Identification of long-lived proteins reveals exceptional stability of essential cellular structures.

Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell's life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process. PAPERCLIP:

Specificity and nonspecificity in RNA-protein interactions.

To fully understand the regulation of gene expression, it is critical to quantitatively define whether and how RNA-binding proteins (RBPs) discriminate between alternative binding sites in RNAs. Here, we describe new methods that measure protein binding to large numbers of RNA variants, and ways to analyse and interpret data obtained by these approaches, including affinity distributions and free energy landscapes. We discuss how the new methodologies and the associated concepts enable the development of inclusive, quantitative models for RNA-protein interactions that transcend the traditional binary classification of RBPs as either specific or nonspecific.

The effect of climate change on avian offspring production: A global meta-analysis.

Climate change affects timing of reproduction in many bird species, but few studies have investigated its influence on annual reproductive output. Here, we assess changes in the annual production of young by female breeders in 201 populations of 104 bird species (N = 745,962 clutches) covering all continents between 1970 and 2019. Overall, average offspring production has declined in recent decades, but considerable differences were found among species and populations. A total of 56.7% of populations showed a declining trend in offspring production (significant in 17.4%), whereas 43.3% exhibited an increase (significant in 10.4%). The results show that climatic changes affect offspring production through compounded effects on ecological and life history traits of species. Migratory and larger-bodied species experienced reduced offspring production with increasing temperatures during the chick-rearing period, whereas smaller-bodied, sedentary species tended to produce more offspring. Likewise, multi-brooded species showed increased breeding success with increasing temperatures, whereas rising temperatures were unrelated to reproductive success in single-brooded species. Our study suggests that rapid declines in size of bird populations reported by many studies from different parts of the world are driven only to a small degree by changes in the production of young.

The specificity landscape of bacterial ribonuclease P.

Developing quantitative models of substrate specificity for RNA processing enzymes is a key step toward understanding their biology and guiding applications in biotechnology and biomedicine. Optimally, models to predict relative rate constants for alternative substrates should integrate an understanding of structures of the enzyme bound to "fast" and "slow" substrates, large datasets of rate constants for alternative substrates, and transcriptomic data identifying in vivo processing sites. Such data are either available or emerging for bacterial ribonucleoprotein RNase P a widespread and essential tRNA 5' processing endonuclease, thus making it a valuable model system for investigating principles of biological specificity. Indeed, the well-established structure and kinetics of bacterial RNase P enabled the development of high throughput measurements of rate constants for tRNA variants and provided the necessary framework for quantitative specificity modeling. Several studies document the importance of conformational changes in the precursor tRNA substrate as well as the RNA and protein subunits of bacterial RNase P during binding, although the functional roles and dynamics are still being resolved. Recently, results from cryo-EM studies of E. coli RNase P with alternative precursor tRNAs are revealing prospective mechanistic relationships between conformational changes and substrate specificity. Yet, extensive uncharted territory remains, including leveraging these advances for drug discovery, achieving a complete accounting of RNase P substrates, and understanding how the cellular context contributes to RNA processing specificity in vivo.

Kinetic analysis of RNA cleavage by coronavirus Nsp15 endonuclease: Evidence for acid-base catalysis and substrate-dependent metal ion activation.

Understanding the functional properties of severe acute respiratory syndrome coronavirus 2 nonstructural proteins is essential for defining their roles in the viral life cycle, developing improved therapeutics and diagnostics, and countering future variants. Coronavirus nonstructural protein Nsp15 is a hexameric U-specific endonuclease whose functions, substrate specificity, mechanism, and dynamics are not fully defined. Previous studies report that Nsp15 requires Mn2+ ions for optimal activity; however, the effects of divalent ions on Nsp15 reaction kinetics have not been investigated in detail. Here, we analyzed the single- and multiple-turnover kinetics for model ssRNA substrates. Our data confirm that divalent ions are dispensable for catalysis and show that Mn2+ activates Nsp15 cleavage of two different ssRNA oligonucleotide substrates but not a dinucleotide. Biphasic kinetics of ssRNA substrates demonstrates that Mn2+ stabilizes alternative enzyme states that have faster substrate cleavage on the enzyme. However, we did not detect Mn2+-induced conformational changes using CD and fluorescence spectroscopy. The pH-rate profiles in the presence and absence of Mn2+ reveal active-site ionizable groups with similar pKas of ca. 4.8 to 5.2. An Rp stereoisomer phosphorothioate modification at the scissile phosphate had minimal effect on catalysis supporting a mechanism involving an anionic transition state. However, the Sp stereoisomer is inactive because of weak binding, consistent with models that position the nonbridging phosphoryl oxygen deep in the active site. Together, these data demonstrate that Nsp15 employs a conventional acid-base catalytic mechanism passing through an anionic transition state, and that divalent ion activation is substrate dependent.

What would primary care practitioners do differently after a delayed cancer diagnosis? Learning lessons from their experiences.

OBJECTIVE: Diagnosis of cancer is challenging in primary care due to the low incidence of cancer cases in primary care practice. A prolonged diagnostic interval may be due to doctor, patient or system factors, or may be due to the characteristics of the cancer itself. The objective of this study was to learn from Primary Care Physicians' (PCP) experiences of incidents when they had failed to think of, or act on, a cancer diagnosis. DESIGN: A qualitative, online survey eliciting PCP narratives. Thematic analysis was used to analyse the data. SETTING AND SUBJECTS: A primary care study, with narratives from 159 PCPs in 23 European countries. MAIN OUTCOME MEASURES: PCPs' narratives on the question 'If you saw this patient with cancer presenting in the same way today, what would you do differently? RESULTS: The main themes identified were: thinking broadly; improvement in communication and clinical management; use of other available resources and 'I wouldn't do anything differently'. CONCLUSION (IMPLICATIONS): To achieve more timely cancer diagnosis, PCPs need to provide a long-term, holistic and active approach with effective communication, and to ensure shared decision-making, follow-up and continuing re-assessment of the patients' clinical conditions.

Diagnosing cancer in primary care is challenging due to the low incidence of cancer in practice and the multiple confounding factors that are involved in the diagnostic process.The need to think broadly, make improvements in communication and clinical management, and use other available resources were the main themes from Primary Care Physicians' (PCPs') narratives about their learning experiences from missed or late cancer diagnoses.A long-term, holistic and active approach with effective communication, follow-up and continuing re-assessment of the patients' clinical conditions was another theme for making improvements.Some PCPs, on reflection, would not have done anything differently.

Congenitally Corrected Transposition of the Great Arteries in Utero: Morphological Spectrum, Outcomes and Pitfalls in Fetal Diagnosis.

Congenitally corrected transposition of the great arteries (ccTGA) is a rare malformation with diverse morphology. We assessed features of fetuses with ccTGA and evaluated neonatal and pediatric outcomes. This was a retrospective review of fetuses with ccTGA at Birmingham Women's and Children's Hospital born from 2005 to 2019. Of thirty-six fetuses identified, six had unavailable prenatal data, one was postnatally diagnosed with isomerism and 29 fetuses were evaluated. ccTGA without associated cardiac lesions was found in 28% (8/29), ccTGA with significant VSD in 31% (9/29), ccTGA with pulmonary obstruction in 24% (7/29) and ccTGA with complex anomalies in 17% (5/29). Tricuspid regurgitation (TR) was observed in 17% (5/29) and heart block (HB) in 10% (3/29) prenatally. Six, that is 21% underwent genetic testing of which one was abnormal. Five extra-cardiac anomalies were reported prenatally and postnatally. Pregnancy was discontinued in five, of which two had moderate TR. There were thirty-one liveborn. Coarctation of the aorta was found in five postnatally but not suspected prenatally. In one, pulmonary stenosis was underestimated; otherwise, prenatal morphology was confirmed. Cardiac interventions were performed in 77% (24/31) liveborn with 39% (12/31) undergoing neonatal intervention. Overall, 6/31 liveborn died including all three with prenatal heart block and one with TR. Estimated survival for all liveborn at 1, 5 and 10 years was 87% (95% CI 76-100%), 83% (95% CI 72-98%) and 80% (95% CI 66-96%) respectively. Accurate prenatal diagnosis of ccTGA is critical for counseling. Early outcomes are favorable with 77% of liveborn undergoing surgery. Fetuses with prenatal diagnosis of complex associated abnormalities, HB and TR appear to do less well.

Optimal timing of faculty teaching when combined with near-peer teaching: A mixed methods analysis.

BACKGROUND: Near-peer teaching is increasingly used in medical education, supporting or replacing faculty teaching. It has positive aspects for learners and tutors, some of which are explained by higher social and cognitive congruence between learners and near-peer tutors (NPTs). This study investigates the optimal combination of faculty tutors (FTs) and NPTs in an abdominal ultrasound course. METHODS: Sixty-four third-year medical students underwent a basic ultrasound course, with 75% of lessons taught by NPTs and 25% by FTs. Each of four groups had a different faculty teaching timing. A mixed methods approach used a survey and semi-structured interviews at the course end to elicit learners' preferences, and end-of-course examination scores to look for differences in outcomes. RESULTS: Most learners preferred having faculty teaching in the second half of the course, saying it would be overwhelming to start with FTs. Learners preferred between a quarter and a third of the teaching to be from FTs, with NPTs rated better at teaching basics, and FTs contributing unique, helpful clinical knowledge. There was no significant between-group difference in examination scores. CONCLUSIONS: Medical students preferred most of their teaching to be from NPTs, with some faculty input in the second half of the course.

Why are medical students so motivated to learn ultrasound skills? A qualitative study.

BACKGROUND: The introduction of ultrasound (US) courses into medical undergraduate courses is usually met with a particularly high level of student motivation. The reasons for this are unclear. The aim of this study was to investigate the factors that contribute to undergraduate medical students' motivation to learn US skills. Understanding what motivates students to learn US will inform the efforts of faculty to foster students' motivation to learn. METHODS: We carried out in-depth semi-structured one-to-one interviews with medical students participating in an optional US course at two Swiss universities. The interview guide consisted of 10 main questions. The content was informed by experts in the field of medical education and US, as well as by a literature review of motivation theories for learning, in particular by self-determination theory (SDT). SDT was used to guide the development of the interview guide and to reflect on the resulting themes in the discussion section. The interview guide was piloted with two medical students. The interviews lasted an average of 45 min and were audio recorded and transcribed. Thematic analysis was used to analyse the data. RESULTS: Fourteen undergraduate medical students in their preclinical (year 3) and clinical studies (years 4 and 5) elaborated on a wide range of reasons for their high motivation to learn US. They were motivated for US training because of the positive nimbus of the US modality, emphasising the advantages of visualisation. Students acknowledged the potential professional benefits of learning US and described it as a fun, exciting group activity. CONCLUSIONS: The four themes we found in our analysis can all be related to the three universal needs described in SDT. The strong focus on the visual aspect and the positive nimbus of the modality goes beyond that and reflects the visuo-centric Zeitgeist, which claims the superiority of visual information over other data. Educators should be aware that motivation to learn is affected by the Zeitgeist and ensuing preconceptions, such as the perception of the positive nimbus surrounding a topic. Other key elements that can be implemented to motivate students are just-in-time feedback, enabling group experiences and creating awareness of the clinical relevance of learning content.

Comparison Between Movement Pattern Training and Strengthening on Kinematics and Kinetics in Patients With Chronic Hip-Related Groin Pain.

The purpose of this study was to compare the preliminary effects of movement pattern training (MoveTrain) versus strengthening/flexibility (standard) treatment on hip and pelvic biomechanics in patients with chronic hip-related groin pain. This is a secondary analysis of data collected during a pilot randomized clinical trial. Thirty patients with hip pain, between the ages of 15 and 40 years, were randomized to MoveTrain or standard. Both groups completed 10 treatment sessions over 12 weeks along with a daily home exercise program. Three-dimensional motion analysis was used to collect kinematic and kinetic data of the pelvis and hip during a single-leg squat task at pretreatment and immediately posttreatment. Compared with the standard group, the MoveTrain group demonstrated smaller hip adduction angles (P = .006) and smaller hip external adduction moments (P = .008) at posttreatment. The desired changes to hip joint biomechanics, as found in this study, may require specificity in training that could allow health care professionals to better customize the rehabilitation of patients with hip pain. These findings can also be applied to the design and implementation of future clinical trials to strengthen our understanding of the long-term implications of different rehabilitation techniques for patients with hip pain.

OGFOD1 modulates the transcriptional and proteomic landscapes to alter isoproterenol-induced hypertrophy susceptibility.

Cardiac hypertrophy is associated with increased translation. However, little is known of the mechanisms that regulate translation in hypertrophy. Members of the 2-oxoglutarate-dependent dioxygenase family regulate several aspects of gene expression, including translation. An important member of this family is OGFOD1. Here, we show OGFOD1 accumulates in failing human hearts. Upon OGFOD1 deletion, murine hearts showed transcriptomic and proteomic changes, with only 21 proteins and mRNAs (0.6%) changing in the same direction. Additionally, OGFOD1-KO mice were protected from induced hypertrophy, supporting a role for OGFOD1 in the cardiac response to chronic stress.

Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.

Pistol ribozyme (Psr) is a distinct class of small endonucleolytic ribozymes, which are important experimental systems for defining fundamental principles of RNA catalysis and designing valuable tools in biotechnology. High-resolution structures of Psr, extensive structure-function studies, and computation support a mechanism involving one or more catalytic guanosine nucleobases acting as a general base and divalent metal ion-bound water acting as an acid to catalyze RNA 2'-O-transphosphorylation. Yet, for a wide range of pH and metal ion concentrations, the rate of Psr catalysis is too fast to measure manually and the reaction steps that limit catalysis are not well understood. Here, we use stopped-flow fluorescence spectroscopy to evaluate Psr temperature dependence, solvent H/D isotope effects, and divalent metal ion affinity and specificity unconstrained by limitations due to fast kinetics. The results show that Psr catalysis is characterized by small apparent activation enthalpy and entropy changes and minimal transition state H/D fractionation, suggesting that one or more pre-equilibrium steps rather than chemistry is rate limiting. Quantitative analyses of divalent ion dependence confirm that metal aquo ion pKa correlates with higher rates of catalysis independent of differences in ion binding affinity. However, ambiguity regarding the rate-limiting step and similar correlation with related attributes such as ionic radius and hydration free energy complicate a definitive mechanistic interpretation. These new data provide a framework for further interrogation of Psr transition state stabilization and show how thermal instability, metal ion insolubility at optimal pH, and pre-equilibrium steps such as ion binding and folding limit the catalytic power of Psr suggesting potential strategies for further optimization.

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.

Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.

Hierarchical Variation in Phenotypic Flexibility across Timescales and Associated Survival Selection Shape the Dynamics of Partial Seasonal Migration.

AbstractPopulation responses to environmental variation ultimately depend on within-individual and among-individual variation in labile phenotypic traits that affect fitness and resulting episodes of selection. Yet complex patterns of individual phenotypic variation arising within and between time periods, as well as associated variation in selection, have not been fully conceptualized or quantified. We highlight how structured patterns of phenotypic variation in dichotomous threshold traits can theoretically arise and experience varying forms of selection, shaping overall phenotypic dynamics. We then fit novel multistate models to 10 years of band-resighting data from European shags to quantify phenotypic variation and selection in a key threshold trait underlying spatioseasonal population dynamics: seasonal migration versus residence. First, we demonstrate substantial among-individual variation alongside substantial between-year individual repeatability in within-year phenotypic variation ("flexibility"), with weak sexual dimorphism. Second, we demonstrate that between-year individual variation in within-year phenotypes ("supraflexibility") is structured and directional, consistent with the threshold trait model. Third, we demonstrate strong survival selection on within-year phenotypes-and hence on flexibility-that varies across years and sexes, including episodes of disruptive selection representing costs of flexibility. By quantitatively combining these results, we show how supraflexibility and survival selection on migratory flexibility jointly shape population-wide phenotypic dynamics of seasonal movement.

Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome.

MOTIVATION: Short-read whole-genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences and sequencing bias reduces the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. To benchmark short-read variant calling, we used 36 diverse clinical Mycobacterium tuberculosis (Mtb) isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically studied the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias and GC content. RESULTS: Reference-based Illumina variant calling demonstrated a maximum recall of 89.0% and minimum precision of 98.5% across parameters evaluated. The approach that maximized variant recall while still maintaining high precision (<99%) was tuning the mapping quality filtering threshold, i.e. confidence of the read mapping (recall = 85.8%, precision = 99.1%, MQ ≥ 40). Additional masking of repetitive sequence content is an alternative conservative approach to variant calling that increases precision at cost to recall (recall = 70.2%, precision = 99.6%, MQ ≥ 40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52/168 PE/PPE genes (34.5%). From these results, we present a refined list of low confidence regions across the Mtb genome, which we found to frequently overlap with regions with structural variation, low sequence uniqueness and low sequencing coverage. Our benchmarking results have broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems and more generally for WGS applications in other organisms. AVAILABILITY AND IMPLEMENTATION: All relevant code is available at https://github.com/farhat-lab/mtb-illumina-wgs-evaluation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Increased parental effort fails to buffer the cascading effects of warmer seas on common guillemot demographic rates.

Climate warming can reduce food resources for animal populations. In species exhibiting parental care, parental effort is a 'barometer' of changes in environmental conditions. A key issue is the extent to which variation in parental effort can buffer demographic rates against environmental change. Seabirds breed in large, dense colonies and globally are major predators of small fish that are often sensitive to ocean warming. We explored the causes and consequences of annual variation in parental effort as indicated by standardised checks of the proportions of chicks attended by both, one or neither parent, in a population of common guillemots Uria aalge over four decades during which there was marked variation in marine climate and chick diet. We predicted that, for parental effort to be an effective buffer, there would be a link between environmental conditions and parental effort, but not between parental effort and demographic rates. Environmental conditions influenced multiple aspects of the prey delivered by parents to their chicks with prey species, length and energy density all influenced by spring sea surface temperature (sSST) in the current and/or previous year. Overall, the mean annual daily energy intake of chicks declined significantly when sSST in the current year was higher. In accordance with our first prediction, we found that parental effort increased with sSST in the current and previous year. However, the increase was insufficient to maintain chick daily energy intake. In contrast to our second prediction, we found that increased parental effort had major demographic consequences such that growth rate and fledging success of chicks, and body mass and overwinter survival of breeding adults all decreased significantly. Common guillemot parents were unable to compensate effectively for temperature-mediated variation in feeding conditions through behavioural flexibility, resulting in immediate consequences for breeding population size because of lower adult survival and potentially longer-term impacts on recruitment because of lower productivity. These findings highlight that a critical issue for species' responses to future climate change will be the extent to which behavioural buffering can offer resilience to deteriorating environmental conditions.

Raising offspring increases ageing: Differences in senescence among three populations of a long-lived seabird, the Atlantic puffin.

Actuarial senescence, the decline of survival with age, is well documented in the wild. Rates of senescence vary widely between taxa, to some extent also between sexes, with the fastest life histories showing the highest rates of senescence. Few studies have investigated differences in senescence among populations of the same species, although such variation is expected from population-level differences in environmental conditions, leading to differences in vital rates and thus life histories. We predict that, within species, populations differing in productivity (suggesting different paces of life) should experience different rates of senescence, but with little or no sexual difference in senescence within populations of monogamous, monomorphic species where the sexes share breeding duties. We compared rates of actuarial senescence among three contrasting populations of the Atlantic puffin Fratercula arctica. The dataset comprised 31 years (1990-2020) of parallel capture-mark-recapture data from three breeding colonies, Isle of May (North Sea), Røst (Norwegian Sea) and Hornøya (Barents Sea), showing contrasting productivities (i.e. annual breeding success) and population trends. We used time elapsed since first capture as a proxy for bird age, and productivity and the winter North Atlantic Oscillation Index (wNAO) as proxies for the environmental conditions experienced by the populations within and outside the breeding season, respectively. In accordance with our predictions, we found that senescence rates differed among the study populations, with no evidence for sexual differences. There was no evidence for an effect of wNAO, but the population with the lowest productivity, Røst, showed the lowest rate of senescence. As a consequence, the negative effect of senescence on the population growth rate (λ) was up to 3-5 times smaller on Røst (Δλ = -0.009) than on the two other colonies. Our findings suggest that environmentally induced differences in senescence rates among populations of a species should be accounted for when predicting effects of climate variation and change on species persistence. There is thus a need for more detailed information on how both actuarial and reproductive senescence influence vital rates of populations of the same species, calling for large-scale comparative studies.

Safe Today, Unsafe Tomorrow: Tanzanian Households Experience Variability in Drinking Water Quality.

Measuring Escherichia coli in a single-grab sample of stored drinking water is often used to characterize drinking water quality. However, if water quality exhibits variability temporally, then one-time measurement schemes may be insufficient to adequately characterize the quality of water that people consume. This study uses longitudinal data collected from 193 households in peri-urban Tanzania to assess variability in stored water quality and to characterize uncertainty with different data collection schemes. Households were visited 5 times over the course of a year. At each visit, information was collected on water management practices, and a sample of stored drinking water was collected for E. coli enumeration. Water quality was poor for households, with 80% having highly contaminated (>100 CFU per 100 mL) water during at least one visit. There was substantial variability of water quality for households, with only 3% of households having the same category (low, medium, or high) of water quality for all five visits. These data suggest a single sample would inaccurately characterize a household's drinking water quality over the course of a year and lead to misestimates of population level access to safe drinking water.

Biallelic variants of ATP13A3 cause dose-dependent childhood-onset pulmonary arterial hypertension characterised by extreme morbidity and mortality.

BACKGROUND: The molecular genetic basis of pulmonary arterial hypertension (PAH) is heterogeneous, with at least 26 genes displaying putative evidence for disease causality. Heterozygous variants in the ATP13A3 gene were recently identified as a new cause of adult-onset PAH. However, the contribution of ATP13A3 risk alleles to child-onset PAH remains largely unexplored. METHODS AND RESULTS: We report three families with a novel, autosomal recessive form of childhood-onset PAH due to biallelic ATP13A3 variants. Disease onset ranged from birth to 2.5 years and was characterised by high mortality. Using genome sequencing of parent-offspring trios, we identified a homozygous missense variant in one case, which was subsequently confirmed to cosegregate with disease in an affected sibling. Independently, compound heterozygous variants in ATP13A3 were identified in two affected siblings and in an unrelated third family. The variants included three loss of function variants (two frameshift, one nonsense) and two highly conserved missense substitutions located in the catalytic phosphorylation domain. The children were largely refractory to treatment and four died in early childhood. All parents were heterozygous for the variants and asymptomatic. CONCLUSION: Our findings support biallelic predicted deleterious ATP13A3 variants in autosomal recessive, childhood-onset PAH, indicating likely semidominant dose-dependent inheritance for this gene.

Primary care practitioners' priorities for improving the timeliness of cancer diagnosis in primary care: a European cluster-based analysis.

BACKGROUND: Diagnosing cancer at an early stage increases the likelihood of survival, and more advanced cancers are more difficult to treat successfully. Primary care practitioners (PCPs) play a key role in timely diagnosis of cancer. PCPs' knowledge of their own patient populations and health systems could help improve the planning of more effective approaches to earlier cancer recognition and referral. How PCPs act when faced with patients who may have cancer is likely to depend on how their health systems are organised, and this may be one explanation for the wide variation on cancer survival rates across Europe. OBJECTIVES: To identify and characterise clusters of countries whose PCPs perceive the same factors as being important in improving the timeliness of cancer diagnosis. METHODS: A cluster analysis of qualitative data from an online survey was carried out. PCPs answered an open-ended survey question on how the speed of diagnosis of cancer in primary care could be improved. Following coding and thematic analysis, we identified the number of times per country that an item in a theme was mentioned. k-means clustering identified clusters of countries whose PCPs perceived the same themes as most important. Post-hoc testing explored differences between these clusters. SETTING: Twenty-five primary care centres in 20 European countries. Each centre was asked to recruit at least 50 participants. PARTICIPANTS: Primary care practitioners of each country. RESULTS: In all, 1,351 PCPs gave free-text answers. We identified eighteen themes organising the content of the responses. Based on the frequency of the themes, k-means clustering identified three groups of countries. There were significant differences between clusters regarding the importance of: access to tests (p = 0.010); access to specialists (p = 0.014), screening (p < 0.001); and finances, quotas & limits (p < 0.001). CONCLUSIONS: Our study identified three distinct clusters of European countries within which PCPs had similar views on the factors that would improve the timeliness of cancer diagnosis. Further work is needed to understand what it is about the clusters that have produced these patterns, allowing healthcare systems to share best practice and to reduce disparities.