A systems biology-based mathematical model demonstrates the potential anti-stress effectiveness of a multi-nutrient botanical formulation.

Stress is an adaptive response to the stressors that adversely affects physiological and psychological health. Stress elicits HPA axis activation, resulting in cortisol release, ultimately contributing to oxidative, inflammatory, physiological and mental stress. Nutritional supplementations with antioxidant, anti-inflammatory, and stress-relieving properties are among widely preferred complementary approaches for the stress management. However, there is limited research on the potential combined impact of vitamins, minerals and natural ingredients on stress. In the present study, we have investigated the effect of a multi-nutrient botanical formulation, Nutrilite® Daily Plus, on clinical stress parameters. The stress-modulatory effects were quantified at population level using a customized sub-clinical inflammation mathematical model. The model suggested that combined intervention of botanical and micronutrients lead to significant decline in physical stress (75% decline), mental stress (70% decline), oxidative stress (55% decline) and inflammatory stress (75% decline) as evident from reduction in key stress parameters such as ROS, TNF-α, blood pressure, cortisol levels and PSS scores at both individual and population levels. Further, at the population level, the intervention relieved stress in 85% of individuals who moved towards a healthy state. The in silico studies strongly predicts the use of Gotukola based Nutrilite® Daily Plus as promising anti-stress formulation.

Efficacy of optimal nutraceutical combination in treating PCOS characteristics: an in-silico assessment.

BACKGROUND: Polycystic ovary syndrome (PCOS) is a serious health condition affecting women of reproductive age. High prevalence of PCOS and associated metabolic complications needs effective treatment and management. This study evaluated the efficacy of optimal nutraceutical combinations in improving PCOS characteristics using system biology-based mathematical modelling and simulation. METHODS: A shortlisting of eight potent nutraceuticals was carried out with literature search. Menstrual cycle model was used to perform simulations on an in-silico population of 2000 individuals to test individual and combined effects of shortlisted nutraceuticals on five PCOS characteristics [oligomenorrhea, anovulation, hirsutism, infertility, and polycystic ovarian morphology (PCOM)] for a duration of 6 months. Efficacy was tested across lean and obese phenotypes and age groups. RESULTS: Individual assessment of nutraceuticals revealed seven most potent compounds. Myo-inositol among them was observed to be the most effective in alleviating the PCOS characteristics. The in-silico population analysis showed that the combination of melatonin and ALA along with myo-inositol was efficacious in restoring the hormonal balance across age-groups and Body Mass Index (BMI) categories. CONCLUSION: Supplementation with the combination of myo-inositol, melatonin, and ALA demonstrated potential in managing PCOS symptoms in our in-silico analysis of a heterogeneous population, including lean and obese phenotypes across various severities and age groups, over a 6-month period. Future clinical studies are recommended to validate these findings.

FAIR, ethical, and coordinated data sharing for COVID-19 response: a scoping review and cross-sectional survey of COVID-19 data sharing platforms and registries.

Data sharing is central to the rapid translation of research into advances in clinical medicine and public health practice. In the context of COVID-19, there has been a rush to share data marked by an explosion of population-specific and discipline-specific resources for collecting, curating, and disseminating participant-level data. We conducted a scoping review and cross-sectional survey to identify and describe COVID-19-related platforms and registries that harmonise and share participant-level clinical, omics (eg, genomic and metabolomic data), imaging data, and metadata. We assess how these initiatives map to the best practices for the ethical and equitable management of data and the findable, accessible, interoperable, and reusable (FAIR) principles for data resources. We review gaps and redundancies in COVID-19 data-sharing efforts and provide recommendations to build on existing synergies that align with frameworks for effective and equitable data reuse. We identified 44 COVID-19-related registries and 20 platforms from the scoping review. Data-sharing resources were concentrated in high-income countries and siloed by comorbidity, body system, and data type. Resources for harmonising and sharing clinical data were less likely to implement FAIR principles than those sharing omics or imaging data. Our findings are that more data sharing does not equate to better data sharing, and the semantic and technical interoperability of platforms and registries harmonising and sharing COVID-19-related participant-level data needs to improve to facilitate the global collaboration required to address the COVID-19 crisis.

Pandemic preparedness and response: beyond the Access to COVID-19 Tools Accelerator.

Nationalism has trumped solidarity, resulting in unnecessary loss of life and inequitable access to vaccines and therapeutics. Existing intellectual property (IP) regimens, trade secrets and data rights, under which pharmaceutical firms operate, have also posed obstacles to increasing manufacturing capacity, and ensuring adequate supply, affordable pricing, and equitable access to COVID-19 vaccines and other health products in low-income and middle- income countries. We propose: (1) Implementing alternative incentive and funding mechanisms to develop new scientific innovations to address infectious diseases with pandemic potential; (2) Voluntary and involuntary initiatives to overcome IP barriers including pooling IP, sharing data and vesting licences for resulting products in a globally agreed entity; (3) Transparent and accountable collective procurement to enable equitable distribution; (4) Investments in regionally distributed research and development (R&D) capacity and manufacturing, basic health systems to expand equitable access to essential health technologies, and non-discriminatory national distribution; (5) Commitment to strengthen national (and regional) initiatives in the areas of health system development, health research, drug and vaccine manufacturing and regulatory oversight and (6) Good governance of the pandemic prevention, preparedness and response accord. It is important to articulate principles for deals that include reasonable access conditions and transparency in negotiations. We argue for an equitable, transparent, accountable new global agreement to provide rewards for R&D but only on the condition that pharmaceutical companies share the IP rights necessary to produce and distribute them globally. Moreover, if countries commit to collective procurement and fair pricing of resulting products, we argue that we can greatly improve our ability to prepare for and respond to pandemic threats.

Analytics Pipeline for Visualization of Single Cell RNA Sequencing Data from Brochoaveolar Fluid in COVID-19 Patients: Assessment of Neuro Fuzzy-C-Means and HDBSCAN.

Since the mutation in SARS-COV2 poses new challenges in designing vaccines, it is imperative to develop advanced tools for visualizing the genetic information. Specially, it remains challenging to address the patient-to-patient variability and identify the signature for severe/critical conditions. In this endeavor we analyze the large-scale RNA-sequencing data collected from broncho-alveolar fluid. In this work, we have used PCA and tSNE for the dimension-reduction. The novelty of the current work is to depict a detailed comparison of k-means, HDBSAN and neuro-fuzzy method in visualization of high-dimension data on gene expression. Clinical Relevance- The subpopulation profiling can be used to study the patient-to patient variability when infected by SARS-COV-2 and its variants. The distribution of cell types can be relevant in designing new drugs that are targeted to control the distribution of epithelial cells T cells and macrophages.

Considerations of sex and gender dimensions by research ethics committees: a scoping review.

Despite a growing consensus on the importance of integrating sex and gender in health research, research across disciplines continues to be conducted and reported without a gender focus. Research ethics committees (RECs) can play a particularly powerful role in identifying the gender gaps at an early stage of the development of research protocols. Their role is missing in the dialogue related to improving gender awareness and analysis in health research. A scoping review was conducted to examine the extent to which RECs discuss and consider the inclusion and analysis of sex and gender in health research and to examine the literature regarding the gender balance of RECs. The limited literature around gender and research ethics reveals the power and potential of RECs to ensure that gender dimensions are thoughtfully included in health research, and sheds light on the gaps that exist. These include an under-representation of women on RECs, a lack of awareness of the importance of gender-related aspects in health research and a paucity of gender-related training to RECs. Guidelines such as the Sex and Gender Equity in Research guidelines are required for RECs to strengthen the ways in which health research is gendered from conception of a research protocol to its publication.

Mathematical modeling of viral infection dynamics and immune response in SARS-CoV-2: A computational framework for testing drug efficacy.

SARS-CoV-2 has emerged to cause the outbreak of COVID-19, which has expanded into a worldwide human pandemic. Although detailed experimental data on animal experiments would provide insight into drug efficacy, the scientists involved in these experiments would be exposed to severe risks. In this context, we propose a computational framework for studying infection dynamics that can be used to capture the growth rate of viral replication and lung epithelial cell in presence of SARS-CoV-2. Specifically, we formulate the model consisting of a system of non-linear ODEs that can be used for visualizing the infection dynamics in a cell population considering the role of T cells and Macrophages. The major contribution of the proposed simulation method is to utilize the infection progression model in testing the efficacy of the drugs having various mechanisms and analyzing the effect of time of drug administration on virus clearance.Clinical Relevance-The proposed computational framework incorporates viral infection dynamics and role of immune response in Covid-19 that can be used to test the impact of drug efficacy and time of drug administration on infection mitigation.

Guidance for ensuring fair and ethical broad consent for future use. A scoping review protocol.

Introduction: Broad consent for future use is the reuse of data and/or samples collected by a study by researchers who may not be affiliated with the original study team for purposes that may differ from the objectives of the original study. Sharing participant-level data and samples collected from research participants facilitates reuse and transparency and can accelerate drug or vaccine development, research findings, and translation. Data reuse and synthesis help prevent unnecessary research, thereby respecting research participants time and efforts and building their trust in the research process. Despite these myriad benefits, data and sample sharing represent a significant investment of time for the team that collected the data or samples, and may present additional risks for research participants, including that of re-identifiability and incidental findings, or for the source community. This scoping review will summarize existing guidance on broad consent for future use and highlight evidence gaps related to the ethical, equitable implementation of broad consent for future use. Methods and analysis: We will apply the Arskey and O'Malley scoping review methodology and best practice as outlined in the Joanna Briggs scoping review guidelines.  The research questions have been identified through a literature review and consultation with subject-matter experts. The systematic search will be conducted in three databases using a tailored search strategy. We will search the reference lists of included articles or related systematic reviews for additional citations. The title-abstract and full text screening and charting the data will be conducted independently by two reviewers. Discrepancies will be resolved by a third reviewer. Results will be summarized in narrative form. Ethics and dissemination: This scoping review summarizes findings from existing publications and grey literature rather than primary data and, as such, does not require ethics review. Findings will be disseminated through an open access publication and webinar.

Proceedings of an expert workshop on community agreement for gene drive research in Africa - Co-organised by KEMRI, PAMCA and Target Malaria.

Gene drive research is progressing towards future field evaluation of modified mosquitoes for malaria control in sub-Saharan Africa. While many literature sources and guidance point to the inadequacy of individual informed consent for any genetically modified mosquito release, including gene drive ones, (outside of epidemiological studies that might require blood samples) and at the need for a community-level decision, researchers often find themselves with no specific guidance on how that decision should be made, expressed and by whom. Target Malaria, the Kenya Medical Research Institute and the Pan African Mosquito Control Association co-organised a workshop with researchers and practitioners on this topic to question the model proposed by Target Malaria in its research so far that involved the release of genetically modified sterile male mosquitoes and how this could be adapted to future studies involving gene drive mosquito releases for them to offer reflections about potential best practices. This paper shares the outcomes of that workshop and highlights the remaining topics for discussion before a comprehensive model can be designed.

WHO guidance on ethics in outbreaks and the COVID-19 pandemic: a critical appraisal.

In 2016, following pandemic influenza threats and the 2014-2016 Ebola virus disease outbreaks, the WHO developed a guidance document for managing ethical issues in infectious disease outbreaks. In this article, we analyse some ethical issues that have had a predominant role in decision making in response to the current COVID-19 pandemic but were absent or not addressed in the same ways in the 2016 guidance document. A pandemic results in a health crisis and social and political crises both nationally and globally. The ethical implications of these global effects should be properly identified so that appropriate actions can be taken globally and not just in national isolation. Our analysis, which is a starting point to test the broader relevance of the 2016 WHO document that remains the only available guidance document applicable globally, concludes that the WHO guidance should be updated to provide reasoned and thoughtful comprehensive ethics advice for the sound management of the current and future pandemics.

A survey of national ethics and bioethics committees.

OBJECTIVE: To assess the current state of national ethics committees and the challenges they face. METHODS: We surveyed national ethics committees between 30 January and 21 February 2018. FINDINGS: In total, representatives of 87 of 146 national ethics committees (59.6%) participated. The 84 countries covered were in all World Bank income categories and all World Health Organization regions. Many national ethics committees lack resources and face challenges in several domains, like independence, funding or efficacy. Only 40.2% (35/87) of committees expressed no concerns about independence. Almost a quarter (21/87) of committees did not make any ethics recommendations to their governments in 2017, and the median number of reports, opinions or recommendations issued was only two per committee Seventy-two (82.7%) national ethics committees included a philosopher or a bioethicist. CONCLUSION: National ethics (or bioethics) committees provide recommendations and guidance to governments and the public, thereby ensuring that public policies are informed by ethical concerns. Although the task is seemingly straightforward, implementation reveals numerous difficulties. Particularly in times of great uncertainty, such as during the current coronavirus disease 2019 pandemic, governments would be well advised to base their actions not only on technical considerations but also on the ethical guidance provided by a national ethics committee. We found that, if the advice of national ethics committees is to matter, they must be legally mandated, independent, diverse in membership, transparent and sufficiently funded to be effective and visible.

A detailed model and Monte Carlo simulation for predicting DIP genome length distribution in baculovirus infection of insect cells.

Baculoviruses have enormous potential for use as biopesticides to control insect pest populations without the adverse environmental effects posed by the widespread use of chemical pesticides. However, continuous baculovirus production is susceptible to DNA mutation and the subsequent production of defective interfering particles (DIPs). The amount of DIPs produced and their genome length distribution are of great interest not only for baculoviruses but for many other DNA and RNA viruses. In this study, we elucidate this aspect of virus replication using baculovirus as an example system and both experimental and modeling studies. The existing mathematical models for the virus replication process consider DIPs as a lumped quantity and do not consider the genome length distribution of the DIPs. In this study, a detailed population balance model for the cell-virus culture is presented, which predicts the genome length distribution of the DIP population along with their relative proportion. The model is simulated using the kinetic Monte Carlo algorithm, and the results agree well with the experimental results. Using this model, a practical strategy to maintain the DIP fraction to near to its maximum and minimum limits has been demonstrated.

Programmatic norms change to eliminate violence against children: Insights for practitioners and researchers from a UNICEF global mapping study.

Interest in gender norms is rising within the field of global health and among its funders. With more resources available for norms change work, international institutions seek to develop thoughtful strategic and programmatic responses to a variety of issues, including violence against children. Yet changing deeply rooted gender norms requires sensitivity to local context. This can present a challenge for mid- to large sized organisations, as well as funders, who are typically required to develop strategies that encompass multiple contexts. This paper presents practical lessons learned from a mapping study of UNICEF's existing work to change discriminatory gender norms. As the world's leading children's rights organisation, preventing violence against children (0-9) and adolescents (ages 10-19) is a key component of UNICEF's work. This mapping formed the foundation of the institution's efforts to build out a coordinated strategy and programme of work around 'positive gender socialisation.' The mapping was unique in that it accounted for differences across and within regions and sought to develop an institutional programme of work based on local experience and existing priorities. The lessons learned are relevant to other organisations and practice-oriented research programmes embarking on work to change norms that lead to violence against children.

Informed consent for controlled human infection studies in low- and middle-income countries: Ethical challenges and proposed solutions.

In controlled human infection studies (CHIs), participants are deliberately exposed to infectious agents in order to better understand the mechanism of infection or disease and test therapies or vaccines. While most CHIs have been conducted in high-income countries, CHIs have recently been expanding into low- and middle-income countries (LMICs). One potential ethical concern about this expansion is the challenge of obtaining the voluntary informed consent of participants, especially those who may not be literate or have limited education. In some CHIs in LMICs, researchers have attempted to address this potential concern by limiting access to literate or educated populations. In this paper, we argue that this practice is unjustified, as it does not increase the chances of obtaining valid informed consent and therefore unfairly excludes illiterate populations and populations with lower education. Instead, we recommend that investigators improve the informed consent process by drawing on existing data on obtaining informed consent in these populations and interventions aimed at improving their understanding. Based on a literature review, we provide concrete suggestions for how to follow this recommendation and ensure that populations with lower literacy or education are given a fair opportunity to protect their rights and interests in the informed consent process.

Statistical modeling of cell-to-cell variability in viral infection during passaging in suspension cell culture: Application in Monte-Carlo simulation.

Packaging during the passaging of viruses in cell cultures yields various phenotypes and is regulated by viral protein expression in infected cells. Although such a packaging mechanism has a profound effect in controlling the virus yield, little is known about the underlying statistical models followed by virus packaging and protein expression among cells infected with the virus. A predictive framework combining identification of the probability density function (PDF) based on log-likelihood and using the PDF for Monte-Carlo simulations is developed. The Birnbaum-Saunders distribution was found to be consistent with all three-virus packaging levels, including nucleocapsids/occlusion-derived virus (ODV), ODVs/polyhedra, and polyhedra/cell for both wild-type and genetically modified AcMNPV. Next, it was demonstrated that PDF fitting could be used to compare two viruses having distinctly different genetic configurations. Finally, the identified PDF can be incorporated in RNA synthesis parameters for baculovirus infection to predict the cell-to-cell variability in protein expression using Monte-Carlo simulations. The proposed tool can be used for the estimation of uncertainty in the kinetic parameter and prediction of cell-to-cell variability for other biological systems.

Beyond Research Ethics: Novel Approaches of 3 Major Public Health Institutions to Provide Ethics Input on Public Health Practice Activities.

Public health institutions increasingly realize the importance of creating a culture in their organizations that values ethics. When developing strategies to strengthen ethics, institutions will have to take into account that while public health research projects typically undergo thorough ethics review, activities considered public health practice may not be subjected to similar oversight. This approach, based on a research-practice dichotomy, is increasingly being criticized as it does not adequately identify and manage ethically relevant risks to those affected by nonresearch activities. As a reaction, 3 major public health institutions (the World Health Organization, US Centers for Disease Control and Prevention, and Public Health Ontario) have implemented mechanisms for ethics review of public health practice activities. In this article, we describe and critically discuss the different modalities of the 3 approaches. We argue that although further evaluation is necessary to determine the effectiveness of the different approaches, public health institutions should strive to implement procedures to ensure that public health practice adheres to the highest ethical standards.

Informed consent for controlled human infection studies in low‐ and middle‐income countries: ethical challenges and proposed solutions

In controlled human infection studies (CHIs), participants are deliberately exposed to infectious agents in order to better understand the mechanism of infection or disease and test therapies or vaccines. While most CHIs have been conducted in high‐income countries, CHIs have recently been expanding into low‐ and middle‐income countries (LMICs). One potential ethical concern about this expansion is the challenge of obtaining the voluntary informed consent of participants, especially those who may not be literate or have limited education. In some CHIs in LMICs, researchers have attempted to address this potential concern by limiting access to literate or educated populations. In this paper, we argue that this practice is unjustified, as it does not increase the chances of obtaining valid informed consent and therefore unfairly excludes illiterate populations and populations with lower education. Instead, we recommend that investigators improve the informed consent process by drawing on existing data on obtaining informed consent in these populations and interventions aimed at improving their understanding. Based on a literature review, we provide concrete suggestions for how to follow this recommendation and ensure that populations with lower literacy or education are given a fair opportunity to protect their rights and interests in the informed consent process.

Ethics preparedness: facilitating ethics review during outbreaks - recommendations from an expert panel.

BACKGROUND: Ensuring that countries have adequate research capacities is essential for an effective and efficient response to infectious disease outbreaks. The need for ethical principles and values embodied in international research ethics guidelines to be upheld during public health emergencies is widely recognized. Public health officials, researchers and other concerned stakeholders also have to carefully balance time and resources allocated to immediate treatment and control activities, with an approach that integrates research as part of the outbreak response. Under such circumstances, research "ethics preparedness" constitutes an important foundation for an effective response to infectious disease outbreaks and other health emergencies. MAIN TEXT: A two-day workshop was convened in March 2018 by the World Health Organisation Global Health Ethics Team and the African coaLition for Epidemic Research, Response and Training, with representatives of National Ethics Committees, to identify practical processes and procedures related to ethics review preparedness. The workshop considered five areas where work might be undertaken to facilitate rapid and sound ethics review: preparing national ethics committees for outbreak response; pre-review of protocols; multi-country review; coordination between national ethics committees and other key stakeholders; data and benefit sharing; and export of samples to third countries. In this paper, we present the recommendations that resulted from the workshop. In particular, the participants recommended that Ethics Committees would develop a formal national standard operating procedure for emergency response ethical review; that there is a need to clarify the terminology and expectations of pre-review of generic protocols and agree upon specific terminology; that there is a need to explore mechanisms for multi-country emergency ethical consultation, and to establish procedures for communication between national ethics committees and other oversight bodies and public health authorities. In addition, it was suggested that ethics committees should request from researchers, at a minimum, a preliminary data sharing and sample sharing plan that outlines the benefit to the population from which data and samples are to be drawn. This should be followed in due time by a full plan. CONCLUSION: It is hoped that the national ethics committees, supported by the WHO, relevant collaborative research consortia and external funding agencies, will work towards bringing these recommendations into practice, for supporting the conduct of effective research during outbreaks.