Glass box machine learning for retrospective cohort studies using many patient records. The complex example of bleeding peptic ulcer

Glass Box Machine Learning is, in this study, a type of partially supervised data mining and prediction technique, like a neural network in which each weight or pattern of mutually relevant weights is now replaced by a meaningful "probabilistic knowledge element." We apply it to retrospective cohort studies using large numbers of structured medical records to help select candidate patients for future cohort studies and similar clinical trials. Here it is applied to aid analysis of approaches to aid Deep Learning, but the method lends itself well to direct computation of odds with "explainability" in study design that can complement "Black Box" Deep Learning. Cohort studies and clinical trials traditionally involved at least one 2 × 2 contingency table, but in the age of emerging personalized medicine and the use of machine learning to discover and incorporate further relevant factors, these tables can extend into many extra dimensions as a 2 × 2 x 2 × 2 x ….data structure by considering different conditional demographic and clinical factors of a patient or group, as well as variations in treatment. We consider this in terms of multiple 2 × 2 x 2 data substructures where each one is summarized by an appropriate measure of risk and success called DOR*. This is the diagnostic odds ratio DOR for a specified disease conditional on a favorable outcome divided by the corresponding DOR conditional on an unfavorable outcome. Bleeding peptic ulcer was chosen as a complex disease with many influencing factors, one that is still subject to controversy and that highlights the challenges of using Real World Data.

Examining the impact of COVID-19 on Māori:non-Māori health inequities in Aotearoa, New Zealand: an observational study protocol

INTRODUCTION

The COVID-19 pandemic has had both direct and indirect impacts on the health of populations worldwide. While racial/ethnic health inequities in COVID-19 infection are now well known (and ongoing), knowledge about the impact of COVID-19 pandemic management on non-COVID-19-related outcomes for Indigenous peoples is less well understood. This article presents the study protocol for the Health Research Council of New Zealand funded project 'Mā te Mōhio ka Mārama: Impact of COVID-19 on Māori:non-Māori inequities'. The study aims to explore changes in access to healthcare, quality of healthcare and health outcomes for Māori, the Indigenous peoples of Aotearoa New Zealand (NZ) and non-Māori during the COVID-19 outbreak period across NZ.

METHODS AND ANALYSIS

This observational study is framed within a Kaupapa Māori research positioning that includes Kaupapa Māori epidemiology. National datasets will be used to report on access to healthcare, quality of healthcare and health outcomes between Māori and non-Māori during the COVID-19 pandemic in NZ. Study periods are defined as (a) prepandemic period (2015-2019), (b) first pandemic year without COVID-19 vaccines (2020) and (c) pandemic period with COVID-19 vaccines (2021 onwards). Regional and national differences between Māori and non-Māori will be explored in two phases focused on identified health priority areas for NZ including (1) mortality, cancer, long-term conditions, first 1000 days, mental health and (2) rheumatic fever.

ETHICS AND DISSEMINATION

This study has ethical approval from the Auckland Health Research Ethics Committee (AHREC AH26253). An advisory group will work with the project team to disseminate the findings of this project via project-specific meetings, peer-reviewed publications and a project-specific website. The overall intention of the project is to highlight areas requiring health policy and practice interventions to address Indigenous inequities in health resulting from COVID-19 pandemic management (both historical and in the future).

Support for and potential impacts of key Smokefree 2025 strategies among Māori who smoke

AIM

The recently passed Smokefree Environments and Regulated Products (Smoked Tobacco) Amendment Act has the potential to profoundly reduce smoking prevalence and related health inequities experienced among Māori. This study examined support for, and potential impacts of, key measures included within the legislation.

METHOD

Data came from Wave 1 (2017-2019) of the Te Ara Auahi Kore longitudinal study, which was conducted in partnership with five primary health organisations serving Māori communities. Participants were 701 Māori who smoked. Analysis included both descriptive analysis and logistic regression.

RESULTS

More Māori participants supported than did not support the Smokefree 2025 (SF2025) goal of reducing smoking prevalence to below 5%, and the key associated measures. Support was greatest for mandating very low nicotine cigarettes (VLNCs). Participants also believed VLNCs would prompt high rates of quitting. Participants who had made more quit attempts or reported less control over their life were more likely to support VLNCs.

CONCLUSION

There was support for the SF2025 goal and for key measures that could achieve it. In particular, VLNCs may have significant potential to reduce smoking prevalence among Māori. As part of developing and implementing these measures it will be important to engage with Māori who smoke and their communities.

Equity of Cancer and Diabetes Co-Occurrence: A National Study With 44 Million Person-Years of Follow-Up

PURPOSE

The co-occurrence of diabetes and cancer is becoming increasingly common, and this is likely to compound existing inequities in outcomes from both conditions within populations.

METHODS

In this study, we investigate the co-occurrence of cancer and diabetes by ethnic groups in New Zealand. National-level diabetes and cancer data on nearly five million individuals over 44 million person-years were used to describe the rate of cancer in a national prevalent cohort of peoples with diabetes versus those without diabetes, by ethnic group (Māori, Pacific, South Asian, Other Asian, and European peoples).

RESULTS

The rate of cancer was greater for those with diabetes regardless of ethnic group (age-adjusted rate ratios, Māori, 1.37; 95% CI, 1.33 to 1.42; Pacific, 1.35; 95% CI, 1.28 to 1.43; South Asian, 1.23; 95% CI, 1.12 to 1.36; Other Asian, 1.31; 95% CI, 1.21 to 1.43; European, 1.29; 95% CI, 1.27 to 1.31). Māori had the highest rate of diabetes and cancer co-occurrence. Rates of GI, endocrine, and obesity-related cancers comprised a bulk of the excess cancers occurring among Māori and Pacific peoples with diabetes.

CONCLUSION

Our observations reinforce the need for the primordial prevention of risk factors that are shared between diabetes and cancer. Also, the commonality of diabetes and cancer co-occurrence, particularly for Māori, reinforces the need for a multidisciplinary, joined-up approach to the detection and care of both conditions. Given the disproportionate burden of diabetes and those cancers that share risk factors with diabetes, action in these areas is likely to reduce ethnic inequities in outcomes from both conditions.

We still don't count: the under-counting and under-representation of Māori in health and disability sector data

AIM

To examine ethnicity data quality; in particular, the representation and potential under-counting of Māori in health and disability sector data, as well as implications for inequities.

METHODS

Māori and non-Māori ethnicity data are analysed at: 1) a population aggregate level across multiple 2018 datasets (Estimated Resident Population, Census Usually Resident Population, Health Service User (HSU) population and Primary Health Organisation (PHO) enrolments); and 2) an individual level for those linked in PHO and 2018 Census datasets. Ethnicity is drawn from the National Health Index (NHI) in health datasets and variations by age and gender are explored.

RESULTS

Aggregate analyses show that Māori are considerably under-represented in HSU and PHO data. In linked analysis Māori were under-counted on the NHI by 16%. Under-representation in data and under-counting occur across both genders but are more pronounced for Māori men with variations by age.

CONCLUSION

High quality ethnicity data are fundamental for understanding and monitoring Māori health and health inequities as well as in the provision of targeted services and interventions that are responsive to Māori aspirations and needs. The continued under-counting of Māori in health and disability sector data is a breach of Te Tiriti o Waitangi and must be addressed with urgency.

Analysis of deprivation distribution in New Zealand by ethnicity, 1991-2013

AIMS

To compare the distribution of Māori and New Zealand (NZ) European populations in Aotearoa New Zealand by neighbourhood deprivation, for the five censuses between 1991 and 2013, and to identify changes in the distribution pattern over time.

METHODS

Geographical meshblock data from the 1991-2013 New Zealand censuses, by NZDep Index deprivation score, and by prioritised ethnic group population, were combined to analyse ethnic population counts by deprivation decile and deprivation score. Trends over time were analysed.

RESULTS

Māori were over-represented in the more deprived NZDep deciles and under-represented in the least deprived deciles for all census periods. The NZ European population were over-represented in the least deprived deciles, and under-represented in the more deprived deciles. In each census, over 40% of the Māori population have been living in the two most deprived deciles, compared to less than 15% for NZ European.

CONCLUSION

The patterns of inequity in socio-economic deprivation between Māori and NZ Europeans have remained virtually unchanged since 1991, despite various Government commitments to reduce inequity. Socio-economic deprivation for Māori is a key determinant of health inequity, and bolder Government measures prioritised for Māori are needed to change this socio-economic gradient if health equity goals are to be met.

A kia ora, a wave and a smile: an urban marae-led response to COVID-19, a case study in manaakitanga

BACKGROUND

When COVID-19 emerged, there were well-founded fears that Māori (indigenous peoples of Aotearoa (New Zealand)) would be disproportionately affected, both in terms of morbidity and mortality from COVID-19 itself and through the impact of lock-down measures. A key way in which Kōkiri (a Māori health provider) responded was through the establishment of a pātaka kai (foodbank) that also provided a gateway to assess need and deliver other support services to whānau (in this case, client). Māori values were integral to this approach, with manaakitanga (kindness or providing care for others) at the heart of Kōkiri's actions. We sought to identify how Kōkiri operated under the mantle of manaakitanga, during Aotearoa's 2020 nationwide COVID-19 lockdown and to assess the impact of their contributions on Māori whānau.

METHODS

We used qualitative methods underpinned by Māori research methodology. Twenty-six whānau interviews and two focus groups were held, one with eight kaimahi (workers) and the other with seven rangatahi (youth) kaimahi. Data was gathered between June and October 2020 (soon after the 2020 lockdown restrictions were lifted), thematically analysed and interpreted using a Māori worldview.

RESULTS

Three key themes were identified that aligned to the values framework that forms the practice model that Kōkiri kaimahi work within. Kaitiakitanga, whānau and manaakitanga are also long-standing Māori world values. We identified that kaitiakitanga (protecting) and manaakitanga (with kindness) - with whānau at the centre of all decisions and service delivery - worked as a protective mechanism to provide much needed support within the community Kōkiri serves.

CONCLUSIONS

Māori health providers are well placed to respond effectively in a public-health crisis when resourced appropriately and trusted to deliver. We propose a number of recommendations based on the insights generated from the researchers, kaimahi, and whānau. These are that: Māori be included in pandemic planning and decision-making, Māori-led initiatives and organisations be valued and adequately resourced, and strong communities with strong networks be built during non-crisis times.

Regional variation in post-operative mortality in New Zealand

Background

There is a growing body of evidence that access to best practice perioperative care varies within our population. In this study, we use national‐level data to begin to address gaps in our understanding of regional variation in post‐operative outcomes within New Zealand.

Methods

Using National Collections data, we examined all inpatient procedures in New Zealand public hospitals between 2005 and 2017 (859 171 acute, 2 276 986 elective/waiting list), and identified deaths within 30 days. We calculated crude and adjusted rates per 100 procedures for the 20 district health boards (DHBs), both for the total population and stratified by ethnicity (Māori/European). Odds ratios comparing the risk of post‐operative mortality between Māori and European patients were calculated using crude and adjusted Poisson regression models.

Results

We observed regional variations in post‐operative mortality outcomes. Māori, compared to European, patients experienced higher post‐operative mortality rates in several DHBs, with a trend to higher mortality in almost all DHBs. Regional variation in patterns of age, procedure, deprivation and comorbidity (in particular) largely drives regional variation in post‐operative mortality, although variation persists in some regions even after adjusting for these factors. Inequitable outcomes for Māori also persist in several regions despite adjustment for multiple factors, particularly in the elective setting.

Conclusions

The persistence of variation and ethnic disparities in spite of adjustment for confounding and mediating factors suggests that multiple regions require additional resource and support to improve outcomes. Efforts to reduce variation and improve outcomes for patients will require both central planning and monitoring, as well as region‐specific intervention.

Towards faster response against emerging epidemics and prediction of variants of concern

The author, the journal, Computers in Biology and Medicine (CBM), and Elsevier Press more generally, played a helpful very early role in responding to COVID-19. Within a few days of the appearance of the "Wuhan Seafood isolate" genome on GenBank, a bioinformatics study was posted by the present author in ResearchGate in January 2020, "Preliminary Bioinformatics Studies on the Design of Synthetic Vaccines and Preventative Peptidomimetic Antagonists against the Wuhan Seafood Market Coronavirus. Possible Importance of the KRSFIEDLLFNKV Motif" DOI: 10.13140/RG.2.2.18275.09761. On February 2nd^, 2020, a more thorough analysis was submitted to CBM, e-published on February 26, and formally published in April 2020, at about the same time as the virus named as 2019n-CoV was identified as essentially SARS and renames SARS-COV-2. This was followed by four further papers describing in more detail some previously unreported aspects of the early investigation. The speed of research and writing of the papers was made possible by knowledge-gathering tools. Based on this and earlier experiences with fast responses to emerging epidemics such as HIV and Mad Cow Disease, it is possible to envisage the nature of a speedier response to emerging epidemics and new variants of concern in established epidemics.

How is family health history discussed in routine primary healthcare? A qualitative study of archived family doctor consultations

OBJECTIVES

Family health history underpins genetic medicine. Our study aimed to explore language and patterns of communication relating to family health history observed in interactions between general practitioners (GPs) and their patients within routine primary care consultations.

DESIGN

Secondary analysis of patient and GP routine consultation data (n=252).

PARTICIPANTS

Consultations that included 'family health history' were eligible for inclusion (n=58).

PRIMARY OUTCOMES

A qualitative inductive analysis of the interactions from consultation transcripts.

RESULTS

46/58 conversations about family health history were initiated by the GP. Most discussions around family history lasted for between approximately 1 to 2 min. Patients were invited to share family health history through one of two ways: non-specific enquiry (eg, by asking the patient about 'anything that runs in the family'); or specific enquiry where they were asked if they had a 'strong family history' in relation to a particular condition, for example, breast cancer. Patients often responded to either approach with a simple no, but fuller negative responses also occurred regularly and typically included an account of some kind (eg, explaining family relationships/dynamics which impeded or prevented the accessibility of information).

CONCLUSIONS

Family health history is regarded as a genetic test and is embedded in the sociocultural norms of the patient from whom information is being sought. Our findings highlight that it is more complex than asking simply if 'anything' runs in the family. As the collection of family health history is expected to be more routine, it will be important to also consider it from sociocultural perspectives in order to help mitigate any inequities in how family history is collected, and therefore used (or not) in a person's healthcare. Orientating an enquiry away from 'anything' and asking more specific details about particular conditions may help facilitate the dialogue.

Disparities in post-operative mortality between Māori and non-Indigenous ethnic groups in New Zealand

AIM

To describe disparities in post-operative mortality experienced by Indigenous Māori compared to non-Indigenous New Zealanders.

METHODS

We completed a national study of all those undergoing a surgical procedure between 2005 and 2017 in New Zealand. We examined 30-day and 90-day post-operative mortality for all surgical specialties and by common procedures. We compared age-standardised rates between ethnic groups (Māori, Pacific, Asian, European, MELAA/Other) and calculated hazard ratios (HRs) using Cox proportional hazards regression modelling adjusted for age, sex, deprivation, rurality, comorbidity, ASA score, anaesthetic type, procedure risk and procedure specialty.

RESULTS

From nearly 3.9 million surgical procedures (876,976 acute, 2,990,726 elective/waiting list), we observed ethnic disparities in post-operative mortality across procedures, with the largest disparities occurring between Māori and Europeans. Māori had higher rates of 30- and 90-day post-operative mortality across most broad procedure categories, with the disparity between Māori and Europeans strongest for elective/waiting list procedures (eg, elective/waiting list musculoskeletal procedures, 30-day mortality: adj. HR 1.93, 95% CI 1.56-2.39).

CONCLUSIONS

The disparities we observed are likely driven by a combination of healthcare system, process and clinical team factors, and we have presented the key mechanisms within these factors.

He Tamariki Kokoti Tau: Tackling preterm incidence and outcomes of preterm births by ethnicity in Aotearoa New Zealand 2010-2014

OBJECTIVE

To explore preterm birth among Māori indigenous peoples through Kaupapa Māori research of preterm birth in Aotearoa New Zealand.

METHODS

Linked maternity, mortality, and hospital data were analyzed for women and their infants born between January 1, 2010 and December 31, 2014. Relative risks (RR) were calculated for each ethnic group for preterm birth, small for gestational age (SGA), and mortality.

RESULTS

Adjusted rates showed that compared with Māori women, European women were at significantly less risk of having extremely and very preterm infants (RR 0.86, 95% confidence interval [CI] 0.76-0.95). Preterm infants of European women had a significantly lower adjusted RR of early neonatal death (RR 0.65, 95% CI 0.45-0.93) or post-neonatal death (RR 0.41, 95% CI 0.26-0.64). In addition to ethnicity, preterm rates were influenced by maternal age, body mass index, smoking status, and SGA status.

CONCLUSION

This study demonstrates that the Aotearoa New Zealand maternity system privileges whiteness, suggesting that clinical pathways for evidence-based medical care are not delivered systemically and equitably for all. Health pathways that focus on equity as a fundamental right will enhance health outcomes for Māori women and their infants.

When personal experience overlaps with study

BACKGROUND

Health professional education programmes increasingly seek to train a generation of clinicians who reflect the population they serve. However, teaching approaches in health professional education have not always kept pace with this drive, and some educators tend to assume a lack of overlap between students' life experience and aspects of the curriculum.

METHOD

In-depth interviews were conducted with 22 health professional students and graduates, who self-identified as having experienced a significant overlap between their personal life and their course of study. These interviews were analysed thematically to explore the role of teaching practices that created either alienating or inclusive learning environments.

RESULTS

Participants identified areas where clinical teachers could modify their teaching approach and assumptions about the student cohort to be more inclusive of students whose life experience overlapped with the curriculum. They wanted educators to treat any teaching topic as if it could be personal for some students, which may include teaching inequities carefully, acknowledging family members' perspectives, moderating discussions, and avoiding stereotyping patients. Participants also wanted educators to practice shared decision-making about alternative arrangements or time off.

DISCUSSION

Clinical educators have a key role in shaping an inclusive health sciences programme. Their assumptions, attitudes and teaching strategies can either strengthen or undermine the development of a diverse health workforce.

Bowel cancer screening age range for Māori: what is all the fuss about?

The current New Zealand Bowel Screening Programme (BSP) is inequitable. At present, just over half of bowel cancers in Māori present before the age of 60 years (58% in females and 52% in males), whereas just under a third of bowel cancers in non-Māori are diagnosed before the same age (27% in females and 29% in males). The argument for extending the bowel screening age range down to 50 years for Māori is extremely simple-in comparison to non-Māori, a greater percentage of bowel cancers in Māori occur before the age of 60 years (when screening starts). Commencing the BSP at 50 years of age for Māori with high coverage will help fix this inequity. In this paper we review the current epidemiology of colorectal cancer with respect to the age range extension for Māori.

Techniques assisting peptide vaccine and peptidomimetic design. Sidechain exposure in the SARS-CoV-2 spike glycoprotein

The aim of the present study is to discuss the design of peptide vaccines and peptidomimetics against SARS-COV-2, to develop and apply a method of protein structure analysis that is particularly appropriate to applying and discussing such design, and also to use that method to summarize some important features of the SARS-COV-2 spike protein sequence. A tool for assessing sidechain exposure in the SARS-CoV-2 spike glycoprotein is described. It extends to assessing accessibility of sidechains by considering several different three-dimensional structure determinations of SARS-CoV-2 and SARS-CoV-1 spike protein. The method is designed to be insensitive to a distance limit for counting neighboring atoms and the results are in good agreement with the physical chemical properties and exposure trends of the 20 naturally occurring sidechains. The spike protein sequence is analyzed with comment regarding exposable character. It includes studies of complexes with antibody elements and ACE2. These indicate changes in exposure at sites remote to those at which the antibody binds. They are of interest concerning design of synthetic peptide vaccines, and for peptidomimetics as a basis of drug discovery. The method was also developed in order to provide linear (one-dimensional) information that can be used along with other bioinformatics data of this kind in data mining and machine learning, potentially as genomic data regarding protein polymorphisms to be combined with more traditional clinical data.

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Bioinformatics studies are carried out on SARS-CoV-2 spike, studying solvent exposure.

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The methods are particularly suited for synthetic vaccines and d-amino acid peptidomimetics.

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Methods of generating d-amino acid peptidomimetics are described and reviewed.

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The effect of antibody binding in stabilizing loop conformation and exposing remote sites is noted.

The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target

Knowledge management tools that assist in systematic review and exploration of scientific knowledge generally are of obvious potential importance in evidence based medicine in general, but also to the design of therapeutics based on the protein subsequences and fold motifs of virus proteins as considered here. Rapid access to bundles (clusters) of related elements of knowledge gathered from diverse sources on the Internet and from growing knowledge repositories seem particularly helpful when exploring less obvious therapeutic targets in viruses (for which knowledge new to the researcher is important), and when using the following concept. Subsequences of amino acid residue sequences of proteins that are conserved across strains and species are (a) more likely to be important targets and (b) less likely to exhibit escape mutations that would make them resistant to vaccines and therapeutic agents. However, the terms "conserved" and even "highly conserved" used by authors are matters of degree, depending on how distant from SARS-CoV-2 they wished to go in comparing other sequences. The binding site to the human ACE2 protein as virus receptor and human antibody CR3022 binding site on the spike glycoprotein are rather variable by the criteria used in the present and preceding studies. To look for more strongly conserved targets, open reading frames of SARS-CoV-2 were examined for extremely highly conserved regions, meaning recognizable across many viruses and organisms. Most prominent is a motif found in SARS-CoV-2 non-structural protein 3 (Nsp3). It relates to a fold called type called the macro domain and has remarkably wide distribution across organisms including humans with significant homologies involving three especially conserved subsequences (a) VVVNAANVYLKHGGGVAGALNK, (b) LHVVGPNVNKG, and (c) PLLSAGIFG. Careful study of the variations of these and of the more variable sequences between and around them might provide a finer "scalpel" to ensure inhibition of a vital function of the virus without impairing the functions of related host macro domains.

The most commonly diagnosed and most common causes of cancer death for Māori New Zealanders

Cancer is an important cause of morbidity and avoidable mortality for Māori-and substantial disparities exist in cancer incidence, mortality and survival for Māori compared to non-Māori New Zealanders. In this viewpoint, we draw together cancer incidence, mortality and survival data from the previous decade, in order to provide clarity regarding the most important causes of cancer burden for Māori. Covering the decade 2007-2016, our manuscript directly leads on from the landmark Unequal Impact II report (which covered 1996-2006), and provides the most up-to-date record of this burden as is currently possible. While focusing on the absolute burden of cancer for Māori, we also compare this burden to that experienced by non-Māori, and consider how this relative disparity may (or may not) have changed over time. Finally, we discuss how to reduce the occurrence and the overall cancer mortality burden for Māori, with a focus on those cancers that confer the greatest burden.

Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans

SARS-CoV and SARS-CoV-2 do not appear to have functions of a hemagglutinin and neuraminidase. This is a mystery, because sugar binding activities appear essential to many other viruses including influenza and even most other coronaviruses in order to bind to and escape from the glycans (sugars, oligosaccharides or polysaccharides) characteristic of cell surfaces and saliva and mucin. The S1 N terminal Domains (S1-NTD) of the spike protein, largely responsible for the bulk of the characteristic knobs at the end of the spikes of SARS-CoV and SARS-CoV-2, are here predicted to be “hiding” sites for recognizing and binding glycans containing sialic acid. This may be important for infection and the ability of the virus to locate ACE2 as its known main host cell surface receptor, and if so it becomes a pharmaceutical target. It might even open up the possibility of an alternative receptor to ACE2. The prediction method developed, which uses amino acid residue sequence alone to predict domains or proteins that bind to sialic acids, is naïve, and will be advanced in future work. Nonetheless, it was surprising that such a very simple approach was so useful, and it can easily be reproduced in a very few lines of computer program to help make quick comparisons between SARS-CoV-2 sequences and to consider the effects of viral mutations.

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This paper extends the studies of the author's previous SARS-CoV-2 papers.

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Designing vaccine and drugs must seek to avoid escape mutations.

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Strangely, SARS-CoV and SARS-CoV-2 appear to lack sialic acid binding functions.

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Sequence motifs are found, but they require a simple prediction method.

COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles' heel conserved region to minimize probability of escape mutations and drug resistance

This paper continues a recent study of the spike protein sequence of the COVID-19 virus (SARS-CoV-2). It is also in part an introductory review to relevant computational techniques for tackling viral threats, using COVID-19 as an example. Q-UEL tools for facilitating access to knowledge and bioinformatics tools were again used for efficiency, but the focus in this paper is even more on the virus. Subsequence KRSFIEDLLFNKV of the S2′ spike glycoprotein proteolytic cleavage site continues to appear important. Here it is shown to be recognizable in the common cold coronaviruses, avian coronaviruses and possibly as traces in the nidoviruses of reptiles and fish. Its function or functions thus seem important to the coronaviruses. It might represent SARS-CoV-2 Achilles’ heel, less likely to acquire resistance by mutation, as has happened in some early SARS vaccine studies discussed in the previous paper. Preliminary conformational analysis of the receptor (ACE2) binding site of the spike protein is carried out suggesting that while it is somewhat conserved, it appears to be more variable than KRSFIEDLLFNKV. However compounds like emodin that inhibit SARS entry, apparently by binding ACE2, might also have functions at several different human protein binding sites. The enzyme 11β-hydroxysteroid dehydrogenase type 1 is again argued to be a convenient model pharmacophore perhaps representing an ensemble of targets, and it is noted that it occurs both in lung and alimentary tract. Perhaps it benefits the virus to block an inflammatory response by inhibiting the dehydrogenase, but a fairly complex web involves several possible targets.

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This paper “drills down” into the studies of the author's previous COVID-19 paper.

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Designing vaccine and drugs must seek to avoid escape mutations.

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Subsequence KRSFIEDLLFNKV seems recognizable across many coronaviruses.

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The ACE2 binding domain is a target, but shows variation.

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A steroid dehydrogenase is argued to remain an interesting model pharmacophore.

Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus

This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a peptidomimetic therapeutic, and to explore some design possibilities. The project was originally directed towards a use case for the Q-UEL language and its implementation in a knowledge management and automated inference system for medicine called the BioIngine, but focus here remains mostly on the virus itself. However, using Q-UEL systems to access relevant and emerging literature, and to interact with standard publically available bioinformatics tools on the Internet, did help quickly identify sequences of amino acids that are well conserved across many coronaviruses including 2019-nCoV. KRSFIEDLLFNKV was found to be particularly well conserved in this study and corresponds to the region around one of the known cleavage sites of the SARS virus that are believed to be required for virus activation for cell entry. This sequence motif and surrounding variations formed the basis for proposing a specific synthetic vaccine epitope and peptidomimetic agent. The work can, nonetheless, be described in traditional bioinformatics terms, and readily reproduced by others, albeit with the caveat that new data and research into 2019-nCoV is emerging and evolving at an explosive pace. Preliminary studies using molecular modeling and docking, and in that context the potential value of certain known herbal extracts, are also described.

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Bioinformatics studies are carried out on the COVID-19 virus.

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A sequence motif KRSFIEDLLFNKV is of particular interest.

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Based on the above, synthetic peptides are designed.

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Preliminary considerations are also given to non-peptide organic molecules.

Gestational Age, Health, and Educational Outcomes in Adolescents

BACKGROUND AND OBJECTIVES

As outcomes for extremely premature infants improve, up-to-date, large-scale studies are needed to provide accurate, contemporary information for clinicians, families, and policy makers. We used nationwide New Zealand data to explore the impact of gestational age on health and educational outcomes through to adolescence.

METHODS

We performed a retrospective cohort study of all births in New Zealand appearing in 2 independent national data sets at 23 weeks' gestation or more. We report on 2 separate cohorts: cohort 1, born January 1, 2005 to December 31, 2015 (613 521 individuals), used to study survival and midterm health and educational outcomes; and cohort 2, born January 1, 1998 to December 31, 2000, and surviving to age 15 years (146 169 individuals), used to study high school educational outcomes. Outcomes described by gestational age include survival, hospitalization rates, national well-being assessment outcomes at age 4 years, rates of special education support needs in primary school, and national high school examination results.

RESULTS

Ten-year survival increased with gestational age from 66% at 23 to 24 weeks to >99% at term. All outcomes measured were strongly related to gestational age. However, most extremely preterm children did not require special educational support and were able to sit for their national high school examinations.

CONCLUSIONS

Within a publicly funded health system, high-quality survival is achievable for most infants born at periviable gestations. Outcomes show improvement with gestational ages to term. Outcomes at early-term gestation are poorer than for children born at full term.

Fine sediment and particulate organic matter: A review and case study on ridge-to-reef transport, transformations, fates, and impacts on marine ecosystems

Studies documenting the effects of land-derived suspended particulate matter (SPM, i.e., particulate organic matter and mineral sediment) on marine ecosystems are typically disconnected from terrestrial studies that determine their origin, transport and fate. This study reviews sources, transport, transformations, fate and effects of SPM along the 'ridge-to-reef' continuum. We show that some of the SPM can be transported over long distances and transformed into large and easily resuspendible organic-rich sediment flocs. These flocs may lead to prolonged reductions in water clarity, impacting upon coral reef, seagrass and fish communities. Using the Great Barrier Reef (NE Australia) as a case study, we identify the latest research tools to determine thresholds of SPM exposure, allowing for an improved appreciation of marine risk. These tools are used to determine ecologically-relevant end-of-basin load targets and reliable marine water quality guidelines, thereby enabling enhanced prioritisation and management of SPM export from ridge-to-reef.

Testicular Cancer in New Zealand (TCNZ) study: protocol for a national case-control study

Testicular cancer (TC) is by far the most common cancer to affect young men; however, the exposures that cause this disease are still poorly understood. Our own research has shown that Māori men have the highest rates of this disease in New Zealand-a puzzling observation, since internationally TC is most commonly a disease of men of European ancestry. These trends provide us with a unique opportunity: to learn more about the currently unknown exposures that cause TC, and to explain why Māori have the highest rates of this disease in New Zealand. Using epidemiology and genetics, our experienced research team will conduct a nationwide study which aims to answer these internationally important questions.

AIM OF STUDY

The overall aim of the current national case-control study is to identify the key exposures in the development of TC in New Zealand, and explore which factors might explain the difference in the incidence of TC between Māori and non-Māori.

METHODS AND ANALYSIS

Outside of our own investigations into cryptorchidism, we still do not know which exposures are driving the significant incidence disparity between ethnic groups in NZ. The aim of the proposed research is to use a population-based case-control study to identify the key exposures in the development of TC in New Zealand. We will recruit 410 TC cases and 410 controls, and collect (1) environmental exposure data, via interview and (2) genetic information, via genome-wide genotyping.

ETHICS AND DISSEMINATION

Ethical approval for this study was sought and received from the New Zealand Ministry of Health's Health and Disability Ethics Committee (reference # 17/NTA/248). Following a careful data interpretation process, we will disseminate the findings of this study to a wide and varied audience ranging from general academia, community groups and clinical settings, as well as to the participants themselves.

He Tamariki Kokoti Tau-Tackling Preterm: a data-linkage methodology to explore the clinical care pathway in preterm deliveries

Background

Significant health inequities exist around maternal and infant health for Māori, the indigenous people of Aotearoa New Zealand – and in particular around a premature (preterm) delivery. Māori babies are more likely to be born preterm (8.1%, compared to an overall rate of 7.4%) and they are more likely to have a preterm death. An essential part of redressing these disparities is to examine the clinical care pathway and outcomes associated with preterm deliveries. This paper describes a protocol utilising national and local health collections to enable such a study.

Design

This is a retrospective cohort study comprising 5 years data pertaining to preterm deliveries from 2010 to 2014. These data are generated from linked national administrative and local health information collections to explore a range of neonatal outcomes and infant mortality in relation to the antenatal care pathway and known risk factors for preterm delivery. This study is being conducted within a Kaupapa Māori paradigm that dismisses victim blaming and seeks to intervene at structural levels to improve the health and wellbeing of Māori whānau (family).

Significance of the study

Our data-linkage methodology optimises the utility of New Zealand health collections to address a significant health issue. Our findings will fill the information gaps around the burden of preterm delivery by quantifying the incidence of preterm delivery and adverse neonatal and infant outcomes in Aotearoa New Zealand. It will explore access to evidenced based care including use of steroids before birth, and appropriate place of delivery. The results from this study will inform maternity care services to improve management of preterm deliveries – both locally and internationally. This in turn will improve the preterm sequela by reducing the long-term health burden and health inequities.

Measuring cancer in indigenous populations

It is estimated that there are 370 million indigenous peoples in 90 countries globally. Indigenous peoples generally face substantial disadvantage and poorer health status compared with nonindigenous peoples. Population-level cancer surveillance provides data to set priorities, inform policies, and monitor progress over time. Measuring the cancer burden of vulnerable subpopulations, particularly indigenous peoples, is problematic. There are a number of practical and methodological issues potentially resulting in substantial underestimation of cancer incidence and mortality rates, and biased survival rates, among indigenous peoples. This, in turn, may result in a deprioritization of cancer-related programs and policies among these populations. This commentary describes key issues relating to cancer surveillance among indigenous populations including 1) suboptimal identification of indigenous populations, 2) numerator-denominator bias, 3) problems with data linkage in survival analysis, and 4) statistical analytic considerations. We suggest solutions that can be implemented to strengthen the visibility of indigenous peoples around the world. These include acknowledgment of the central importance of full engagement of indigenous peoples with all data-related processes, encouraging the use of indigenous identifiers in national and regional data sets and mitigation and/or careful assessment of biases inherent in cancer surveillance methods for indigenous peoples.

Indigenous and tribal peoples' health (The Lancet-Lowitja Institute Global Collaboration): a population study

BACKGROUND

International studies of the health of Indigenous and tribal peoples provide important public health insights. Reliable data are required for the development of policy and health services. Previous studies document poorer outcomes for Indigenous peoples compared with benchmark populations, but have been restricted in their coverage of countries or the range of health indicators. Our objective is to describe the health and social status of Indigenous and tribal peoples relative to benchmark populations from a sample of countries.

METHODS

Collaborators with expertise in Indigenous health data systems were identified for each country. Data were obtained for population, life expectancy at birth, infant mortality, low and high birthweight, maternal mortality, nutritional status, educational attainment, and economic status. Data sources consisted of governmental data, data from non-governmental organisations such as UNICEF, and other research. Absolute and relative differences were calculated.

FINDINGS

Our data (23 countries, 28 populations) provide evidence of poorer health and social outcomes for Indigenous peoples than for non-Indigenous populations. However, this is not uniformly the case, and the size of the rate difference varies. We document poorer outcomes for Indigenous populations for: life expectancy at birth for 16 of 18 populations with a difference greater than 1 year in 15 populations; infant mortality rate for 18 of 19 populations with a rate difference greater than one per 1000 livebirths in 16 populations; maternal mortality in ten populations; low birthweight with the rate difference greater than 2% in three populations; high birthweight with the rate difference greater than 2% in one population; child malnutrition for ten of 16 populations with a difference greater than 10% in five populations; child obesity for eight of 12 populations with a difference greater than 5% in four populations; adult obesity for seven of 13 populations with a difference greater than 10% in four populations; educational attainment for 26 of 27 populations with a difference greater than 1% in 24 populations; and economic status for 15 of 18 populations with a difference greater than 1% in 14 populations.

INTERPRETATION

We systematically collated data across a broader sample of countries and indicators than done in previous studies. Taking into account the UN Sustainable Development Goals, we recommend that national governments develop targeted policy responses to Indigenous health, improving access to health services, and Indigenous data within national surveillance systems.

FUNDING

The Lowitja Institute.

Indigenous and tribal peoples' health (The Lancet-Lowitja Institute Global Collaboration): a population study

BACKGROUND

International studies of the health of Indigenous and tribal peoples provide important public health insights. Reliable data are required for the development of policy and health services. Previous studies document poorer outcomes for Indigenous peoples compared with benchmark populations, but have been restricted in their coverage of countries or the range of health indicators. Our objective is to describe the health and social status of Indigenous and tribal peoples relative to benchmark populations from a sample of countries.

METHODS

Collaborators with expertise in Indigenous health data systems were identified for each country. Data were obtained for population, life expectancy at birth, infant mortality, low and high birthweight, maternal mortality, nutritional status, educational attainment, and economic status. Data sources consisted of governmental data, data from non-governmental organisations such as UNICEF, and other research. Absolute and relative differences were calculated.

FINDINGS

Our data (23 countries, 28 populations) provide evidence of poorer health and social outcomes for Indigenous peoples than for non-Indigenous populations. However, this is not uniformly the case, and the size of the rate difference varies. We document poorer outcomes for Indigenous populations for: life expectancy at birth for 16 of 18 populations with a difference greater than 1 year in 15 populations; infant mortality rate for 18 of 19 populations with a rate difference greater than one per 1000 livebirths in 16 populations; maternal mortality in ten populations; low birthweight with the rate difference greater than 2% in three populations; high birthweight with the rate difference greater than 2% in one population; child malnutrition for ten of 16 populations with a difference greater than 10% in five populations; child obesity for eight of 12 populations with a difference greater than 5% in four populations; adult obesity for seven of 13 populations with a difference greater than 10% in four populations; educational attainment for 26 of 27 populations with a difference greater than 1% in 24 populations; and economic status for 15 of 18 populations with a difference greater than 1% in 14 populations.

INTERPRETATION

We systematically collated data across a broader sample of countries and indicators than done in previous studies. Taking into account the UN Sustainable Development Goals, we recommend that national governments develop targeted policy responses to Indigenous health, improving access to health services, and Indigenous data within national surveillance systems.

FUNDING

The Lowitja Institute.

Pounamu: E Hine: access to contraception for indigenous Mãori teenage mothers

ABSTRACT INTRODUCTION Timely and equitable access to contraception enables teenage mothers to make informed choices about their sexual and reproductive health. This study aimed to identify barriers and facilitators to contraception for Māori teenagers who become mothers. METHODS ‘E Hine’ is a longitudinal qualitative Kaupapa Māori (by Māori for Māori) study involving Māori women (aged 14–19 years), following them through pregnancy (n = 44) and the birth of their babies until their babies’ first birthdays (n = 41). This analysis focusses on contraception access pre-and post-pregnancy. FINDINGS Pre-pregnancy most participants accessed contraception or advice. Contraception use was compromised by a lack of information, negative side effects, and limited follow up. All reported their subsequent pregnancies as unplanned. Participants gave considerable thought to post-pregnancy contraception. Despite this many experienced clinical and service delays, financial barriers, and negative contraceptive side effects. There was little focus on contraception initiation and a lack of integrated care between midwives and other primary care services, leaving many participants without timely effective contraception. The system worked well when there was a contraception plan that included navigation, free access, and provision of contraception. CONCLUSION The majority of participants actively sought contraception pre- and post-conception. Despite a publicly funded system, a lack of health sector integration resulted in multiple missed opportunities to meet the needs of these teenagers for effective contraception. Health service funding formulas should define the goal as initiation of contraception rather than advice and provide funding to improve timely access to long acting reversible contraception. KEYWORDS Indigenous teenage pregnancy; contraception; barriers to contraception; Māori mothers

Uterine cancer: exploring access to services in the public health system

BACKGROUND

Māori are the indigenous peoples of New Zealand and experience higher rates of uterine cancer and poorer survival rates. Postmenopausal bleeding (PMB) is the most common presenting symptom for uterine cancer. Prompt investigation is essential with 28 days being viewed as an appropriate time from first medical contact (FMC) to first specialist appointment (FSA).

AIMS

To compare access to services for the investigation of PMB between Māori and non-Māori women.

MATERIALS AND METHODS

The time interval between FMC to FSA was obtained from medical records for women presenting to gynaecology clinics for PMB. Dates of first bleeding symptoms, knowledge and access issues were collected in a nurse-administered questionnaire.

RESULTS

A total of 154 women (n = 27 Māori and 127 non-Māori) participated in the study. 23% of women had their FSA from FMC within 28 days and 67% waited more than six weeks. The 75th percentile was approximately two weeks longer for Māori women. 25% (n = 37) of women were not aware that they needed to see a doctor about PMB, and this was significantly more common for Māori women (44%; 95% CI 25-65) than non-Māori women (20%; 95% CI 13-28; P = 0.011).

CONCLUSIONS

The majority of women were not seen for FSA within 28 days of their FMC. Māori women were more likely to experience lengthy delays and to report that they did not know they should see a doctor about PMB. Further investigation into reasons for delays and initiatives to improve access to services and health information appears warranted.

Initiation of maternity care for young Maori women under 20 years of age

AIM

To explore the lived realities of pregnant Maori women <20 years through pregnancy and motherhood, to identify barriers to, and facilitators of, access to maternity care.

METHOD

Using a Kaupapa Maori research paradigm, 44 pregnant or recently pregnant Maori woman <20 years of age were recruited in two case study sites. Participants completed a series of interviews during different stages of pregnancy and motherhood. Interview transcripts were read, re-read and cross-compared by the two interviewing researchers to identify emergent themes, and organised using the software programme Nvivo. Thematic data was grouped, and re-grouped into topic areas for further analysis.

RESULTS

Participants engaged early with health care services both to confirm their pregnancy and to initiate maternity care. Barriers to access occurred at the first contact with a lack of information, and support along the maternity care pathway to mainly community based midwifery care. Many participants felt inadequately supported to be able to identify, confirm, and enrol with a midwife or hospital care. Participants who received proactive support at the first interaction with health services had an appropriate maternity care pathway toward obtaining early and seamless maternity care.

CONCLUSION

Interviews with participants identified that contrary to published literature young Maori women are engaging early with health services (GP services, school and community based youth health services) for maternity care, but system barriers from this first health contact lead to avoidable delays to them accessing a seamless maternity care pathway. There is a lack of sufficient and appropriate information and support for this young population group who have limited resources and experience to navigate through health services. These inequities in access to maternity care could be reduced through an integrated model of care that sees maternity care beginning at the first interaction with health care services. The service, primarily general practitioners, would then take responsibility for first trimester screening and navigation to a lead maternity carer.

Clinical engagement: improving healthcare together

Clinical engagement can achieve lasting change in the delivery of healthcare. In October 2011, Healthcare Improvement Scotland formulated a clinical engagement strategy to ensure that a progressive and sustainable approach to engaging healthcare professionals is firmly embedded in its health improvement and public assurance activities. The strategy was developed using a 90-day process, combining an evidence base of best practice and feedback from semi-structured interviews and focus groups.

The strategy aims to create a culture where clinicians view working with Healthcare Improvement Scotland as a worthwhile venture, which offers a number of positive benefits such as training, career development and research opportunities. The strategy works towards developing a respectful partnership between Healthcare Improvement Scotland, the clinical community and key stakeholders whereby clinicians’ contributions are recognised in a non-financial reward system. To do this, the organisation needs a sustainable infrastructure and an efficient, cost-effective approach to clinical engagement. There are a number of obstacles to achieving successful clinical engagement and these must be addressed as key drivers in its implementation. The implementation of the strategy is supported by an action and resource plan, and its impact will be monitored by a measurement plan to ensure the organisation reviews its approaches towards clinical engagement.

Distinguishing human and possum faeces using PCR markers

Specificity testing of two published polymerase chain reaction (PCR) markers for the detection of human faecal pollution, revealed 100% false-positive rates to brush-tailed possum faeces (n = 10), but low false-positive rates against other potential pollution sources. Cross-reaction with possums could be a problem with other human-specific markers; therefore, a possum PCR marker was developed for use in conjunction with human PCR markers. The possum PCR marker was based on Bacteroidales 16S ribosomal ribonucleic acid sequences, and was tested on 233 individual faecal samples from 11 other animal species. Sensitivity of the possum marker in possum faeces (n = 36) was high at 83.3%. Cross-reactivity of the possum marker was limited to black swan (7/20 samples), human (2/48 samples) and rabbit (1/10) faecal samples, all at marker concentrations at least four orders of magnitude lower than possum faeces. The possum marker was not detected in human sewage or the faeces of other animal species. Specificity of the possum PCR marker, therefore, was high at 95.7%. To exclude the possibility that only possum pollution is being detected, additional testing by other faecal source tracking methods is required where the water sample is positive for both human and possum markers.

Wāhine hauora: linking local hospital and national health information datasets to explore maternal risk factors and obstetric outcomes of New Zealand Māori and non-Māori women in relation to infant respiratory admissions and timely immunisations

Background

Significant health inequities exist around maternal and infant health for Māori, the indigenous people of New Zealand. The infants of Māori are more likely to die in their first year of life and also have higher rates of hospital admission for respiratory illnesses, with the greatest burden of morbidity being due to bronchiolitis in those under one year of age. Timely immunisations can prevent some respiratory related hospitalisations, although for Māori, the proportion of infants with age appropriate immunisations are lower than for non-Māori. This paper describes the protocol for a retrospective cohort study that linked local hospital and national health information datasets to explore maternal risk factors and obstetric outcomes in relation to respiratory admissions and timely immunisations for infants of Māori and non-Māori women.

Methods/Design

The study population included pregnant women who gave birth in hospital in one region of New Zealand between 1995 and 2009. Routinely collected local hospital data were linked via a unique identifier (National Health Index number) to national health information databases to assess rates of post-natal admissions and access to health services for Māori and non-Māori mothers and infants. The two primary outcomes for the study are: 1. The rates of respiratory hospitalisations of infants (≤ 1 yr of age) calculated for infants of both Māori and non-Māori women (for mothers under 20 years of age, and overall) accounting for relationship to parity, maternal age, socioeconomic deprivation index, maternal smoking status. 2. The proportion of infants with age appropriate immunisations at six and 12 months, calculated for both infants born to Māori women and infants born to non-Māori women, accounting for relationship to parity, maternal age, socioeconomic deprivation index, smoking status, and other risk factors.

Discussion

Analysis of a wide range of routinely collected health information in which maternal and infant data are linked will allow us to directly explore the relationship between key maternal factors and infant health, and provide a greater understanding of the causes of health inequalities that exist between the infants of Māori and non-Māori mothers.

Improving survival disparities in cervical cancer between Māori and non-Māori women in New Zealand: a national retrospective cohort study

OBJECTIVE

Māori women in New Zealand have higher incidence of and mortality from cervical cancer than non-Māori women, however limited research has examined differences in treatment and survival between these groups. This study aims to determine if ethnic disparities in treatment and survival exist among a cohort of Māori and non-Māori women with cervical cancer.

METHODS

A retrospective cohort study of 1911 women (344 Māori and 1567 non-Māori) identified from the New Zealand Cancer Register with cervical cancer (adenocarcinoma, adenosquamous or squamous cell carcinoma) between 1 January 1996 and 31 December 2006.

RESULTS

Māori women with cervical cancer had a higher receipt of total hysterectomies, and similar receipt of radical hysterectomies and brachytherapy as primary treatment, compared to non-Māori women (age and stage adjusted). Over the cohort period, Māori women had poorer cancer specific survival than non-Māori women (mortality hazard ratio (HR) 2.07, 95% confidence interval (CI): 1.63-2.62). From 1996 to 2005, the survival for Māori improved significantly relative to non-Māori.

CONCLUSION

Māori continue to have higher incidence and mortality than non-Māori from cervical cancer although disparities are improving. Survival disparities are also improving. Treatment (as measured) by ethnicity is similar.

IMPLICATIONS

Primary prevention and early detection remain key interventions for addressing Māori needs and reducing inequalities in cervical cancer in New Zealand.