Bayesian emulation and history matching of JUNE.

We analyze JUNE: a detailed model of COVID-19 transmission with high spatial and demographic resolution, developed as part of the RAMP initiative. JUNE requires substantial computational resources to evaluate, making model calibration and general uncertainty analysis extremely challenging. We describe and employ the uncertainty quantification approaches of Bayes linear emulation and history matching to mimic JUNE and to perform a global parameter search, hence identifying regions of parameter space that produce acceptable matches to observed data, and demonstrating the capability of such methods. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Mental health of staff working in intensive care during Covid-19.

BACKGROUND: Staff working in intensive care units (ICUs) have faced significant challenges during the COVID-19 pandemic which have the potential to adversely affect their mental health. AIMS: To identify the rates of probable mental health disorder in staff working in ICUs in nine English hospitals during June and July 2020. METHODS: An anonymized brief web-based survey comprising standardized questionnaires examining depression, anxiety symptoms, symptoms of post-traumatic stress disorder (PTSD), well-being and alcohol use was administered to staff. RESULTS: Seven hundred and nine participants completed the surveys comprising 291 (41%) doctors, 344 (49%) nurses and 74 (10%) other healthcare staff. Over half (59%) reported good well-being; however, 45% met the threshold for probable clinical significance on at least one of the following measures: severe depression (6%), PTSD (40%), severe anxiety (11%) or problem drinking (7%). Thirteen per cent of respondents reported frequent thoughts of being better off dead, or of hurting themselves in the past 2 weeks. Within the sample used in this study, we found that doctors reported better mental health than nurses across a range of measures. CONCLUSIONS: We found substantial rates of probable mental health disorders, and thoughts of self-harm, amongst ICU staff; these difficulties were especially prevalent in nurses. Whilst further work is needed to better understand the real level of clinical need amongst ICU staff, these results indicate the need for a national strategy to protect the mental health, and decrease the risk of functional impairment, of ICU staff whilst they carry out their essential work during COVID-19.

Economic consequences incurred by living kidney donors: a Canadian multi-center prospective study.

Some living kidney donors incur economic consequences as a result of donation; however, these costs are poorly quantified. We developed a framework to comprehensively assess economic consequences from the donor perspective including out-of-pocket cost, lost wages and home productivity loss. We prospectively enrolled 100 living kidney donors from seven Canadian centers between 2004 and 2008 and collected and valued economic consequences ($CAD 2008) at 3 months and 1 year after donation. Almost all (96%) donors experienced economic consequences, with 94% reporting travel costs and 47% reporting lost pay. The average and median costs of lost pay were $2144 (SD 4167) and $0 (25th-75th percentile 0, 2794), respectively. For other expenses (travel, accommodation, medication and medical), mean and median costs were $1780 (SD 2504) and $821 (25th-75th percentile 242, 2271), respectively. From the donor perspective, mean cost was $3268 (SD 4704); one-third of donors incurred cost >$3000, and 15% >$8000. The majority of donors (83%) reported inability to perform usual household activities for an average duration of 33 days; 8% reported out-of-pocket costs for assistance with these activities. The economic impact of living kidney donation for some individuals is large. We advocate for programs to reimburse living donors for their legitimate costs.

DTC genetic testing: pendulum swings and policy paradoxes.

After decades of optimistic portrayals, there has been a shift in the way that the popular press represents genomic research. A skeptical view has become more common. The central reason for this pendulum swing away from popular support is the harsh truth that most genetic risk information just isn't that predictive. This reality has created a fascinating policy paradox. If, as many in the scientific community are now saying, genetic information is not the oracle of our future health as we were once led to believe, and if access does not, for most, cause harm, why regulate the area? Why worry about shoddy direct-to-consumer (DTC) genetic testing companies? One primary justification, and one endorsed by the recent Canadian College of Medical Geneticists (CCMG) Policy Statement on DTC Genetics Testing, is that information that is conveyed to the public about genetics via marketing and to those who access DTC tests should, at a minimum, be accurate.

Genome Canada precision medicine strategy for structured national implementation of epitope matching in renal transplantation.

Advances in immunology support the understanding that precise structural epitopes on the antibody-accessible region of the HLA molecule determine antigenicity and challenge the need for identity across the full HLA molecule to minimize graft immunogenicity. Retrospective studies confirm that quantitative measurement of epitope-level mismatching between donor and recipient is an informative marker of graft rejection and survival and suggest that prospective allocation of donor organs based on this principle may improve graft survival. Here we describe the process for rigorous prospective evaluation of this hypothesis in a formal national proof-of-concept program for epitope-based matching. This encompasses broad societal consultation to engage the public, patients and providers; the development of clear allocation policies with strategies to support candidates who may be difficult to match; molecular and sequencing methods and web-based calculators enabling rapid epitope typing and recipient selection; precise immunological monitoring of the graft response; information systems permitting real-time monitoring of clinical outcomes; and assessment of health benefit and economic cost. The results of this objective evaluation can then be provided to payers and policy-makers for review, and adoption if of proven benefit.

Direct-to-consumer genetic testing: good, bad or benign?

A wide variety of genetic tests are now being marketed and sold in direct-to-consumer (DTC) commercial transactions. However, risk information revealed through many DTC testing services, especially those based on emerging genome wide-association studies, has limited predictive value for consumers. Some commentators contend that tests are being marketed prematurely, while others support rapid translation of genetic research findings to the marketplace. The potential harms and benefits of DTC access to genetic testing are not yet well understood, but some large-scale studies have recently been launched to examine how consumers understand and use genetic risk information. Greater consumer access to genetic tests creates a need for continuing education for health care professionals so they can respond to patients' inquiries about the benefits, risks and limitations of DTC services. Governmental bodies in many jurisdictions are considering options for regulating practices of DTC genetic testing companies, particularly to govern quality of commercial genetic tests and ensure fair and truthful advertising. Intersectoral initiatives involving government regulators, professional bodies and industry are important to facilitate development of standards to govern this rapidly developing area of personalized genomic commerce.

Media portrayal of herbal remedies versus pharmaceutical clinical trials: impacts on decision.

The use of Complementary and Alternative Medicines (CAM) in Europe and North America is increasing significantly with a concomitant growth in business interest. Users are educated and self-empowered and rely on information sources beyond mainstream medical practitioners. Not surprisingly, media coverage, much of dubious quality, has increased to meet demand for information. Here we present data from a study that explores how knowledge is translated in the socioeconomic-political context of CAM as compared to conventional pharmaceuticals. Specifically, we are interested in the nature of the information provided by clinical trials and the media and how this might impact decision-making regarding the use of CAM versus conventional pharmaceuticals and the reporting of conflicts of interest and industry funding of research. Our results suggest that, in the media, there were significant errors of omission in describing clinical trial quality and a serious under-reporting of risks of herbal remedies. Consumers, who often self-administer CAM are not being provided with information sufficient to make informed choices about treatment alternatives. The next step in the research is to determine whether these reporting dynamics in describing CAM clinical trials differ from those of reporting on pharmaceutical clinical trials.

Waldenstrom macroglobulinemia cells devoid of BTKC481S or CXCR4WHIM-like mutations acquire resistance to ibrutinib through upregulation of Bcl-2 and AKT resulting in vulnerability towards venetoclax or MK2206 treatment.

Although ibrutinib is highly effective in Waldenstrom macroglobulinemia (WM), no complete remissions in WM patients treated with ibrutinib have been reported to date. Moreover, ibrutinib-resistant disease is being steadily reported and is associated with dismal clinical outcome (overall survival of 2.9-3.1 months). To understand mechanisms of ibrutinib resistance in WM, we established ibrutinib-resistant in vitro models using validated WM cell lines. Characterization of these models revealed the absence of BTKC481S and CXCR4WHIM-like mutations. BTK-mediated signaling was found to be highly attenuated accompanied by a shift in PI3K/AKT and apoptosis regulation-associated genes/proteins. Cytotoxicity studies using the AKT inhibitor, MK2206±ibrutinib, and the Bcl-2-specific inhibitor, venetoclax±ibrutinib, demonstrated synergistic loss of cell viability when either MK22016 or venetoclax were used in combination with ibrutinib. Our findings demonstrate that induction of ibrutinib resistance in WM cells can arise independent of BTKC481S and CXCR4WHIM-like mutations and sustained pressure from ibrutinib appears to activate compensatory AKT signaling as well as reshuffling of Bcl-2 family proteins for maintenance of cell survival. Combination treatment demonstrated greater (and synergistic) antitumor effect and provides rationale for development of therapeutic strategies encompassing venetoclax+ibrutinib or PI3K/AKT inhibitors+ibrutinib in ibrutinib-resistant WM.

Coinhibition of the deubiquitinating enzymes, USP14 and UCHL5, with VLX1570 is lethal to ibrutinib- or bortezomib-resistant Waldenstrom macroglobulinemia tumor cells.

The survival of Waldenstrom macroglobulinemia (WM) tumor cells hinges on aberrant B-cell receptor (BCR) and MYD88 signaling. WM cells upregulate the proteasome function to sustain the BCR-driven growth while maintaining homeostasis. Clinically, two treatment strategies are used to disrupt these complementary yet mutually exclusive WM survival pathways via ibrutinib (targets BTK/MYD88 node) and bortezomib (targets 20 S proteasome). Despite the success of both agents, WM patients eventually become refractory to treatment, highlighting the adaptive plasticity of WM cells and underscoring the need for development of new therapeutics. Here we provide a comprehensive preclinical report on the anti-WM activity of VLX1570, a novel small-molecule inhibitor of the deubiquitinating enzymes (DUBs), ubiquitin-specific protease 14 (USP14) and ubiquitin carboxyl-terminal hydrolase isozyme L5 (UCHL5). Both DUBs reside in the 19 S proteasome cap and their inhibition by VLX1570 results in rapid and tumor-specific apoptosis in bortezomib- or ibrutinib-resistant WM cells. Notably, treatment of WM cells with VLX1570 downregulated BCR-associated elements BTK, MYD88, NFATC, NF-κB and CXCR4, the latter whose dysregulated function is linked to ibrutinib resistance. VLX1570 administered to WM-xenografted mice resulted in decreased tumor burden and prolonged survival (P=0.0008) compared with vehicle-treated mice. Overall, our report demonstrates significant value in targeting USP14/UCHL5 with VLX1570 in drug-resistant WM and carries a high potential for clinical translation.

Likelihood of spontaneous conversion of atrial fibrillation to sinus rhythm.

OBJECTIVES: We sought to determine the likelihood and predictors of spontaneous conversion to sinus rhythm of recent-onset atrial fibrillation (symptoms <72 h). BACKGROUND: Although spontaneous conversion of recent-onset atrial fibrillation is common, the likelihood and clinical and echocardiographic predictors have not been fully defined. Such data would be important for management of patients in whom early cardioversion is desired: Cardioversion could be delayed in patients with a high likelihood of spontaneous conversion, and it could be expeditiously pursued if spontaneous conversion is unlikely. METHODS: We screened 1,822 consecutive adults admitted to the hospital with atrial fibrillation and prospectively identified 356 patients (45% male, mean age +/- SD 68 +/- 16 years) with atrial fibrillation of <72-h duration. The occurrence of spontaneous conversion to sinus rhythm and clinical and echocardiographic data were identified through retrospective chart review. RESULTS: Spontaneous conversion to sinus rhythm occurred in 68% of the study group (n = 242; 95% confidence interval [CI] 63% to 73%). Among patients with spontaneous conversion, the total duration of atrial fibrillation was <24 h in 159 (66%), 24 to 48 h in 42 (17%) and >48 h in 41 (17%) (p < 0.001). Logistic regression analysis of clinical data identified presentation <24 h from onset of symptoms as the only predictor of spontaneous conversion (odds ratio 1.8, 95% CI 1.4 to 2.4, p < 0.0001). Normal left ventricular systolic function was more common among patients with spontaneous conversion (p = 0.03), but it was not an independent predictor of conversion. Left atrial dimension was similar between groups. CONCLUSIONS: Spontaneous conversion to sinus rhythm occurs in almost 70% of patients presenting with atrial fibrillation of <72-h duration. Presentation with symptoms of <24-h duration is the best predictor of spontaneous conversion.

Prospective identification of biologically active structures by topomer shape similarity searching.

The principle of bioisosterism-similarly shaped molecules are more likely to share biological properties than are other molecules-has long helped to guide drug discovery. An algorithmic implementation of this principle, based on shape comparisons of a single rule-generated "topomer" conformation per molecule, had been found to be the descriptor most consistently predictive of similar biological properties, in retrospective studies, and also to be well-suited for searching large (>10(12)) "virtual libraries" of potential reaction products. Therefore a prospective trial of this shape similarity searching method was carried out, with synthesis of 425 compounds and testing of them for inhibition of binding of angiotensin II (A-II). The 63 compounds that were identified by shape searching as most similar to any of four query structures included all of the seven compounds found to be highly active, with none of the other 362 structures being highly active (p < 0.001). Additional consistent relations (p < 0.05) were found, among all 425 compounds, between the degree of shape similarity to the nearest query structure and the frequency of various levels of observed activity. Known "SAR" (rules specifying structural features required for A-II antagonism) were also regenerated within the biological data for the 63 shape similar structures.

The law, adolescents, and the APOE epsilon 4 genotype: a view from Canada.

The presence of an apolipoprotein E (APOE) epsilon 4 allele may be a risk factor for the severity of the consequences of head trauma, both short-term and long-term. If this proves to be true, genetic testing for APOE status might be encouraged, or required, to minimize the costs of participation in high-contact sports, such as ice hockey, soccer, rugby, and boxing, where head injury is likely to occur. Under some circumstances, testing minors for this purpose might be justifiable. This would raise complex ethical and legal questions about respective powers and rights of adolescents and parents. The wishes of the "nearly competent" adolescent not to be tested should override parental desires for testing, although such a conclusion has only limited warrant in Canadian law. If a mature adolescent wishes testing, but the parents do not, testing may be permissible--although Canadian law is again unclear. The physician should not be able to inform the parents of the test results without the adolescent's consent, nor should the adolescent be forced to disclose those results.

Total synthesis of globotriaosylceramide (Gb3) and lysoglobotriaosylceramide (lysoGb3).

We have recently reported a highly efficient and stereocontrolled synthesis of globotriaosylceramide (Gb3, 1) in optically pure form. Key to our synthetic strategy was the implementation of the two-stage activation of thioglycosides for formation of the glycosidic bonds and the utilization of (2S, 3S, 4E)-2-azido-3-O-(tert-butyldimethylsilyl)-4-octadecen-1,3-di ol (9) as a sphingosine equivalent. The syntheses of Gb3 (1) and lysoGb3 (2) were achieved by stereocontrolled coupling of 2,3,4,6-tetra-O-benzyl-alpha-D-galactosyl fluoride (15) with phenyl O-(6-O-benzoyl-2,3-di-O-pivaloyl-beta-D-galactopyranosyl)- (1----4)-2,3,6-tri-O-pivaloyl-1-thio-beta-D-glucopyranoside (14) to form the P kappa antigen trisaccharide masked as a phenyl 1-thioglycoside at the reducing end. Thioglycoside 16 was converted into glycosyl fluoride 19, which was coupled to 9 in high yield. The coupled product 20 was converted into the title compounds 1 and 2 in four and three steps, respectively. This article presents the total synthesis of 1 and 2 in full experimental detail.

Xenotransplantation and public health: identifying the legal issues.

The debate over the acceptability of clinical trials for xenotransplantation has focussed primarily on analyses of: 1) the medical benefits that might accrue to individual patients in need of organ replacement therapy; 2) the risk of introducing new infectious disease(s) into the population; and 3) the ability of public safety measures to minimize that risk. It is now generally accepted that if we are to proceed with xenobiotechnology, sufficient public safety measures must first be adopted. Despite the growing consensus as to the indispensability of scientific safeguards, few authors have questioned the ability of current or novel legal frameworks to sustain and enforce such safeguards. A legal analysis of the public health concerns must be incorporated into the debate if we are to ensure a thorough and responsible decision-making process.

Relative kinematics of the rib cage and abdomen during speech and nonspeech behaviors of 15-month-old children.

Speech motor control emerges in the neurophysiologic context of widely distributed, powerful coordinative mechanisms, including those mediating respiratory function. It is unknown, however, whether developing children are able to exploit the capabilities of neural circuits controlling homeostasis for the production of speech and voice. Speech and rest breathing were investigated in eleven 15-month-old children using inductance plethysmography (Respitrace). Rib cage and abdominal kinematics were studied using a time-varying correlational index of thoracoabdominal coupling (i.e., reflecting the synchrony of movement of the rib cage and abdomen) as well as simple classification of the moment-to-moment kinematic relationship of these two functional components (i.e., concurrent expansion or compression, or oppositional movement). Results revealed markedly different patterns of movement for rest breathing and speech breathing, although within types of vocalization (nonspeech vocalization, babbling, true word production) no differences were apparent. Whereas rest breathing was characterized by tight coupling of rib cage and abdominal movement (average correlation coefficients usually exceeded .90), speech breathing exhibited weak coupling (the correlation coefficient ranged widely, but averaged about .60). Furthermore, speech production by these toddlers included the occurrence of both rib cage and abdominal paradoxing, which are observed infrequently in adult speakers. These results fail to support the suggestion that speech emerges from the extant coordinative organization of rest breathing. Rather, even in its earliest stages breathing for speech and voice exhibits kinematic properties distinct from those of other observed behaviors.

Xenotransplantation: consent, public health and charter issues.

There is a growing body of literature and commentary analyzing the ethical and public policy concerns associated with xenotransplantation. While this technology holds great promise to provide an almost limitless supply of organs for transplantation, there remains grave concern about possible public health ramifications. As a result, it has been recommended that patients who undergo xenotransplantations will need to agree, inter alia, to a lifetime of close health monitoring, participation in an international database and autopsy upon death. It has been suggested that this agreement would transform the nature of informed consent into a "binding contract." Though such draconian measures are understandable given the magnitude of the risks involved, would existing common law and legislation allow their implementation? This paper analyzes relevant Canadian consent and public health law in the context of the xenotransplantation. Canada is a country with a particularly rich body of informed consent jurisprudence--jurisprudence firmly rooted (rightly or not) in the ethical principle of autonomy. In this climate, many of the suggested monitoring strategies would find little support from Canadian law. Before xenotransplantations proceed, policy makers must be sensitive to the legal barriers which exist to the implementation [of] effective public health measures. Effective surveillance programs will require novel approaches to consent and the enactment of specific public health laws.

Tissue banking, patient rights, and confidentiality: tensions in law and policy.

The collection, storage and analysis of tissue samples, including genetic data, has become an increasingly common part of biomedical research. Though there are many scientific justifications for the creation of tissue and DNA databanks, the storage and use of human tissue continues to create legal dilemmas. In this paper, the impact and relevance of existing common law principles are reviewed. It is noted that the Canadian common law rules covering consent and confidentiality may create challenges for the research community. Emerging health information legislation does, however, create a somewhat more lenient research environment, largely because these laws allow, in some circumstances, research on identifiable health information without consent. Nevertheless, conflicts between existing common law, research ethics policy and new health information legislation illustrate profound policy dilemmas created by research involving storage and use of tissue and genetic material.

Nimbolide targets BCL2 and induces apoptosis in preclinical models of Waldenströms macroglobulinemia.

Neem leaf extract (NLE) has medicinal properties, which have been attributed to its limonoid content. We identified the NLE tetranorterpenoid, nimbolide, as being the key limonoid responsible for the cytotoxicity of NLE in various preclinical models of human B-lymphocyte cancer. Of the models tested, Waldenströms macroglobulinemia (WM) cells were most sensitive to nimbolide, undergoing significant mitochondrial mediated apoptosis. Notably, nimbolide toxicity was also observed in drug-resistant (bortezomib or ibrutinib) WM cells. To identify putative targets of nimbolide, relevant in WM, we used chemoinformatics-based approaches comprised of virtual in silico screening, molecular modeling and target-ligand reverse docking. In silico analysis revealed the antiapoptotic protein BCL2 was the preferential binding partner of nimbolide. The significance of this finding was further tested in vitro in RS4;11 (BCL2-dependent) tumor cells, in which nimbolide induced significantly more apoptosis compared with BCL2 mutated (Jurkat BCL2(Ser70-Ala)) cells. Lastly, intraperitoneal administration of nimbolide in WM tumor xenografted mice, significantly reduced tumor growth and IgM secretion in vivo, while modulating the expression of several proteins as seen on immunohistochemistry. Overall, our data demonstrate that nimbolide is highly active in WM cells, as well as other B-cell cancers, and engages BCL2 to exert its cytotoxic activity.

Science and the sources of hype.

It has been suggested that genomic research is frequently inappropriately hyped, in both the popular press and the scientific literature, and that this hype has the potential to create a range of social concerns. This paper maps the complex array of social forces that contribute to the phenomenon of hype, including the pressure to publish, the increasingly intense commercialization agenda, the messaging emanating from research institutions, the news media and, even, the public itself. These numerous and interrelated factors create a 'hype pipeline' that will be difficult to counter without the utilization of a wide range of policy strategies.