cardiac injury; however, they are short-lived and have not been validated in preclinical animal models. In this study, we have used filter-aided sample preparation (FASP) and tandem mass tag (TMT) labeling to investigate serum protein alterations in isoproterenol-treated African green monkeys. Our results showed that the combination of FASP and TMT labeling provided highly reproducible and efficient sample preparation, which enables us to identify and quantify serum proteins with high confidence. We focused on the proteins that exhibit long-term alteration upon isoproterenol injection and discovered nine proteins exhibiting significant changes at 48 and 72 h postdosing. We further chose three proteins, serum amyloid A (SAA), frutose biphosphate aldolase A (FBAA), and fetuin A, for validation using enzyme-linked immunosorbent assay (ELISA). The serum concentration of SAA showed a ∼ 50 fold increase, while concentration of FBAA and fetuin A exhibited a significant decrease accompanying isoproterenol-induced cardiotoxicity. This work provides valuable insights for multimarker evaluation of long-term cardiac injury.

Evolution of the closely related, sex-related genes DM-W and DMRT1 in African clawed frogs (Xenopus).

DM-W is a dominant, female-specific, regulator of sex determination in the African clawed frog Xenopus laevis. This gene is derived from partial duplication of DMRT1, a male-related autosomal gene. We set out to better understand sex determination in Xenopus by studying this pair of genes. We found that DM-W evolved in Xenopus after divergence from the sister genus Silurana but before divergence of X. laevis and X. clivii, and that DM-W arose from partial duplication of DMRT1ß, which is one of the two DMRT1 paralogs in the tetraploid ancestor of Xenopus. Using the rate ratio of nonsynonymous to synonymous substitutions per site and multilocus polymorphism data, we show that DM-W evolved non-neutrally. By cloning paralogs and using a pyrosequencing assay, we also demonstrate that DMRT1 underwent phylogenetically biased pseudogenization after polyploidization, and that expression of this gene is regulated by mechanisms that vary through development. One explanation for these observations is that the expression domain of DMRT1ß was marginalized, which would explain why this paralog is dispensable in Xenopus polyploids and why DM-W has a narrow expression domain. These findings illustrate how evolution of the genetic control of stable phenotypes is facilitated by redundancy, degeneration, and compartmentalized regulation.