The rapid identification and adoption of effective innovations in healthcare is a known challenge. The strongest evidence base for innovations can be provided by evidence synthesis, but this is frequently a lengthy process and even rapid versions of this can be time-consuming and complex. In the UK, the Accelerated Access Review and Academic Health Science Network (AHSN) have provided the impetus to develop a consistently rapid process to support the identification and adoption of high-value innovations in the English NHS.The Greater Manchester Applied Research Collaboration (ARC-GM) developed a framework for a rapid evidence synthesis (RES) approach, which is highly integrated within the innovation process of the Greater Manchester AHSN and the associated healthcare and research ecosystem. The RES uses evidence synthesis approaches and draws on the GRADE Evidence to Decision framework to provide rapid assessments of the existing evidence and its relevance to specific decision problems. We implemented this in a real-time context of decision-making around adoption of innovative health technologies.Key stakeholders in the Greater Manchester decision-making process for healthcare innovations have found that our approach is both timely and flexible; it is valued for its combination of rigour and speed.Our RES approach rapidly and systematically identifies, appraises and contextualises relevant evidence, which can then be transparently incorporated into decisions about the wider adoption of innovations. The RES also identifies limitations in existing evidence for innovations and this can inform subsequent evaluations. There is substantial interest from other ARCs and AHSNs in implementing a similar process. We are currently exploring methods to make completed RES publicly available. We are also exploring methods to evaluate the impact of using RES as more implementation decisions are made.The RES framework we have implemented combines transparency and consistency with flexibility and rapidity. It therefore maximises utility in a real-time decision-making context for healthcare innovations.The online version contains supplementary material available at 10.1186/s13643-022-02106-z. Whilst evidence synthesis can represent the strongest evidence base for innovations, conventional systematic reviews may often take up to 2 years to produce , 2, whilChallenges in getting proven innovations rapidly adopted into systems, policies or practice have long been recognised. In the UK, the Accelerated Access Review provided fresh policy impetus to efforts to develop a faster pathway to identify and adopt high-value innovations in the National Health Service (NHS) in England . The AccIn Greater Manchester, Health Innovation Manchester (HInM) is the AHSN with the remit to implement beneficial health innovations across the region , 13. OurDecisions about innovation adoption may need to be made rapidly but this does not negate the need for evidence-informed decision-making, although for some novel technologies the available evidence may be limited. It remains important that there should be transparency about the evidence used, its reliability and relevance to the decision problem and what, if any, further evaluation may be warranted.To ensure that decisions in Greater Manchester on innovation adoption and roll-out are informed by evidence, we developed a framework for the production of RES for innovations being considered for implementation. This framework has been made publicly available and registered  and is p”.The RES we produce are designed to be requested, undertaken, and delivered in a time period of 2 weeks. We use a systematic but streamlined process to enable replicable, transparent yet consistently very rapid delivery compared with other rapid evidence synthesis processes –9. Our RThe production of RES is embedded within, and integral to, the Greater Manchester innovation adoption decision-making process, rather than representing an input from a separate organisation. This integration means that key stakeholders and reviewers can work closely together to co-produce the RES. HInM uses a high-level, broad framework which involves identifying and prioritising innovations which are assessed and selected via an ongoing “pipeline” process , wherebyThe RES team attends relevant meetings where innovations are discussed, and the need for RES is explored on a case-by-case basis. Where a RES is requested, the review plan is developed iteratively between reviewers and decision-makers. This enables resolution of queries at each stage, maximises the relevance of the RES and supports integration of the evidence appraisal into decision-making.RES is recognised as one of the necessary components of the early stage of the decision-making process around innovation adoption, alongside public patient involvement and engagement (PPIE) input, business case assessment and consultation with local health and social care stakeholders. The assessment of evidence, its relevance and certainty, is integrated into the considerations before decisions are made as to whether to proceed with the development of the implementation plans. This consideration of evidence may include wider evidence about the impact of interventions for similar decision problems. The RES does not produce recommendations, and decisions are not determined solely by the findings of the RES, but the RES ensures that decisions are evidence informed. In a small number of instances, the RES proves critical to the decision, usually where a decision is made not to proceed. For example, one RES identified that the innovation was addressed by a national guideline that recommended that a particular intervention should not be offered. Usually the contribution is more nuanced, however.The principles of the GRADE evidence to decision framework are central to our approach to RES, which makes the RES, and the decision process to which it contributes, more transparent, consistent and reproducible , 21. GRAThe RES uses GRADE approaches to consider the applicability of the evidence to the Greater Manchester context as well as its reliability. Context, both broadly and narrowly considered, can be key to the impact of introducing an intervention . In the Although in the first instance our RES consider relevance in terms of a UK-wide NHS context, we also consider the local Greater Manchester context. We do not generally undertake RES where an innovation is already a nationally mandated priority, so local context is potentially important to all the innovations assessed. Local context includes the existing service models, relevant infrastructure, and area and population characteristics including urbanicity, relative deprivation, etc. GRADE helps to ensure that relevance can be given equal prominence to certainty in evidence summaries. An example of identified limited relevance at the national level is where an RES of an innovation in asthma care identified only evidence from US trials. This is not directly relevant to asthma control in people with asthma in the UK, who at the population level have higher baseline control and use of preventative medication . At the We present a full example of an RES in the The key elements of the completed RES are shown in Table The RES is designed to produce a “good-enough” (rather than perfect) summary of the evidence as a contribution to decision-making in a short timeframe. “Good-enough” is considered to be an up-to-date evidence summary which is based on the most relevant and methodologically rigorous evidence available, with uncertainties clearly articulated and acknowledged. The methods described are implemented using a median of up to 2 days of time for an experienced researcher with a background in evidence synthesis, spread over an approximately 2-week period. More complex innovations may entail more resources for RES production and may involve more input from an information specialist. More details are provided in the framework see  15]..15].The first stage is to briefly describe the innovation in terms of its nature and purpose Table . This esUsing the description of the intervention, we formulate a series of questions based on the innovation description Table . These bIf the innovation is an intervention, then the questions will be ones of effectiveness and safety; where the innovation is (for example) a diagnostic test or screening tool, we consider accuracy as well as the impact on participants and health systems of implementing the technology. For complex interventions, each core feature is described and underpins the formulation of several questions. When evaluating evidence for particular components of a complex intervention, we are mindful of the fact that effectiveness in such an intervention may derive not solely from the additive effect of components but from their interaction with each other, as well as with the (often complex) system context . We woulWhilst we first focus on effectiveness evidence for the specific innovation being assessed, where this is limited, we will explore evidence for (2) the category of innovations (“innovations like this”) and then (3) wider categories of relevant innovation (e.g. “innovations with a similar aim”). Categories are sometimes not obvious, particularly where the innovation is complex , 28, 38.These subsequent questions are designed to ensure that useful evidence can be provided where the evidence for the innovation itself is absent, limited or not directly relevant. Development of these questions involves consultation with key individuals to ensure the focus is relevant. For example, such consultation determined that the widest appropriate question in an appraisal of a particular digital care plan for dementia was “digital care plans for any condition” rather than “care plans for dementia”. These additional questions are designed to be addressed only where the evidence for the first question(s) is considered insufficient. Implementation of the sequential question set is then flexible and sensitive to the nature of the identified evidence. Additional questions are also required when innovations are tests, where the evidence for available treatments should be considered as a whole in the absence of test-and-treat evaluations .Our focus is always on those study designs best able to answer the questions we have developed. We focus on the identification of existing evidence synthesis (systematic reviews) where possible; where this is not possible, we focus on the most informative primary evidence. In the case of most innovations, this is from comparative studies, giving priority to randomised controlled trials. Where appropriate to the questions, we also include diagnostic accuracy or prognostic studies. There are also questions, especially where the focus of an innovation is on patient experience, where mixed methods or qualitative studies will be the most appropriate form of primary evidence.We adopt a pragmatic and iterative approach to identifying evidence. This uses an initially narrow focus to maximise relevance and progresses to a broader evidence base as necessary. We search key resources including NICE guidance , PubMed Where relevant, we increasingly encourage those putting forward an innovation for consideration to provide research evidence, as would be the case with a single technology submission to NICE , and we Where appropriate, we use subject/domain-specific resources, such as the webpage of a particular Cochrane Group  or the OWe use appropriate methods to critically appraise the different types of evidence we identify. Cochrane reviews are generally considered to represent reliable evidence , and we Where there is no existing evidence synthesis, or we have concerns about the robustness or relevance of a systematic review, we consider primary evidence for the question. We also move to assessing primary research where the existing synthesis has only partially addressed a question, for example because eligibility criteria were narrower. Conversely, where a review has a broader remit, we may look at the included primary studies relevant to our question. In the example of the Phagenyx RES, we looked at the subgroup of RCTs assessing Phagenyx within the Cochrane review of interventions for dysphagia in stroke .capacity of the study design(s) to answer the question and an assessment of the risk of bias in the identified studies of the review to produce overall judgements of reliability. Because of our narrow timescale, we do not undertake full assessments but, as with ROBIS, are guided by the domains used. For example, for randomised controlled trials, we are guided by the criteria and considerations of the Cochrane Risk of Bias tool [Assessment of primary studies considers both the ias tool ; for othias tool , 49.In forming judgements about the certainty of the evidence, we are guided by the principles of GRADE , 50. GRAApart from the risk of bias, the domains most relevant to our rapid evidence syntheses are usually imprecision  and indirectness (often a function of context): there is often insufficient evidence to determine inconsistency between studies for the initial questions because there are usually only a small number of studies. The evidence for category-level questions is often of higher certainty than the evidence for the innovation itself; here, the domains of inconsistency (and completeness of evidence (publication bias)) are more likely to be considerations.We bear in mind that where inconsistency is present (as at the wider category level), this may be a consequence of either—or both—differences in the interventions or the systems in which they are evaluated as well as differences in participants or outcome measures. Whilst some interventions are clearly complex, even apparently simple interventions are frequently implemented into complex health systems and this is especially true of those which would represent changes in patient management . We therIn our RES approach, we explore possible reasons for identified inconsistency and attempt to relate these to the Greater Manchester context. For example, in one RES, we identified a pilot study that reported between-site differences in the impact of an intervention on increasing staff participation in a specific form of mental health assessment. It appeared likely, after considering the qualitative data in the case studies, that this differential was likely to be due to one of the sites being part of a large urban area, whilst the other was very rural . As we nImprecision is usually the consequence of small studies with insufficient participants; this results in wide confidence intervals and effect estimates which would be highly likely to change with further evidence. Indirectness is also often an issue for some or all of the evidence. This may be because of inconsistency (as discussed above). However, because innovations assessed are novel, there is also often only a partial evidence base, where the evidence may be only indirectly relevant to many of the people in question, although directly relevant to the group represented in the studies.Our considerations of relevance (which GRADE considers as (in)directness) are key to our assessments. In addition to the consideration of indirectness which informs our assessment of the certainty of the evidence, we also consider the relevance of the evidence to the context and health system in which the innovation would be implemented—in this case, Greater Manchester in the UK.We use the identified evidence to produce narrative summaries of the evidence for the key questions in the RES. We always summarise evidence for core question(s) relating to the innovation, although we may identify little or no (useful) evidence. We provide a separate answer to each question addressed.Where possible, we summarise existing evidence syntheses, together with either their existing GRADE assessment or, if these are not available, a judgement based on our assessment of the GRADE considerations. We also provide an assessment of how relevant the evidence from the existing synthesis is to the question.Where we have been unable to identify relevant existing evidence synthesis, we summarise the primary studies identified. We use a narrative summary to report effect estimates  and their certainty and relevance, very rarely would we seek to undertake meta-analysis.We outline the certainty and relevance of the evidence for each outcome in the question, distinguishing where appropriate the population or subgroup to whom it is directly relevant. So in the Phagenyx population, the evidence is directly relevant to people who have dysphagia following stroke, who represent a subgroup of people with dysphagia. We adopt the GRADE principle of assigning judgements around certainty to a particular outcome rather than at the study level. Where appropriate, we report the evidence for each component of an intervention or intervention bundle (where there is no or very limited evidence for the whole). We provide as nuanced a summary of the evidence as possible, clarifying where evidence has different levels of certainty for different populations, components, or outcomes. An example of a full RES is provided in the We provide two levels of summary information, written in non-technical language.The first provides a single brief summary of the evidence picture and highlights its certainty and relevance Table .Table 4EThe second provides a bulleted summary of the certainty and relevance of the evidence for each key question, including (e.g.) nuances of the population to which the evidence is directly relevant Table . This maAs described above, our question series has three possible levels: these relate to (1) evidence for the specific innovation, (2) evidence for innovation category and (3) evidence for wider relevant innovations. Our process involves addressing these questions sequentially, stopping at the point at which we have identified evidence of sufficient certainty and relevance. For the Phagenyx example, suitable innovation-specific (level 1) evidence was identified and no further evidence was required , 53. In The use of these question sets allows us to be agile in our approach to RES. Where we consider a multicomponent or bundled innovation, we can rapidly review evidence for the innovation as a whole and, where required, evidence for the innovation components. An example of this is the RES we carried out for RESTORE-2, a tool for care home staff which consists of three key components: identification of “softs signs” of possible physical decline, an early warning score and a structured communication plan. We identified limited evidence for the intervention as a whole , so lookThe relevance of evidence reported in the RES is considered during subsequent decision-making, with transparent and cautious extrapolation of indirect data where required. For example, in a RES for an innovation for both people with asthma and people with chronic obstructive pulmonary disease (COPD), we found only randomised evidence for people with asthma , 62, andThe need for evidence-informed decision-making is increasingly apparent for a wide range of healthcare organisations in a climate of increasing and competing demands for services. Decision-making is informed by multiple considerations, including costs and opportunity costs, acceptability and existing infrastructure. Whilst it is critical that decisions are informed by evidence, it is also important that this process is both transparent and consistent. As with all rapid evaluation work, there is a necessary trade-off between rigour, speed and available research resources .The RES we undertake are not conducted as an alternative to full systematic reviews, or even more conventional rapid reviews. Rather they represent the introduction into decision-making of some synthesis of existing research evidence. Rapid evidence synthesis itself is widely used in the form of rapid reviews , and theThe framework presented here is grounded in the GRADE evidence to decision approach as well as previous work in evidence briefing services , 20. It The framework is intended for use where there may be relatively limited evidence available for the innovation, as well as where more research is available. It is envisaged that this approach is used by researchers from organisations involved in decisions about innovation adoption, so that queries are rapidly resolved in the innovation description and question formulation stages. In our process, researchers attend relevant meetings, enabling them to answer queries and discuss issues with stakeholders and decision-makers which arise from the RES. The RES does not therefore exist only as a stand-alone document but as part of a broader integration of relevant research evidence in the decision-making process. This may distinguish the process we present from other evidence briefing services which have tended to be externally commissioned , 16.The principal limitation of the process is the necessary trade-off between rapidity and both comprehensiveness and rigour which all rapid evaluation confronts . This isWe have not formally compared the results of our RES with those of a systematic review: although the need for a full systematic review may be identified, there is often insufficient time or resource to commission a further piece of evidence synthesis for the current decision problem, and this limitation is flagged. Where a systematic review is identified as being a high priority, the scope for this can be explored within the wider ARC-GM. We are currently developing a full systematic review informed by the RES process, although with a narrower review question; we plan to compare the full review findings with those of the RES once it has been completed.It is likely that we will not identify all relevant evidence for some questions, particularly broader category-level questions. This is particularly likely to be the case where we do not identify any relevant evidence syntheses and are summarising primary studies. The iterative process we use, which includes citation searching and a saturation-based approach, mitigates this risk, as does the focus on existing evidence syntheses. The fact that the RES is produced by a single researcher also makes it necessarily vulnerable to bias and error. The potential for error may be mitigated by the researcher being relatively experienced in evidence synthesis ; a possiWe are especially conscious of the difference that the involvement of an information specialist or medical librarian may make to a systematic review , 73, andWe also acknowledge that searching a limited selection of databases  can have an impact on the findings of an evidence synthesis . We acceWe have considered the potential for information supplied by commercial sponsors to have undue influence on the process. As is the case in our experience of the NICE single technology appraisal approach , only veThe approach to rapid evidence synthesis outlined here has the advantage that it can be undertaken very rapidly: it is designed to be undertaken in the 2 weeks between the initial decision that an innovation has potential merit and a subsequent meeting, where an adoption decision will be made. This represents a very short timescale, even for evidence briefing production –9, 19, aThe RES approach outlined is designed to be extremely flexible, both in terms of the questions which can be addressed and the process of answering those questions; it is an iterative and pragmatic process whereby researcher judgement can be used to refine the approach at every stage. This means it is easily adapted for the assessment of a wide range of innovations: those we have so far assessed include medical devices, screening and prognosis testing, bundled service process interventions and digital mHealth apps.Our approach to rapid evidence synthesis has been developed and implemented in a real-time context of decision-making around the adoption of innovative health technologies. Key stakeholders in this decision-making process have found that it is sufficiently timely and flexible to be a useful input and have engaged actively with its production and interpretation. There is substantial interest from other ARCs and AHSNs in implementing a similar process; creating a common resource database of RES undertaken by any organisation would further minimise research waste and improve evidence-informed decision-making. We are exploring options to enable this, including making some RES publicly available. Although we consider local relevance, the RES first consider the relevance of evidence to the NHS in England, meaning that they are also relevant to other regional decision-makers.We track the progress of innovations for which we have undertaken RES; decisions to date have included adoption, requests for further information from the sponsor, and decisions not to progress. For innovations now adopted for roll-out, the RES can inform subsequent evaluation questions. Published evaluations of the use of evidence briefings are limited , and we Additional file 1. The NIHR ARC-GM and Health Innovation Manchester approach to rapid evidence synthesis to support health system decision making.Additional file 2. Rapid evidence synthesis: Phagenyx.


Calls for supporting sustainability through more and better research rest on an incomplete understanding of scientific evidence use. We argue that a variety of barriers to a transformative impact of evidence arises from diverse actor motivations within different stages of evidence use. We abductively specify this variety in policy and practice arenas for three actor motivations  and five stages . Our interdisciplinary synthesis focuses on the sustainability challenge of reducing environmental and human health risks of agricultural pesticides. It identifies barriers resulting from (1) truth-seekers’ desire to reduce uncertainty that is complicated by evidence gaps, (2) sense-makers’ evidence needs that differ from the type of evidence available, and (3) utility-maximizers’ interests that guide strategic evidence use. We outline context-specific research–policy–practice measures to increase evidence use for sustainable transformation in pesticides and beyond. To support sustainable development and biodiversity conservation, scholars have been calling for expanding sustainability science  in five stages . Combining motivations and stages expands actor-centered work on science impacts and promises fine-grained assessments that can inform context-specific research–policy–practice strategies to increase evidence use for sustainability.We illustrate our argument using the environmental and human health risks of agricultural pesticides as a typical sustainability problem. Pesticide risk reduction is a complex socio-ecological challenge at the food-health-environment nexus of several UN Sustainable Development Goals (SDGs)—food security (SDG 2), good health (SDG 3), clean water (SDG 6), economic growth (SDG 8), responsible consumption and production (SDG 12), and protection of life on land (SDG 15). It involves goal conflicts, conflicts between actors, and uncertainties regarding pesticides’ effects on human and environmental health and the economic implications of plant protection alternatives. Pesticide use causes pollution risks globally  and food security and safety without posing excessive risks for environmental and human health.We empirically explored evidence use for sustainability in agricultural pesticide policy and practice Fig. . Pests aWe synthesized insights from environmental and health sciences, political science, decision analysis, agricultural economics, and agronomy. Our focus was on cutting-edge research from these disciplines and fields that helps infer barriers to evidence use for sustainability. We focused on the Global North, especially Europe, where recent policy initiatives   Donley  reflect ) Donley . Owing t) Donley . In the ) Donley . Farmers) Donley .Box 1 Value trade-offs and scientific evidenceThe trade-offs inherent in sustainability problems mean that all actors’ objectives cannot be achieved simultaneously. As confirmed by studies that assessed agricultural sustainability with a multi-criteria approach, trade-offs exist between socio-economic, environmental, and other objectives   can increase effectiveness  in the 1940s. From the late 1940s onwards, Swiss apple farmers started increasingly using the insecticide classes organochlorines , organophosphates , and carbamates and fungicide classes like dithiocarbamates  and phthalimides .Silent Spring (1962) collected problem-oriented evidence on adverse pesticide impacts and solution-oriented evidence on alternatives. This evidence uptake increased public awareness and led to a DDT ban in agriculture. In the 1960s and 1970s, several ‘modern’ pesticides became available, including new fungicides  and insecticides . Their intensive use transformed apple production into highly productive orchards but adversely affected other sustainability outcomes .Public doubts regarding intensive pesticide use arose globally in the early 1960s. Rachel Carson’s The 1960s and 1970s saw an increasingly unsustainable Swiss apple production but also innovative farmers and advisors who adopted the novel concept of Integrated Pest Management (IPM), including the idea of applying pesticides only when pests surpass economically damaging thresholds. Farmers, researchers, and advisors jointly began to develop IPM systematically for Swiss apple production. Regional farmer groups fostered knowledge transfer and the development of a premium brand, and one of the two major Swiss retailers, Migros, promoted IPM practices with a distinct label (‘M-Sano’). Additionally, organic farming organizations disseminated evidence-based guidance on biological and biotechnical methods .In the 1980s and 1990s, with the emergence of more problem- and solution-oriented evidence, the transformation of Swiss apple production accelerated. Researchers recognized the need to quantify pesticide impacts on non-target organisms, and the Swiss legislator refined the data requirements for pesticide registration and further restricted chemicals. Commercially, the premium brand for IPM (‘IP’) was launched, and the other major Swiss retailer, Coop, initiated its organic brand. In farming, innovative non-chemical alternatives for pest and disease control  allowed for restricting insecticide and fungicide treatments. Elements promoting functional biodiversity  further reduced dependency on insect pest control.In the 2000s and 2010s, the apple production practices continued to become more sustainable. By providing actionable evidence for timely pesticide application, the weather-based Decision Support Systems (DSS) revolutionized scab control, and new scab-resistant apple varieties were introduced to compensate for resistance breakdowns. Recently, retailers have developed new private standards to promote the production of apples with only low levels of pesticide residues. In organic apple production, post-infection treatments with non-synthetic chemicals like lime sulfur or potassium bicarbonate against scab infections have been an evidence-based breakthrough.Today, Swiss apple production complies with IPM standards or certified organic production. Despite such progress, apples still require intensive pest and disease control and the public remains concerned about pesticide impacts. Continuous feedback, production, and uptake of evidence are needed to advance the co-evolution of sustainable policies and practices addressing new pests and diseases.Weak feedback from sustainability outcomes to renewed evidence production can also hinder transformation. A sensitivity for different actor motivations reveals that this may be due to time lags and missing data, diverging results of scientific and experiential evaluations, and strategic impediments by status quo interests.Truth-seeking actors’ efforts to improve pesticide policies and practices using evidence feedback on previous sustainability effects are hampered by gaps in monitoring and evaluation. An example is the environmental effects for which model-based proxies , vertically between levels , and in time . Incorporating evidence feedback into decision-making can be expanded through more financial and human resources for dynamic evidence summaries and transparent evaluation programs with clearly defined purposes and multi-directional information flows , they may also inform strategies for reducing major pesticide risks in the Global South (Tang et al.


Estimating the prevalence or the absolute probability of the presence of a species from presence‐background data has become a controversial topic in species distribution modelling. In this paper, we propose a new method by combining both statistics and machine learning algorithms that helps overcome some of the known existing problems. We have also revisited the popular but highly controversial Lele and Keim (LK) method by evaluating its performance and assessing the RSPF condition it relies on. Simulations show that the LK method with the RSPF assumptions would render fragile estimation/prediction of the desired probabilities. Rather, we propose the local knowledge condition, which relaxes the predetermined population prevalence condition that has so often been used in much of the existing literature. Simulations demonstrate the performance of the new method utilizing the local knowledge assumption to successfully estimate the probability of presence. The local knowledge extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence from presence background without absence data in species distribution modelling. We proposed a new concept of local knowledge that extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence without absence data in species distribution modelling. This paper will focus on the methodologies developed that relate to PB data, which have been used in approximately 50% of SDM papers, according to the survey in Guillera‐Arroita et al.  to help understand how organisms selectively use their resources and the factors which shape their spatial distributions. SDMs have therefore become fundamental for many tasks in modern ecological modelling . Here, the variable y = 1 represents the species’ presence while y = 0 represents its absence at a particular site. More specifically, a key goal is to estimate the conditional probability of Pr(y=1|x), namely the absolute probability of presence at a site, based on the covariate x measured at that site. The overall population prevalence will be denoted as π=Pr(y=1), that is, fraction of sites in the study area in which the species is present. A common practice in statistical modeling is to assume a parametric structure for Pr(y=1|x), for example, the logit functionη(x;β) can be a linear or nonlinear function of x, and β are parameters that need to be estimated.When working with SDMs, we are interested in whether a species is present or absent at a particular site, conditional on environmental covariates . The second sample B of size n0 is drawn independently and identically from all locations in the study area with only the covariates but no information about presence or absence at each location. We use s to represent the sampling stratum, with s = 1 for the observed/labelled samples appearing in P and s = 0 for “unlabelled” samples in B. Pr(s=1) gives the probability of a species being observed or the probability of belonging to the presence samples. The class of y is not observed, but its information can be derived from the value of s. If the sample is labelled s = 1, then it is a “presence” with y = 1; that is Pr(y=1|s=1)=1. But, if s=0 we do not know whether y=1 or y=0. An important assumption underlying the labelling mechanism is that each labelled sample is chosen completely at random with the probability Pr(s=1|y=1). The “selected completely at random” (SCAR) assumption is stated formally as Pr=Pr(s=1|y=1)  of population prevalence empirically, and obtained the following log‐likelihood;Lele and Keim  used theβ that maximizes Equation In Equation , the spelogPr(y=1|x) should be nonlinear, and (2) not all covariates can be categorical. Readers are referred to Solymos and Lele =π0, where π0 is a predetermined population prevalence and n0 is the number of background samples. Note that this is different from just maximizing the function of Equation  proposed by Li et al.  , and absolute probability of presence Pr(y=1|x) as follows  and the conditional probability of the observed presence Pr(s=1|x) under the case‐control sampling scheme. This key relationship was also derived by Phillips et al.  must equal to 1 at certain x value. This property was defined later by Bekker and Davis (Pr(y=1|x)=1. In our framework, a similar assumption will be used to obtain an estimate for π.Elkan and Noto  and Li eand Noto  assume tnd Davis  as the “nd Davis . Similarnd Davis  introducPr(y=1|x)=1, it can be shown from Equation (5) that;c through the predicted values of Pr(s=1|x) at the PPL. For this, we first use ML methods to predict Pr(s=1|x) by training a binary classification model using the presence  and background  data. Popular classification methods, such as logistic regression, k‐nearest neighbours (KNN), support vector machines and neural networks, can be used to model Pr(s=1|x). In this paper, a neural network was used as the classifier which has been shown to perform very well.At PPL, that is, when 5) that;Pr(s=1|xPr(s=1|x). To reduce the effect of noise, Elkan and Noto  at the PPL, the maximum values of Pr(s=1|x) at the PPL, and the ratio between the sum of Pr(s=1|x) at the PPL and the sum of Pr(s=1|x) over the background. Using the average as an example, c can be estimated as follows  for x that belongs to the PPL. According to Equation Pr(y=1|x) is an increasing function of Pr(s=1|x), so we use the locations where Pr(s=1|x) are maximal as the PPL. We rank the predicted Pr(s=1|x) values for all presence and background points, and those locations where predicted Pr(s=1|x) are high are used as the PPL .We then substituted Equation  as the cIn our proposed method, the population prevalence is estimated from the available PB data, provided the LC condition is satisfied. This contrasts with previous studies in which a predetermined value of prevalence  is required  (such as in Equation (Pr(y=1|x), we first generate a random value r on the interval of  for each site. A site is assigned y=1 (presence) if r≤Pr(y=1|x), and y=0 (absence) otherwise. Those sites with probabilities less than one could be randomly allocated as either presence or absence (or just absence) depending on the random value of r. The presences and absences generated at these sites would thus be “inseparable.” In another word, in order for (observed) presences distinguishable from absences (unobserved in PB data), some sites must have Pr(y=1|x)=1  so that a unique region in feature space is only occupied by the presence samples.In the relevant ML literature such as Elkan and Noto  and Li ePry=|x .Figure Machine learning focuses more on classes that are strongly separable. Therefore, to classify presence and absence from the PB data, LC or PPL is a key assumption underlying the case‐control sampling scenario in PBL. Without extra information, the presence and absence points in the second data set would be hard to separate, regardless of the method used.2.5Pr(y=1|x) does not reach the maximal value of one. The scaled logistic example used in Hastie and Fithian  for all observed presences and background points. Those locations with the highest Pr(s=1|x) will be used as the locations with LKN. Using a maximal probability of 0.7 as an example, we can show from Equation  in this case. LKN does not necessarily refer to the information of the maximal probability, and it can also include any nominated probability of presence at a given site or over a particular landscape. In general, if LKN is available so that there are some locations where the probabilities of Pr(y=1|x) are known, it should be possible to make use of the trained value of Pr(s=1|x) at these locations to estimate π from Equation (Pr(y=1|x). In the following simulation section, the scaled logistic example explored in Hastie and Fithian , we can rank the predicted values of Equation  that(11Equation  and to f Fithian  will be  Fithian  that satPr(y=1|x)=1 at these locations. In practice, LKN could be gained through experts’ knowledge or pilot studies.The LKN condition was built under the same framework and extends the LC condition. The PPL assumption given by Elkan and Noto  and Li ePr as follows: Pr(s=1|x), using all presence  and background  data points. A commonly used ML binary classifier, such as the neural network or support vector machine, can be used for modelling Pr(s=1|x);Step 1: Train the model to estimate π^ using Equation Pr(s=1|x) at the PPL or locations with LKN;Step 2: Estimate the population prevalence β, with π substituted by π^ from step 2 and obtain the estimated probability of presence Pr(y=1|x;β).Step 3: Maximize the log‐likelihood function of Equation (4) with respect to At the end of this section, we summarize the steps . Category 1 meets both the RSPF and LC conditions  and Category 3 functions only satisfy the RSPF conditions and not the LC =0.83, Pr(y=1|x)=0.8 and Pr(y=1|x)=0.75, which are the maximal probabilities of the linear, quadratic and cubic logistic functions over the range of x. We also tested the performance of the CLK method with the mis‐specified LKN information, where the LKN used differs the true probability by ±10%. Results are shown in the bottom row of Figure All the functions in Categories 1 and 3 were fitted by logistic functions for both the LK and the refined CLK methods =0.73, Pr(y=1|x)=0.89 and Pr(y=1|x)=0.68 were assumed as the known LKN for fitting the linear, quadratic and cubic functions, respectively  for the refined CLK method. We rank the predicted Pr(s=1|x) for the presence and background points, and those locations whose predicted Pr(s=1|x) lie in the top 10th percentile are used as the PPL or locations with the LKN. The choice for the 10th percentile threshold is arbitrary but was tested sufficient and robust for our simulation studies.The neural network package “nnet” in R  of fitted probabilities against the true probabilities of presence are also calculated and plotted in Figures  of fitteAll model fitting and assessment have been carried out in R version 3.6.1. The R code supplied by Solymos and Lele  has been2.7One of the pivotal publications by Hastie and Fithian  demonstrf1(x)=11+exp(1‐x) while the scaled logistic function is exactly half of that, i.e., f2(x)=12f1(x), where x∈. We first fit both functions by the LK and CLK methods, using a sample of 5000 presences and 50,000, background data points with 1000 iterations =0.8 and Pr(y=1|x)=0.4, which are the maximal probabilities that the full and scaled logistic functions can reach over the range of x. We used the top 10th percentile of sites where Pr(s=1|x) are highest as the locations with LKN.In their paper, Hastie and Fithian  demonstr33.1Pr(y=1|x) is plotted against x. In these figures, the black line gives the original parametric functions selected as given in Table Pr(y=1|x), with the mean estimates close to the true functions. Both methods have similarly small RMSEs for the fitted probabilities against the true probabilities  also improves the accuracy of our method compared to the logistic regression classification method.Figure The brown dashed lines in the bottom panel of Figure Comparable results were also observed for cloglog functions (see Appendix Phillips and Elith  and Soly2.2% of times when the function satisfies the LC condition. The failure rate increases to 31.4% (for the quadratic logistic function in category 3) when the LC is not met, while in both cases, the quadratic functions still satisfy the RSPF condition. Similar behavior is also observed for mis‐specified models  were observed in our simulations. The nonconvergence rate (see Table 3.2f1(x) and a scaled logistic f2(x) which is exactly half of the full logistic function f1(x). The top panels in Figure f1(x) & f2(x) given by Hastie and Fithian (Hastie and Fithian  showed t Fithian .f1(x) and f2(x) are exactly the same. Thus, when we attempted to fit the two different datasets , the LK method gave exactly the same parameter estimates for the βi for both functions. This is confirmed in our simulation when large sample sizes are applied. The LK method yields the same estimates for both the full and the scaled logistic functions. Thus despite the fact that f2(x)=12f1(x) ≈f^1(x). Figure Pr(y=1|x) are available for both the full and scaled logistic regressions. The predicted functions from the refined CLK method align closely with both the true probability functions, with small variations observed between replications  of a species using presence‐background (or use‐availability) data. To estimate the resource selection probability, either a strong parametric assumption such as the logit function requirement for the LK method or extra information such as the population prevalence  has been proposed  probability of presence from the PB data. This condition relaxes the commonly recognised population prevalence and helps overcome the identifiability issue inherent in the proportional LK likelihood function, that is, the problem Hastie and Fithian  elaboratOther related ideas of anchoring the presence probability also exists, such as using extra effort at a subset of sites  or integration of presence‐only with presence‐absence data =1 is satisfied at the PPL  from the observed presences and background points (or the presence locations). As one reviewer pointed out, users could enlarge the study area so that it is more likely to include certain PPL in study area, because under the LC or the positive subdomain assumption there will be locations for which Pr(y=1|x)=1 . In our numerical studies, a simple logistic regression as the classifier gave poor results when compared to the neural network (comparative results not shown). That is the reason we used the neural network in classifying Pr(s=1|x) versus Pr(s=0|x). Similar as other ML methods, our proposed approach also requires reasonably large background samples to enable reliable estimation, whereas the selection of large background samples can be easily achieved in practice.The PBL method  on the LKN at some sites. This could be a potential research to extend the CLK method in the framework of Bayesian analysis. Meanwhile, this paper assumes presence sample is SCAR, where there is either no sampling bias or the sampling effort and presence of species are conditionally independent given5Estimating the absolute probability of presence from presence only data is an ill‐defined problem. In order for the probability identifiable, additional assumption is necessary. This paper first shows that the proper condition to estimate the absolute probability of presence is not the RSPF conditions as the LK method has claimed. We found that the LK method is fragile and often fails to give reliable estimates even when the RSPF conditions are satisfied. Rather, we propose the LKN condition, which relaxes the predetermined population prevalence condition that has so often been used in much of the existing literature. The proposed concept of LKN extends the LC or the PPL assumption when the latter is not satisfied. The concept has significant implications for demonstrating the necessary assumption to possibly estimate the absolute probability of presence from PB data in species distribution modelling.Yan Wang: Conceptualization (lead); Formal analysis ; Funding acquisition (lead); Methodology (lead); Supervision (supporting); Writing—original draft ; Writing—review and editing (lead). Chathuri L. Samarasekara: Conceptualization (supporting); Formal analysis ; Methodology (supporting); Writing—original draft ; Writing—review & editing (supporting). Lewi Stone: Conceptualization ; Methodology (supporting); Supervision (supporting); Writing—original draft (supporting); Writing—review and editing (supporting).There are no conflicted of interest from the authors.


This paper is part of a broader investigation into the ways in which health and social care guideline producers are using qualitative evidence syntheses (QESs) alongside more established methods of guideline development such as systematic reviews and meta-analyses of quantitative data. This study is a content analysis of QESs produced over a 5-year period by a leading provider of guidelines for the National Health Service in the UK  to explore how closely they match a reporting framework for QES.Guidelines published or updated between Jan 2015 and Dec 2019 were identified via searches of the National Institute for Health and Care excellence (NICE) website. These guidelines were searched to identify any QES conducted during the development of the guideline. Data relating to the compliance of these syntheses against a reporting framework for QES (ENTREQ) were extracted and compiled, and descriptive statistics used to provide an analysis of the of QES conduct, reporting and use by this major international guideline producer.QES contributed, in part, to 54 out of a total of 192 guidelines over the five-year period. Although methods for producing and reporting QES have changed substantially over the past decade, this study found that there has been little change in the number or quality of NICE QESs over time. The largest predictor of quality was the centre or team which undertook the synthesis. Analysis indicated that elements of review methods which were similar to those used in quantitative systematic reviews tended to be carried out well and mostly matched the criteria in the reporting framework, but review methods which were more specific to a QES tended to be carried out less well, with fewer examples of criteria in the reporting framework being achieved.The study suggests that use, conduct and reporting of optimal QES methods requires development, as over time the quality of reporting of QES both overall, and by specific centres, has not improved in spite of clearer reporting frameworks and important methodological developments. Further staff training in QES methods may be helpful for reviewers who are more familiar with conventional forms of systematic review if the highest standards of QES are to be achieved. There seems potential for greater use of evidence from qualitative research during guideline development.The online version contains supplementary material available at 10.1186/s12874-022-01743-1. Evidence-based health and social care guidelines  are part of the landscape of evidence-based health and social care in many countries. These guidelines are normally based on one or more analyses of relevant evidence, often in the form of systematic reviews of effectiveness data, and often interpreted by an expert committee.Even though methods for synthesising qualitative research have been around for many years, interest in the use of qualitative evidence to inform the development of these guidelines has grown considerably over recent years. This is partly because of key developments such as more robust methods of synthesis, development of tools like GRADE CERQual and better frameworks for reporting qualitative studies  and partThe World Health Organization (WHO) handbook  affirms A short paper published by Tan and colleagues in 2009  exploredThey further noted that only five of the 22 guidelines which drew on qualitative research used (or documented) specific search strategies for qualitative literature over and above searches that were done for quantitative studies. Only four of the guidelines documented key methodological process details such as inclusion/exclusion criteria for qualitative studies.This study also highlighted a gap in the reporting of the reviews - only half (11/22) of the guidelines reported how critical appraisal of qualitative studies was carried out, and only three of the 22 reported how data were synthesised.The study concluded that “there is no consistency in how qualitative evidence is utilised in the development of NICE clinical guidelines. There are also clear training needs for NICE’s guideline developers in terms of how best to identify, quality appraise and synthesise qualitative evidence” (p.172).The work reported in this current paper updates the study by Tan and colleagues by exploring whether methodological changes within NICE, or development in methodological standards for QES have led to a change in their use in NICE guidelines. It also builds on a review of methodological literature by the current authors . The stuThe study used a content analysis method to analyse textual data.  BerelsonIn order to compare recent NICE guidelines with the sample included by Tan et al. , and to Using inbuilt functionality on the NICE website, a search was conducted for guidelines published between January 2015 and December 2019. This search encompassed the three types of evidence-based guideline produced by the guideline development centres at NICE, classified on the website as ‘public health’, ‘social care’ or ‘clinical’. It does not include guidelines where the method of development differed, that is, antimicrobial guidelines, cancer service guidelines, COVID-19 guidelines and medicines practice guidelines . The resulting list of guidelines was copied to the clipboard  and pasted into an excel spreadsheet .For each included guideline, the individual evidence reviews  were explored using the ‘evidence’ tab on the guideline webpage.Each evidence review was examined to evaluate whether or not a qualitative evidence synthesis  had been undertaken by the technical team (or a contractor) responsible for the development of the guideline. Evidence reviews that did not report the use of qualitative evidence synthesis  were excluded from the sample. Any qualitative reviews and mixed methods reviews identified were downloaded and saved. These formed the sample for the content analysis.Included QES were copied to a new excel spreadsheet and rationalised so that the unit of analysis was the qualitative evidence synthesis rather than the guideline . The coding framework (described below) was added to the spreadsheet to create a data extraction tool.The coding framework used was intended to provide two sets of data – descriptive data and content data.This included key data from the QES – guideline number, year of publication, author  and number of qualitative studies included in the analysis. The use of GRADE CERQual  to assesThe criteria set by ENTREQ  are the Each of the QES was read and descriptive data and content data were coded into an excel spreadsheet according to the framework described above and in Additional file 1. Coding was binary and indicated whether the QES reported on the criterion in the reporting framework or not. For example, did the QES report its aim? Did it report the synthesis methodology it is underpinned by? This approach did not allow for any judgment about the adequacy of each reporting criterion, only whether it was present or not. This approach was taken to allow for analysis of coding.Resulting data are presented predominantly as descriptive statistics to show trends, consistencies and inconsistencies in the data. Data were visualised using Microsoft Excel or were imported into the R program , using tBetween January 2015 and December 2019, NICE published 192 clinical, public health and social care guidelines. The website categorises the breakdown of these guidelines as 156 clinical, 30 public health and 48 social care guidelines, however this includes some guidelines listed in more than one category, hence the discrepancy in numbers. For the purposes of this analysis, pragmatic decisions were made about the main topic area of a guideline to assign each guideline to a single category, resulting in a breakdown of 143 clinically focussed guidelines, 25 public health focussed guidelines and 24 social care focussed guidelines. Each of these guidelines is based on multiple sources of evidence – most often systematic reviews of quantitative evidence, but also prognostic and diagnostic reviews (of the predictive or diagnostic accuracy of tests or indicators), epidemiological studies  and, more rarely, qualitative evidence syntheses. The total number of reviews  conducted for a guideline can range from one review for an update of a single clinical question to around 40 reviews for a large guideline with multiple questions. The reviews are conducted by expert review teams who present them to the guideline committee. The committee who undertake a structured discussion  of the evidence contained in the reviews , alongside any other evidence, and contextualise it using their expertise and experience of the UK health and social care system to make guideline recommendations. When a guideline is published, all of the evidence considered by the committee is also published alongside the guideline.Of the 192 guidelines referred to above, 54 guidelines (28%) had one or more QES as part of their evidence base . Overall, out of a total of approximatelyOf the 54 guidelines with one or more QES, 36  were clinically focussed, 13 (out of 25 [52%]) were public health focussed, 5 (out of 24 [21%]) were social care focussed. This shows that social care and clinically focussed guidelines are roughly half as likely to use qualitative evidence synthesis as public health focussed guidelines.The number of QES used per included guideline ranges from 1 to 6 .In terms of the number of included papers in the QES, there was a large amount of variation. The largest QES contained 69 papers, the smallest QES contained two papers. Distribution of QES by the number of included papers is shown in Fig. Overall, 65% (58 out of 90) of QES had less than 12 papers included, with a mode of four and a median of 10 papers. The four QES with more than 42 papers were from two guidelines ,17] and and17] aFigure There are a range of QES methodologies which vary widely on the epistemological spectrum, and in level of complexity, from aggregative approaches to more configurative/interpretive approaches. QES undertaken for NICE guidelines all use simpler descriptive or aggregative approaches. These syntheses can be used to address a range of issues that concern people’s  views, beliefs and lived experiences. While quantitative evidence is best for addressing questions of efficacy (does treatment A have an effect on condition B?), qualitative evidence can be useful to bridge the gap between efficacy and real-life effectiveness, for example understanding why people do not take their medicines as prescribed, how the medicines impact their lives and how things could be improved. In spite of this, guidelines produced by NICE in the period 2015–2019 seem to address a much more limited range of question types using QES. Almost half of the QES undertaken answer one of two types of question:What are the barriers and/or facilitators to……?What are the information (and support) needs of ……?Many of the remaining questions deal with similar question types, often about support and care needs. This may indicate a limited understanding in the NICE guideline development centres of the potential remit of QES and their flexibility with regards to issues such as service configuration, professional support etc. Other kinds of QES do include occasional innovative questions, for example one QES for guideline NG77 (management of cataracts in adults)  was emplThe 90 QES published by NICE between Jan 2015 and Dec 2019 were assessed against the ENTREQ reporting criteria as described in Table Analysis of number of guidelines meeting each of the ENTREQ criteria is shown in Fig. ENTREQ criteria relating to setting out the aim of the review and to the systematic searching and sifting of studies to generate a pool of included studies was generally done well and described adequately in the included QES. The exception to this was the synthesis methodology criterion . Many QES (40/90) were marked down on this criterion because either they only provided a brief sentence or statement to describe the methods of data synthesis used, for example “We undertook thematic synthesis”, with no methodological detail, or simply provided inadequate descriptions of methodology, often not specifying an approach to synthesis at all.Derivation of themes (described by the ENTREQ statement as “Explain whether the process of deriving the themes or constructs was inductive or deductive”) was demonstrated in a third of QES, and these were mostly undertaken by a particular guideline developer who present a ‘theme map’ as a standard part of their QES.In 70 of the reviews, synthesis output  was reported. This was mostly in the form of NICE evidence statements, although some evidence statements made no attempt at synthesis and simply listed the themes identified by individual studies. Some QES used a Cochrane style ‘Summary of qualitative findings’ table to present synthesised themes and sub-themes along with their CERQual confidence rating. Other than that, CERQual was not often used. This does not seem to be dependent on the age of the review  but seems to depend more on the guideline developer.It might be expected that adherence to reporting frameworks improves over time as methods for undertaking QES become more robust and more widely known. It might also be expected that guideline developers would develop their methods for QES (and train their staff in those methods), and that more recent iterations of the NICE guideline methods manual might give clearer direction on its expectations from QES.Figure Data suggest that in fact there is little variation over time, but that the main determinant of the number of ENTREQ criteria reported is the guideline developer who authored the review. Of the two guideline developers who authored the majority of the QES in the past 5 years, one reasonably consistently reports around 11–13 criteria (Centre 7), whereas the other performs better in 2016 and 2017, but drops to a similar level in 2018 and 2019 (Centre 6). It is unclear what may drive the drop. Two possible confounding factors are the publication of the new NICE methods manual . T. T19]. TThe focus of health guideline producing bodies on the use of systematic reviews of quantitative evidence and the relatively small amount of QES means that there is no noticeable improvement over time in the quality of QES produced. QES that are not produced by contractors who specialise in qualitative methods often lack transparent reporting of those aspects of the qualitative evidence synthesis that differ from the stages of a quantitative systematic review.The clearest factor in the quality of a QES seems to be the team that undertook it. Teams which produce well-reported QES seem to do so consistently, and we can speculate that this may because they have staff with a particular interest or skill set in this area. Solutions to this might include ensuring that staff undertaking QES have appropriate skills and supervision, and providing clearer guidance about how a QES should be undertaken .Below is the link to the electronic supplementary material.Supplementary Material 1Supplementary Material 2


Bile acids (BAs) are important steroidal molecules with a rapidly growing span of applications across a variety of fields such as supramolecular chemistry, pharmacy, and biomedicine. This work provides a systematic review on their transport processes within the enterohepatic circulation and related processes. The focus is laid on the description of specific or less-specific BA transport proteins and their localization. Initially, the reader is provided with essential information about BAs′ properties, their systemic flow, metabolism, and functions. Later, the transport processes are described in detail and schematically illustrated, moving step by step from the liver via bile ducts to the gallbladder, small intestine, and colon; this description is accompanied by descriptions of major proteins known to be involved in BA transport. Spillage of BAs into systemic circulation and urine excretion are also discussed. Finally, the review also points out some of the less-studied areas of the enterohepatic circulation, which can be crucial for the development of BA-related drugs, prodrugs, and drug carrier systems. Bile acids (BAs) are a group of steroids formed during the enzymatic catabolism of cholesterol in the hepatocytes of the liver ,2. The bBAs have a rigid tetracyclic steroid skeleton, which is decorated by various numbers of reactive hydroxy groups of defined stereochemistry and by a flexible alkyl side chain bearing a carboxyl functional group . These u1) will not be absorbed, and a deficiency will occur. The mixed micelle formation also promotes cholesterol elimination. Additional function of BAs in digestive process can be in the form of their solubilization of polyvalent metals, such as iron and calcium in the duodenum, promoting their absorption [Bile is an aqueous solution composed of mostly bile salts, phospholipids, cholesterol, and biliary pigment proteins. Bile is concentrated and stored in the gallbladder and plays a major role in enterohepatic circulation . After fsorption .After performing their role in digestion, bile salts are deconjugated by bacterial enzymes and then almost completely reabsorbed in the small intestine and colon by both active and passive mechanisms of the enterohepatic circulation . It is iBA metabolism is closely related to the metabolism of cholesterol; altering the cholesterol level alters levels of BAs and vice versa. Cholesterol is essential for all animal life. It composes about 30% of animal cell membranes. Cholesterol is also implicated in cell signaling processes and regulation of substrate presentation and is an important chemical precursor for the synthesis of vitamin D, BAs, and all steroid hormones—i.e., adrenal gland hormones cortisol and aldosterone or sex hormones progesterone, estrogen, testosterone, and their derivatives .For a long time, BAs were thought to function purely as compounds that would solubilize lipids and facilitate uptake of lipid-soluble vitamins through the mechanisms described above. It was not until quite recently that the scientific world started to understand that BAs are not only detergents, but also important signaling molecules that affect various receptors ,26,27. BNuclear farnesoid X receptor (FXR) can serve as an example to show the complexity of the subject. FXR plays a major role in BA homeostasis, but also affects, directly or indirectly, glucose metabolism and can influence drug metabolism ,20. For A large amount of experimental data is based on animal models, mainly on mice. Animal models have helped us to better understand biosynthesis, enterohepatic circulation, and metabolism of BAs. However, there are several major differences between mice and humans one must keep in mind when interpreting and extrapolating experimental data ,36. The There are also noteworthy differences between sexes in the biochemistry of BAs. In female mice, the BA pool is approximately 60% larger and more hydrophobic than in males. In humans, however, unlike female mice, women have a lower BA pool size compared to men . As far Apart from more “traditional” animal models, “humanized” mouse models where the liver better resembles that in humans could be used. In such cases, individual or small groups of genes in mice can be replaced by their human counterparts—however, more data are required to demonstrate the accuracy of the evaluation of outcomes ,42. RodeCholestasis is a term which will be used in the following chapters when describing the transport of BAs in the enterohepatic circulation. It refers to impairment of or reduction in bile flow. This pathological condition can occur when the biliary tree is blocked or when bile secretion by hepatocytes into the bile canaliculi is impaired ,45. If bbsep gene in mice resulted in intrahepatic cholestasis [From a general point of view, enterohepatic circulation allows for the recycling of metabolized and non-metabolized compounds . It involestasis ,49.Under normal physiological conditions, BAs follow a defined route of transport within the body . BA flowa of the unconjugated BAs is between 5–6.5 [a of conjugated BAs is lower, between 1–4, thus they are present in their deprotonated form in the duodenum, which makes them significantly more water-soluble and thus able to function as emulsifiers in the digestion process [The pKen 5–6.5  and the  process . However process ,52. A pr process . Some ofA small number of BAs also spills into general circulation, e.g., BAs have been detected in the ovaries, heart, and brain. It is not yet fully clear what purpose they serve in these organs ,52. HoweBas, when present at high concentrations, can exert cytotoxic effects. It is possible that as a way to control and prevent the toxicity of BAs, BA levels can be regulated by nuclear receptor sensing, which is detecting and controlling their concentrations within the body. A major role is played by the nuclear receptor farnesoid X receptor (FXR), also known as bile-acid receptor or NR1H4, which is highly expressed in the liver and gut, likely because hepatocytes and bile duct cells are not only the major cells involved in the synthesis and metabolism of BAs, but are also at the highest risk of cytotoxicity ,20. ManyOne receptor that could potentially protect liver from toxicity of high concentrations of BAs is pregnane X receptor (PXR). This receptor functions as a xenobiotic sensor that can induce the removal of potentially harmful chemicals from the body. PXR could induce the formation of BA conjugation enzymes and, in addition, could suppress CYP7A1 and thus decrease the BA pool. However, it is still being studied if and to what extent this receptor is activated by BAs. The current evidence suggests that PXR is only activated under extreme concentrations of lithocholic acid which even exceed levels observed in patients with severe cholestasis ,57,58.Vitamin D receptor (VDR) is usually activated by vitamin D. VDR is expressed mostly in osteoblasts, kidneys, and in many types of immune cells, but it can also be found in intestines and to some degree in the liver. VDR plays a central role in the biological function of vitamin D—regulation of calcium homeostasis, cellular proliferation, and immunity. Activation of VDR by secondary BAs was found to induce BA-metabolizing cytochrome P450 (CYP3A4) that detoxifies BAs in the intestine. Similarly to PXR, lithocholic acid showed the ability to activate VDR and thus influence the regulation of genes involved in BA metabolism and transport ,59,60.The enterohepatic circulation of BAs involves their transport in the liver from portal blood (liver sinusoids) into bile canaliculi, which occurs across the hepatocytes and against a concentration gradient . Moreove+/taurocholate-co-transporting polypeptide (NTCP) and organic-anion-transporting polypeptides (OATPs) [An overview of hepatocellular transport can be seen in  (OATPs) ,18,52. S (OATPs) , but exp (OATPs) .Efflux of BAs from the basolateral membrane is negligible under normal physiological conditions but can occur in cholestasis. BAs would then be returned to blood by the multi-drug-resistance-associated protein 3 or 4 (MRP3 or MRP4) ,52. UncoIn general, the intracellular transport of BAs across the hepatocyte is not well understood. It is possible that it is facilitated by either intracellular trafficking or by vesicle-mediated transport. Under normal physiological conditions, a large portion of BAs is bound to intracellular binding proteins and diffuses into the canalicular membrane in this form. When presented with higher BA loads, an increasing amount is transported by organelles such as the endoplasmic reticulum or Golgi apparatus ,64.The next step, BA canalicular secretion, determines at what rate the bile is formed. After crossing the hepatocyte, BAs are exported into the canaliculus by BSEP. Phosphatidylcholine (PC) is also transported from the inner part of the apical membrane by multi-drug-resistance protein 3, MDR3 and then is mixed with BAs secreted by BSEP. MRP2 is capable of transporting BAs into the bile canaliculus, but it cannot transport non-sulfated monovalent BAs. Aquaporins  secrete water into bile ,52,64.BAs that escape clearance by hepatocytes are filtered at the glomerulus from plasma into urine. Under normal conditions, the majority of BAs are reabsorbed, and urinary BA levels are therefore minimal. Under cholestasis, renal excretion of BAs can become an important alternative pathway which helps to maintain homeostasis . For exa+-dependent and Na+-independent mechanisms. NTCP is a member of the solute carrier (SLC) group of membrane transport proteins, which is comprised of more than 450 members categorized into 65 superfamilies [slc10a1 [+-dependent uptake of BAs. The Na+-dependent method of transport is considered to be responsible for more than 80% of conjugated taurocholate uptake but also less than 50% of unconjugated cholate uptake [In general, BAs are transported into hepatocytes by both Nafamilies . Specifi[slc10a1 . NTCP, ae uptake ,64,68. Ne uptake ,64.+ gradient. This gradient is maintained by basolateral Na+/K+ ATPase, the outward diffusions of K+, and the cell’s natural intracellular potential. The electronic transport of Na+/taurocholate seems to happen in stoichiometry of at least 2:1 [The force which allows for the transport is provided by the inwardly directed Naeast 2:1 ,69. The east 2:1 .It was reported that NTCP is localized only at the basolateral membrane of hepatocytes . HoweverNTCP deficiency in some patients indicates that there are different ways and mechanisms through which BAs can enter the hepatocytes, as some patients studied with NTCP deficiency had no clinical signs of liver disfunction ,72. Howe+-independent BA transport is mediated by OATPs. This method of transport is currently considered quantitatively less significant than the Na+-dependent method manifested by NTCP [+-dependent transporters evolved more recently [Na by NTCP ,64. Na+-recently ,73.slco genes. Eleven human OATPs have been identified and classified into six subfamilies (1–6). Due to gene duplication and divergence, different orthologs can be found in humans (OATP) and rodents (Oatp): OATP1A2 has five rodent orthologues: Oatp1a1, Oatp1a3 (in rats only), Oatp1a4, Oatp1a5, and Oatp1a6. OATP1B1 and OATP1B3 have a single rodent ortholog, Oatp1b2. The other OATPs and their rodent orthologs are OATP1C1 (Oatp1c1), OATP2A1 (Oatp2a1), OATP2B1 (Oatp2b1), OATP3A1 (Oatp3a1), OATP4A1 (Oatp4a1), OATP4C1 (Oatp4c1), OATP5A1, and OATP6A1  [OATP belongs to SLC family 21, encoded by Oatp6d1) .Members of the OATP family are multispecific transporters responsible primarily for cellular uptake of a broad range of large, fairly hydrophobic, and mostly anionic substrates, including bile acids, steroid conjugates, and numerous xenobiotics. Apart from both conjugated and unconjugated BAs, OATPs have wide substrate specificity which, for example, includes bilirubin and many drugs used clinically such as statins, macrolide antibiotics, and antihistamines ,64,74. O+-independent BA transport is thought to be responsible for 20–25% of total uptake from portal blood, as shown on rat hepatocytes. This transport process is higher for unconjugated Bas, where it seems to be responsible for most of the uptake. Transport of unconjugated BAs can, however, occur by passive diffusion as well [+-dependent or independent mechanism, e.g., BAs with a hydroxy group at carbon position C6 prefer Na+-dependent uptake [Na as well ,62. The t uptake .3− or deprotonated glutathione [The transport mechanism appears to be largely mediated by exchange with intracellular anions such as HCOtathione ,64.abcc3 gene) and MRP2 (encoded by abcc2 gene) are significantly present in the liver, where MRP3 is located at the basolateral surface while MRP2 is located at the canalicular surface (more on this protein in the next section). Function of MRP3 and MRP2 seems to be bound together—levels of MRP3 increase whereas MRP2 decreases under cholestasis conditions. This seems to protect the liver from toxicity of high concentrations of BAs [abcc4 gene), which seems to contribute to the elimination of BAs from the hepatocyte to sinusoidal blood. MRP3 is also expressed the most during cholestasis [In the basolateral membrane of hepatocytes, BA uptake is the predominant path of transport under normal physiological conditions. Increased efflux of BAs can, however, occur under cholestatic conditions. Efflux transport systems are manifested by the MRP subfamily, which belongs to the class of ATP-binding cassette (ABC) transport proteins ,64,78. Ts of BAs . BAs werlestasis . Anotherlestasis .During cholestasis, there is a significantly increased expression of MRP1 and MRP3, which are responsible for the transport and elimination of sulphated and glucuronidated BAs as elimination products excreted in urine .abcb11 gene, which belongs to the ABC superfamily of transporters [Canalicular secretion at the apical side of hepatocytes is often regarded as the rate controlling step of BA transport through the hepatocytes. BSEP is thought to be the most dominant transporter of the canalicular membrane responsible for the excretion of BAs into bile, which runs against a steep concentration gradient. BSEP, also known as a “sister of P-glycoprotein”, is encoded by the sporters ,52,78,81Thus far, it is understood that there is no backup transporter for the canalicular export of BAs in humans, as inactivation of BSEP leads to liver damage. Progressive familial intrahepatic cholestasis type 2 could serve as an example—here, the deficiency of BSEP is inherited and leads to lethal progressive familial intrahepatic cholestasis ,82. On tBSEP mainly transports primary and secondary BA salts as well as UDCA and its conjugates. As an example, chenodeoxycholic acid seems to be eliminated by BSEP at a faster rate compared to cholic acid. This might be because of the fact that chenodeoxycholic acid and its conjugates are potentially more toxic for hepatocytes even at lower concentrations, hence faster elimination is desirable. UDCA showed the lowest toxicity in this study done on mice ,83.Although BSEP does not seem to transport drugs or drug metabolites, some compounds may act as competitive BSEP inhibitors. This can lead to cholestasis and potential liver injury. Thus, many pharmaceutical companies incorporated BSEP inhibition into their in vitro screening panels in preclinical studies . Howeverabcb1 gene) is known to affect the distribution of various drugs in the body. However, it is expressed only at relatively low levels in normal healthy livers. The canalicular membrane of hepatocytes contains MDR3 (encoded by the abcb4 gene), which is structurally similar to MDR1, as it shares 77% of its amino acid composition, but it is functionally a different transporter. MDR3 is a PC transporter which is capable of translocating phospholipids to the outer side of the membrane lipid bilayer. In contrast to MDR1, MDR3 does not seem to be able to transport drugs directly [MDR proteins, or P-glycoproteins, also belong to the superfamily of ABC transporters, which represents ATP-dependent efflux pumps with broad substrate specificity. MDR1, or P-glycoprotein,  is directed towards the canalicular system. It is responsible for the transport of a wide range of substrates—including bilirubin conjugates, drug metabolites, unconjugated drugs and glucuronide, and sulfate or glutathione conjugates—including conjugates of BAs or drugs [In contrast to MRP3 and MRP4, MRP2 —this helps to generate bile flow as well as makes cholangiocytes less likely to undergo apoptosis. Absorbed BAs are then moved across the basolateral membrane by MRP3, organic solute transporter α/β (OST), or by the truncated form of ASBT (tASBT) ,52,93,99slc10a2 gene, which represents another member of SLC family 10, similarly to NTCP. The role of ASBT in bile ducts might not be as obvious as in the small intestine or kidney. Uptake of BAs is sodium-dependent and activates cholehepatic shunting as described previously [ASBT is a protein that was first identified in the renal tubule and is mainly present in the small intestine, thus it is also known as ileal bile acid transporter (IBAT). ASBT is encoded by the eviously ,97. ASBTeviously ,100.3− apical barrier, which might keep certain BA conjugates in a deprotonated and membrane impermeable form, thus protecting the cholangiocytes against potential BA toxicity at high concentrations [It was proposed that the interaction of ASBT with BAs could also lead to a certain protection mechanism, such as stabilization of the HCOtrations .Cholangiocytes were found to express AQP1 at both the apical and basolateral membranes C. Secret+-independent Cl−/HCO3− exchanger, which is encoded by slc4a2 (ae2) gene of SLC family 4 [3− secretion into bile [3−, also known as the HCO3− umbrella, might be a key protective mechanism [CBIE, or anion exchange protein 2, is a Nafamily 4 . CBIE innto bile ,95,103. nto bile . Penetraechanism ,105. Cerechanism ,105.As can be seen from the previous sections, MRP3 can be found in various parts of enterohepatic circulation. It can also transport BAs across the basolateral membrane of cholangiocytes into the peribiliary plexus. Levels of MRP3 can be increased with various forms of cholestasis ,64,106.In addition to AQP1, which is found also in the apical membrane, transport of water across basolateral membrane is also facilitated by AQP4. This allows maintenance of the isosmolar status of the cells during bile formation .slc51a and slc51b [+, K+, H+, and Cl− gradients and ATP levels; hence, it seems to transport substrates by simply allowing them to passively move according to their concentration gradient [OST is a transporter localized in the basolateral membrane of different epithelial cells involved in the enterohepatic circulation. It advocates for Na+-independent efflux of BAs across the basolateral membrane. OST is a heterodimer and requires coexpression of both OSTα and OSTβ proteins, which are encoded by genes from the SLC family 51, d slc51b ,103,107.d slc51b . OST tragradient ,109.The spliced form of ASBT or truncated ASBT which, in contrast to ASBT, can function as a basolateral BA transporter. Its specific contribution to the efflux of BAs, however, seems to be minor or uncertain ,110.+, Cl−, and HCO3−, leading to passive transport of water—this involves AQPs at both the apical and basolateral membranes [− mostly in a Na+-dependent manner achieved by interaction with ASBT at the apical membrane. Na+-independent secretion could be related to the interaction of BAs with OATPs, such as OATP1A2, which are, however, expressed only in low levels and may probably occur across both the apical and basolateral membranes. Mucin secretion serves as a defense mechanism that protects the epithelium surface. Cl− secretion in turn promotes secretion of HCO3− and water—this is most likely the mechanism that aids the gallbladder in emptying [Gallbladder epithelium has also an ability to modify the composition of bile. Gallbladder epithelial cells and cholangiocytes share many functions and are similar in the composition of transport proteins, yet their physiological roles are quite different ,64,92. Tembranes . BAs stiemptying . MRP2 waemptying .a value of 2 for taurine and 4 for glycine conjugates, while the intestinal pH normally exceeds 5, making the BA salts fully ionized. This prevents them from penetrating the cell membranes of enterocytes and thus enables reaching the CMC. Moreover, molecules of BA salts are too large to pass across paracellular junctions [After meal ingestion, but also following olfactory or visual sensing of food, BAs are excreted from the gallbladder into the duodenum, where they participate in the absorption of lipids and lipid-soluble vitamins by acting as biosurfactants ,112,113.unctions .a values can be freely transported by passive diffusion, this only accounts for a small fraction of their transport [BAs are not actually essential to the digestion of dietary fats but are necessary for their effective or complete absorption ,116,117.ransport . The terransport ,120. In ransport . The conransport ,121,122.ransport ,123.Due to the lack of data on the other intestinal pathways, only the ileal transport will be described in more depth. Its overview can be seen in ASBT is a protein which was already introduced in connection to cholangiocytes. Nevertheless, regarding the small intestine and enterocytes, there is more data available. This is partly because the studies in this area are motivated by ASBT’s important role in drug or drug-carrier delivery. Secondly, ASBT is expressed much more in the terminal ileum than in the biliary epithelium ,125,126.+/K+-ATPase, which maintains the Na+-concentration gradient. The binding of the substrates in the extracellular pocket along with Na+ binding drives the conformational change between the outward- and inward-facing states of ASBT, opening the cytoplasmic channel to traverse BAs. Thus far, the crystal structure of mammalian ASBT has not been determined, making the understanding of the exact mechanisms of substrate binding and transport at the molecular level limited [Neisseria meningitidis and Yersinia frederiksenii have been reported [The ASBT is responsible for most BA absorption from the gut lumen. The transport proceeds in an electrogenic and Na+-dependent manner with a stoichiometry of sodium to BA of 2:1. In other words, BA uptake is driven by the negative intracellular potential and Na limited ,126,127.reported .Concerning substrate specificity, ASBT transports hydrophilic conjugated BAs more efficiently than hydrophobic unconjugated BAs. However, dihydroxy BAs seem to have a higher affinity for ASBT-mediated transport than trihydroxy BA . AlthougOral delivery of drugs is a challenging field. The digestive system is naturally designed to degrade proteins and peptides chemically and enzymatically into shorter peptides and amino acids and lipids (triglycerides) into fatty acids, monoglycerides, and free glycerol prior to absorption. For systemic drug absorption, the drug molecule must pass through the gastrointestinal tract intact . Therefoslc10a2 can cause BA malabsorption, chronic diarrhea, fat-soluble vitamin malabsorption, and reduced plasma cholesterol levels [Unsurprisingly, defects in ASBT transport activity or regulation may result in a variety of gastrointestinal disorders, such as Crohn’s disease. Mutation in ASBT gene l levels . On the l levels ,128,132.l levels ,132,133,l levels ,134. On l levels .fabp6 gene. IBABP is primarily expressed by enterocytes, where it is responsible for the shuttling of BAs across the cytosol to the basolateral membrane. Much lower levels of expression of this protein are also shown in cholangiocytes [IBABP, also known as fatty acid binding protein 6, is encoded by the giocytes ,125. Onegiocytes . Currentgiocytes .Proposed transport mechanisms through ileal enterocytes are illustrated in This protein was already introduced in This protein was previously described regarding its function on both hepatocytes and cholangiocytes (2.1 and 2.2). In the intestine, it was assumed that MRP3 plays a significant role in the enterohepatic circulation of BAs. However, it was later discovered that its contribution to intestinal absorption is only minor, as was shown in animal studies ,142,143.Lastly, tASBT is a special form of ASBT with different transporting mechanisms. Its expression was previously mentioned regarding cholangiocytes. It functions as BA efflux protein in the ASBT-expressing epithelium ,126.a of BAs, making passive absorption more likely. Although this is not a major site of transport, colonic absorption may play an important role in cases of BA malabsorption in other parts of enterohepatic circulation [Most BAs encounter low populations of bacteria in the small intestine and return to the liver relatively unchanged. However, the remaining 5% of BAs that avoid active and passive transport in the small intestine enter the colon, which is home to an ecosystem of complex microbial flora. Here, the deconjugation of conjugated BAs via the action of bacterial enzymes occurs ,145,146.culation .Bile acids (BAs) are no longer believed to be just simple molecules involved in digestion. The field of chemistry and biochemistry of BAs has advanced greatly during recent decades, possibly due to their growing role in pharmacy and biomedicine. Quite recently, new discoveries were made about their role as hormone-like signaling molecules. In this review, we summarize up-to-date knowledge obtained about BA transport proteins, their presence, and processes involved in the enterohepatic circulation, which are complemented by graphical illustrations. Moreover, BA transport through the liver, biliary ducts, gallbladder, and intestines are described as well as BA urinary output and spillage into systemic circulation. Major transport proteins such as NTCP, OATP, ASBT, and IBABP involved in BA circulation are described in depth. This overview sets to provide an elemental understanding of the complexity of BA biochemistry, which is crucial in the development of BA-derived drugs, prodrugs, or drug carrier systems.Still, much remains unknown in this field. The crystal structure of mammalian ASBT has not been solved to date, which also represents one of the limiting factors in fully understanding BA transport in the small intestine. It has also been proposed that there is still an undiscovered BA transport mechanism taking place in hepatocytes which could additionally contribute to the understanding of processes involved and ultimately lead to novel approaches in drug design. The transport of BAs in cholangiocytes is not nearly as well studied as transport in enterocytes and hepatocytes. Possible mechanisms of transport of the nanoparticle form of prodrugs have been proposed for enterocytes; however, such studies are missing for hepatocytes. Additionally, the understanding of the transport of nanoparticles from the small intestine into the liver is low.Finally, we anticipate further development and exciting discoveries in the chemistry and biochemistry of BAs, their pathways, and of their role in the enterohepatic circulation and beyond in the years to come, to which we also wish to contribute.TM , Scopus® , and PubMed® . Major search terms  included “Bile acid”, “Bile Salt”, “Enterohepatic circulation”, “NTCP”, “ASBT”, “IBABP”, “OATP”, “MRP”, “MDR” (abbreviated or full names), “Drug delivery”, “Drug carrier”, and their combinations. The search results were manually curated and organized using Zotero . Titles and abstracts of the studies were screened and selected according to their relevance. Full texts were then reviewed, and highly relevant papers  indicated further sources  not found by searching the databases. Relevant information was compiled into a comprehensive narrative synthesis of previously published work (1) to address the key components and processes involved in enterohepatic circulation of BAs, (2) to provide new insights emphasizing previously nonobvious connections between enterohepatic circulation and BA-related drugs, prodrugs, and drug carrier systems.This paper represents a narrative review which consolidates previous work in a descriptive and nonquantitative manner. The literature search was conducted using scientific literature databases Web of Science