Global mismatches between threat mapping research effort and the potential of threat abatement actions to reduce extinction risk.

Threat mapping is a necessary tool for identifying and abating direct threats to species in the ongoing extinction crisis. There are known gaps in the threat mapping literature for particular threats and geographic locations, and it remains unclear if the distribution of research effort is appropriately targeted relative to conservation need. We aimed to determine the drivers of threat mapping research effort and to quantify gaps that, if filled, could inform actions with the highest potential to reduce species' extinction risk. We used a negative binomial generalized linear model to analyze research effort as a function of threat abatement potential (quantified as the potential reduction in species extinction risk from abating threats), species richness, land area, and human pressure. The model showed that threat mapping research effort increased by 1.1 to 1.2 times per standardized unit change in threat abatement potential. However, species richness and land area were stronger predictors of research effort overall. The greatest areas of mismatch between research effort and threat abatement potential, receiving disproportionately low research effort, were related to the threats to species of agriculture, aquaculture, and biological resource use across the tropical regions of the Americas, Asia, and Madagascar. Conversely, the threat of linear infrastructure (e.g., roads and rails) across regions, the threat of biological resource use (e.g., hunting or collection) in sub-Saharan Africa, and overall threats in North America and Europe all received disproportionately high research effort. We discuss the range of methodological and sociopolitical factors that may be behind the overall trends and specific areas of mismatch we found. We urge a stronger emphasis on targeting research effort toward those threats and geographic locations where threat abatement activities could make the greatest contribution to reducing global species extinction risk.

Disparidades mundiales entre la investigación sobre el esfuerzo de mapeo de amenazas y la potencial amenaza de las acciones de abatimiento para reducir el riesgo de extinción Resumen El mapeo de amenazas es una herramienta necesaria para identificar y abatir las amenazas directas para las especies en la actual crisis de extinción. Existen vacíos conocidos en la literatura del mapeo de amenazas para amenazas particulares y ubicaciones geográficas, y todavía no está claro si la distribución de los esfuerzos de investigación está enfocada de forma apropiada en relación con las necesidades de conservación. Buscamos determinar los factores que influyen sobre el esfuerzo de investigación del mapeo de amenazas y cuantificar los vacíos que, si se cierran, podrían guiar las acciones con el potencial más alto para reducir el riesgo de extinción de las especies. Usamos un modelo binomial lineal negativo generalizado para analizar el esfuerzo de investigación como función del potencial de abatimiento de amenazas (cuantificado como la reducción potencial en el riesgo de extinción a partir del abatimiento de amenazas), la riqueza de especies, el área del suelo y la presión humana. El modelo mostró que el esfuerzo de investigación del mapeo de amenazas incrementó entre 1.1 y 1.2 veces por unidad estandarizada de cambio en el potencial de abatimiento de amenazas. Sin embargo, la riqueza de especies y el área del suelo fueron pronósticos más sólidos del esfuerzo de investigación generalizado. Las principales áreas de disparidad entre el esfuerzo de investigación y el potencial de abatimiento de amenazas, las cuales reciben un esfuerzo de investigación desproporcionalmente bajo, estuvieron relacionadas con las amenazas para las especies de agricultura, acuacultura y recursos biológicos que se usan en las regiones tropicales de América, Asia y Madagascar. Al contrario, la amenaza de la infraestructura lineal (p. ej.: carreteras y vías férreas) en las regiones, la amenaza del uso de recursos biológicos (p. ej.: caza o recolección) en la África subsahariana y las amenazas generales en América del Norte y en Europa recibieron un esfuerzo de investigación desproporcionalmente alto. Abordamos el rango de factores metodológicos y sociopolíticos que pueden estar detrás de las tendencias generales y las áreas específicas de disparidad que encontramos. Instamos a un mayor énfasis en el enfoque del esfuerzo de investigación hacia aquellas amenazas y ubicaciones geográficas en donde las actividades de abatimiento de amenazas podrían brindar una mayor contribución para reducir el riesgo mundial de extinción de especies.

Computed tomography-based radiomic markers are independent prognosticators of survival in advanced laryngeal cancer: a pilot study.

OBJECTIVE: Advanced laryngeal cancers are clinically complex; there is a paucity of modern decision-making models to guide tumour-specific management. This pilot study aims to identify computed tomography-based radiomic features that may predict survival and enhance prognostication. METHODS: Pre-biopsy, contrast-enhanced computed tomography scans were assembled from a retrospective cohort (n = 72) with advanced laryngeal cancers (T3 and T4). The LIFEx software was used for radiomic feature extraction. Two features: shape compacity (irregularity of tumour volume) and grey-level zone length matrix - grey-level non-uniformity (tumour heterogeneity) were selected via least absolute shrinkage and selection operator-based Cox regression and explored for prognostic potential. RESULTS: A greater shape compacity (hazard ratio 2.89) and grey-level zone length matrix - grey-level non-uniformity (hazard ratio 1.64) were significantly associated with worse 5-year disease-specific survival (p < 0.05). Cox regression models yielded a superior C-index when incorporating radiomic features (0.759) versus clinicopathological variables alone (0.655). CONCLUSIONS: Two radiomic features were identified as independent prognostic biomarkers. A multi-centre prospective study is necessary for further exploration. Integrated radiomic models may refine the treatment of advanced laryngeal cancers.

Depression in Sjögren's syndrome mediates the relationship between pain, fatigue, sleepiness, and overall quality of life.

Objectives: Sjögren's syndrome (SS) includes many extra-glandular symptoms such as fatigue, pain, sleepiness and depression, which impact on quality of life (QoL). These symptoms also influence each other and could be linked by autonomic nervous system (ANS) dysregulation. Our aim was to model the role of putative predictive variables, including depression in the relationships between ANS function, fatigue, and QoL in SS. Methods: Cross-sectional analysis of self-reported data from the multicentre UK primary SS registry. The Composite Autonomic Symptom Scale (COMPASS) was used to assess autonomic function, the Hospital Anxiety and Depression Scale (HADS) to assess anxiety and depression and the EuroQol-5 Dimension (EQ-5D) to assess QoL. Validated scales were used for other clinical variables. Using multiple regression analysis and structural equation modelling (SEM), we investigated how the QoL of people with SS is impacted by the direct and indirect effects of fatigue, sleepiness, depression, symptom burden and ANS function, and their interactions. Results: Data was obtained for 1046 people with SS, 56% COMPASS completers. Symptoms of ANS dysregulation were common. Participants with ANS dysregulation had more severe depression, anxiety, dryness, fatigue, pain, sleepiness and QoL (P < 0.01 for all). Depression, anxiety, dryness, and pain were independent predictors of ANS function in the multiple regression model (P < 0.05 for all). ANS function could not be included in the SEM. The SEM model had good fit to the data (comparative fit index = 0.998) and showed that, in people with SS, depression mediates the effects of pain, fatigue and sleepiness on QoL. Conclusion: Our results show that diagnosing and treating depression in people with SS could have direct positive impact on QoL, and significantly ameliorate the impact of fatigue and pain.

A systems approach framework for evaluating tree restoration interventions for social and ecological outcomes in rural tropical landscapes.

The science guiding design and evaluation of restoration interventions in tropical landscapes is dominated by ecological processes and outcomes and lacks indicators and methods that integrate human wellbeing into the restoration process. We apply a new systems approach framework for tree restoration in forest-agricultural landscapes to show how this shortcoming can be addressed. Demonstrating 'proof of concept', we tested statistical models underlying the framework pathways with data collected from a case study in Tanzania. Local community perceptions of nature's values were not affected by levels of self-reported wildlife-induced crop damage. But mapped predictions from the systems approach under a tree restoration scenario suggested differential outcomes for biodiversity indicators and altered spatial patterns of crop damage risk, expected to jeopardize human wellbeing. The predictions map anticipated trade-offs in costs and benefits of restoration scenarios, which we have started to explore with stakeholders to identify restoration opportunities that consider local knowledge, value systems and human wellbeing. We suggest that the framework be applied to other landscapes to identify commonalities and differences in forest landscape restoration outcomes under varying governance and land use systems. This should form a foundation for evidence-based implementation of the global drive for forest landscape restoration, at local scales. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

Erratum: Author Correction: The influence of HLA genotype on the development of metal hypersensitivity following joint replacement.

[This corrects the article DOI: 10.1038/s43856-022-00137-0.].

The influence of HLA genotype on the development of metal hypersensitivity following joint replacement.

Background: Over five million joint replacements are performed across the world each year. Cobalt chrome (CoCr) components are used in most of these procedures. Some patients develop delayed-type hypersensitivity (DTH) responses to CoCr implants, resulting in tissue damage and revision surgery. DTH is unpredictable and genetic links have yet to be definitively established. Methods: At a single site, we carried out an initial investigation to identify HLA alleles associated with development of DTH following metal-on-metal hip arthroplasty. We then recruited patients from other centres to train and validate an algorithm incorporating patient age, gender, HLA genotype, and blood metal concentrations to predict the development of DTH. Accuracy of the modelling was assessed using performance metrics including time-dependent receiver operator curves. Results: Using next-generation sequencing, here we determine the HLA genotypes of 606 patients. 176 of these patients had experienced failure of their prostheses; the remaining 430 remain asymptomatic at a mean follow up of twelve years. We demonstrate that the development of DTH is associated with patient age, gender, the magnitude of metal exposure, and the presence of certain HLA class II alleles. We show that the predictive algorithm developed from this investigation performs to an accuracy suitable for clinical use, with weighted mean survival probability errors of 1.8% and 3.1% for pre-operative and post-operative models respectively. Conclusions: The development of DTH following joint replacement appears to be determined by the interaction between implant wear and a patient's genotype. The algorithm described in this paper may improve implant selection and help direct patient surveillance following surgery. Further consideration should be given towards understanding patient-specific responses to different biomaterials.

The COLO-COHORT (Colorectal Cancer Cohort) study: Protocol for a multi-centre, observational research study and development of a consent-for-contact research platform.

AIM: The COLO-COHORT study aims to produce a multi-factorial risk prediction model for colorectal neoplasia that can be used to target colonoscopy to those at greatest risk of colorectal neoplasia, ensuring that people are not investigated unnecessarily and maximizing the use of limited endoscopy resources. The study will also explore the link between neoplasia and the human gut microbiome. Additionally, the study aims to generate a cohort of colonoscopy patients who are 'research ready' through the development of a consent-for-contact (C4C) platform, to facilitate a range of colorectal cancer prevention studies to be conducted at scale and speed. METHODS AND ANALYSIS: This is a multi-centre observational study involving sites across the UK. Recruitment is over a 6-year period (2019-2025). Patients recruited to the study are those attending for colonoscopy. Patients are recruited into two groups, namely observational group A (10 000 patients) and C4C group B (10 000 patients), known as COLO-SPEED (Colorectal Cancer Screening Prevention Endoscopy and Early Diagnosis; https://colospeed.uk). Patients complete a health questionnaire, provide anthropometric measurements and submit biosamples (blood and stool-depending on the part of the study they are recruited into). Patients' colonoscopy and histology findings are also recorded. Models of factors associated with the presence of neoplasia at colonoscopy will be developed using logistic or multinomial regression. For internal validation, model discrimination and calibration will be assessed and bootstrapping and cross-validation approaches used. To enable long-term follow-up for outcomes related to colorectal cancer and polyps, patients are asked to consent to follow-up through data linkage with national databases. DISSEMINATION: In keeping with good research practice, following analysis by the study team the study investigators will make the anonymized dataset available to other researchers. The C4C platform will also be accessible to other researchers. The study findings will be submitted for publication in peer-reviewed journals and lay summaries will be disseminated to participants and the wider public.

Identifying the climatic drivers of honey bee disease in England and Wales.

Honey bee colony health has received considerable attention in recent years, with many studies highlighting multifactorial issues contributing to colony losses. Disease and weather are consistently highlighted as primary drivers of colony loss, yet little is understood about how they interact. Here, we combined disease records from government honey bee health inspections with meteorological data from the CEDA to identify how weather impacts EFB, AFB, CBP, varroosis, chalkbrood and sacbrood. Using R-INLA, we determined how different meteorological variables influenced disease prevalence and disease risk. Temperature caused an increase in the risk of both varroosis and sacbrood, but overall, the weather had a varying effect on the six honey bee diseases. The risk of disease was also spatially varied and was impacted by the meteorological variables. These results are an important step in identifying the impacts of climate change on honey bees and honey bee diseases.

Transmission routes of rare seasonal diseases: the case of norovirus infections.

Norovirus (NoV) is the most commonly recognized cause of acute gastroenteritis, with over a million cases globally per year. While usually self-limiting, NoV poses a substantial economic burden because it is highly contagious and there are multiple transmission routes. Infection occurs through inhalation of vomitus; faecal-oral spread; and food, water and environmental contamination. While the incidence of the disease is predictably seasonal, much less is known about the relative contribution of the various exposure pathways in causing disease. Additionally, asymptomatic excretion and viral shedding make forecasting disease burden difficult. We develop a novel stochastic dynamic network model to investigate the contributions of different transmission pathways in multiple coupled social networks representing schools, hospitals, care-homes and family households in a community setting. We analyse how the networks impact on transmission. We used ward-level demographic data from Northumberland, UK to create a simulation cohort. We compared the results with extant data on NoV cases from the IID2 study. Connectivity across the simulated cohort was high. Cases of NoV showed marked seasonality, peaking in early winter and declining through the summer. For the first time, we show that fomites and food appear to be the most important exposure routes in determining the population burden of disease. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.

Network structure underpinning (dys)homeostasis in chronic fatigue syndrome; Preliminary findings.

INTRODUCTION: A large body of evidence has established a pattern of altered functioning in the immune system, autonomic nervous system and hypothalamic pituitary adrenal axis in chronic fatigue syndrome. However, the relationship between components within and between these systems is unclear. In this paper we investigated the underlying network structure of the autonomic system in patients and controls, and a larger network comprising all three systems in patients alone. METHODS: In a sample of patients and controls we took several measures of autonomic nervous system output during 10 minutes of supine rest covering tests of blood pressure variability, heart rate variability and cardiac output. Awakening salivary cortisol was measured on each of two days with participants receiving 0.5mg dexamethasone during the afternoon of the first day. Basal plasma cytokine levels and the in vitro cytokine response to dexamethasone were also measured. Symptom outcome measures used were the fatigue impact scale and cognitive failures questionnaire. Mutual information criteria were used to construct networks describing the dependency amongst variables. Data from 42 patients and 9 controls were used in constructing autonomic networks, and 15 patients in constructing the combined network. RESULTS: The autonomic network in patients showed a more uneven distribution of information, with two distinct modules emerging dominated by systolic blood pressure during active stand and end diastolic volume and stroke volume respectively. The combined network revealed strong links between elements of each of the three regulatory systems, characterised by three higher modules the centres of which were systolic blood pressure during active stand, stroke volume and ejection fraction respectively. CONCLUSIONS: CFS is a complex condition affecting physiological systems. It is important that novel analytical techniques are used to understand the abnormalities that lead to CFS. The underlying network structure of the autonomic system is significantly different to that of controls, with a small number of individual nodes being highly influential. The combined network suggests links across regulatory systems which shows how alterations in single nodes might spread throughout the network to produce alterations in other, even distant, nodes. Replication in a larger cohort is warranted.

Climate, human behaviour or environment: individual-based modelling of Campylobacter seasonality and strategies to reduce disease burden.

BACKGROUND: With over 800 million cases globally, campylobacteriosis is a major cause of food borne disease. In temperate climates incidence is highly seasonal but the underlying mechanisms are poorly understood, making human disease control difficult. We hypothesised that observed disease patterns reflect complex interactions between weather, patterns of human risk behaviour, immune status and level of food contamination. Only by understanding these can we find effective interventions. METHODS: We analysed trends in human Campylobacter cases in NE England from 2004 to 2009, investigating the associations between different risk factors and disease using time-series models. We then developed an individual-based (IB) model of risk behaviour, human immunological responses to infection and environmental contamination driven by weather and land use. We parameterised the IB model for NE England and compared outputs to observed numbers of reported cases each month in the population in 2004-2009. Finally, we used it to investigate different community level disease reduction strategies. RESULTS: Risk behaviours like countryside visits (t = 3.665, P < 0.001 and t = - 2.187, P = 0.029 for temperature and rainfall respectively), and consumption of barbecued food were strongly associated with weather, (t = 3.219, P = 0.002 and t = 2.015, P = 0.045 for weekly average temperature and average maximum temperature respectively) and also rain (t = 2.254, P = 0.02527). This suggests that the effect of weather was indirect, acting through changes in risk behaviour. The seasonal pattern of cases predicted by the IB model was significantly related to observed patterns (r = 0.72, P < 0.001) indicating that simulating risk behaviour could produce the observed seasonal patterns of cases. A vaccination strategy providing short-term immunity was more effective than educational interventions to modify human risk behaviour. Extending immunity to 1 year from 20 days reduced disease burden by an order of magnitude (from 2412-2414 to 203-309 cases per 50,000 person-years). CONCLUSIONS: This is the first interdisciplinary study to integrate environment, risk behaviour, socio-demographics and immunology to model Campylobacter infection, including pathways to mitigation. We conclude that vaccination is likely to be the best route for intervening against campylobacteriosis despite the technical problems associated with understanding both the underlying human immunology and genetic variation in the pathogen, and the likely cost of vaccine development.

Control of norovirus infection.

PURPOSE OF REVIEW: The purpose of the review is to provide an update on control measures for norovirus (NoV), which is the most commonly implicated pathogen in acute gastroenteritis and outbreaks, causing major disruption in nurseries, schools, hospitals and care homes. RECENT FINDINGS: Important developments include the discovery that virus particles, previously considered to be the infectious unit, also occur in clusters, which appear to be more virulent than individual virus particles; a working culture system using human stem-cell derived enteroids; promising results from early phase clinical trials of candidate NoV vaccines, which appear to be safe and immunogenic; chronic NoV affects patients with primary and secondary immune deficiencies. Although several treatments have been used none are supported by well designed clinical trials; infection control procedures are effective if properly implemented. SUMMARY: NoV remains an important cause of morbidity and mortality. Although there are exciting developments on the vaccine front, the mainstay of control remains good hand hygiene, adherence to infection control procedures and limiting contamination of food, water and the wider environment. Once vaccines are available there will be important decisions to be made about how best to implement them.

Spatio-temporal models to determine association between Campylobacter cases and environment.

Background: Campylobacteriosis is a major cause of gastroenteritis in the UK, and although 70% of cases are associated with food sources, the remainder are probably associated with wider environmental exposure. Methods: In order to investigate wider environmental transmission, we conducted a spatio-temporal analysis of the association of human cases of Campylobacter in the Tyne catchment with weather, climate, hydrology and land use. A hydrological model was used to predict surface-water flow in the Tyne catchment over 5 years. We analysed associations between population-adjusted Campylobacter case rate and environmental factors hypothesized to be important in disease using a two-stage modelling framework. First, we investigated associations between temporal variation in case rate in relation to surface-water flow, temperature, evapotranspiration and rainfall, using linear mixed-effects models. Second, we used the random effects for the first model to quantify how spatial variation in static landscape features of soil and land use impacted on the likely differences between subcatchment associations of case rate with the temporal variables. Results: Population-adjusted Campylobacter case rates were associated with periods of high predicted surface-water flow, and during above average temperatures. Subcatchments with cattle on stagnogley soils, and to a lesser extent sheep plus cattle grazing, had higher Campylobacter case rates. Conclusions: Areas of stagnogley soils with mixed livestock grazing may be more vulnerable to both Campylobacter spread and exposure during periods of high rainfall, with resultant increased risk of human cases of the disease.

Resurgence of scarlet fever in England, 2014-16: a population-based surveillance study.

BACKGROUND: After decades of decreasing scarlet fever incidence, a dramatic increase was seen in England beginning in 2014. Investigations were launched to assess clinical and epidemiological patterns and identify potential causes. METHODS: In this population-based surveillance study, we analysed statutory scarlet fever notifications held by Public Health England from 1911 to 2016 in England and Wales to identify periods of sudden escalation of scarlet fever. Characteristics of cases and outbreaks in England including frequency of complications and hospital admissions were assessed and compared with the pre-upsurge period. Isolates from throat swabs were obtained and were emm typed. FINDINGS: Data were retrieved for our analysis between Jan 1, 1911, and Dec 31, 2016. Population rates of scarlet fever increased by a factor of three between 2013 and 2014 from 8·2 to 27·2 per 100 000 (rate ratio [RR] 3·34, 95% CI 3·23-3·45; p<0·0001); further increases were observed in 2015 (30·6 per 100 000) and in 2016 (33·2 per 100 000), which reached the highest number of cases (19 206) and rate of scarlet fever notifcation since 1967. The median age of cases in 2014 was 4 years (IQR 3-7) with an incidence of 186 per 100 000 children under age 10 years. All parts of England saw an increase in incidence, with 620 outbreaks reported in 2016. Hospital admissions for scarlet fever increased by 97% between 2013 and 2016; one in 40 cases were admitted for management of the condition or potential complications. Analysis of strains (n=303) identified a diversity of emm types with emm3 (43%), emm12 (15%), emm1 (11%), and emm4 (9%) being the most common. Longitudinal analysis identified 4-yearly periodicity in population incidence of scarlet fever but of consistently lower magnitude than the current escalation. INTERPRETATION: England is experiencing an unprecedented rise in scarlet fever with the highest incidence for nearly 50 years. Reasons for this escalation are unclear and identifying these remains a public health priority. FUNDING: None.

Relationship between mean daily energy intake and frequency of consumption of out-of-home meals in the UK National Diet and Nutrition Survey.

BACKGROUND: Out-of-home meals have been characterised as delivering excessively large portions that can lead to high energy intake. Regular consumption is linked to weight gain and diet related diseases. Consumption of out-of-home meals is associated with socio-demographic and anthropometric factors, but the relationship between habitual consumption of such meals and mean daily energy intake has not been studied in both adults and children in the UK. METHODS: We analysed adult and child data from waves 1-4 of the UK National Diet and Nutrition Survey using generalized linear modelling. We investigated whether individuals who report a higher habitual consumption of meals out in a restaurant or café, or takeaway meals at home had a higher mean daily energy intake, as estimated by a four-day food diary, whilst adjusting for key socio-demographic and anthropometric variables. RESULTS: Adults who ate meals out at least weekly had a higher mean daily energy intake consuming 75-104 kcal more per day than those who ate these meals rarely. The equivalent figures for takeaway meals at home were 63-87 kcal. There was no association between energy intake and frequency of consumption of meals out in children. Children who ate takeaway meals at home at least weekly consumed 55-168 kcal more per day than those who ate these meals rarely. Additionally, in children, there was an interaction with socio-economic position, where greater frequency of consumption of takeaway meals was associated with higher mean daily energy intake in those from less affluent households than those from more affluent households. CONCLUSIONS: Higher habitual consumption of out-of-home meals is associated with greater mean daily energy intake in the UK. More frequent takeaway meal consumption in adults and children is associated with greater daily energy intake and this effect is greater in children from less affluent households. Interventions seeking to reduce energy content through reformulation or reduction of portion sizes in restaurants, cafés and takeaways could potentially lead to reductions in mean daily energy intake, and may reduce inequalities in health in children.

Mechanisms Affecting the Gut of Preterm Infants in Enteral Feeding Trials.

Large randomized controlled trials (RCTs) in preterm infants offer unique opportunities for mechanistic evaluation of the risk factors leading to serious diseases, as well as the actions of interventions designed to prevent them. Necrotizing enterocolitis (NEC) a serious inflammatory gut condition and late-onset sepsis (LOS) are common feeding and nutrition-related problems that may cause death or serious long-term morbidity and are key outcomes in two current UK National Institutes for Health Research (NIHR) trials. Speed of increasing milk feeds trial (SIFT) randomized preterm infants to different rates of increases in milk feeds with a primary outcome of survival without disability at 2 years corrected age. Enteral lactoferrin in neonates (ELFIN) randomizes infants to supplemental enteral lactoferrin or placebo with a primary outcome of LOS. This is a protocol for the mechanisms affecting the gut of preterm infants in enteral feeding trials (MAGPIE) study and is funded by the UK NIHR Efficacy and Mechanistic Evaluation programme. MAGPIE will recruit ~480 preterm infants who were enrolled in SIFT or ELFIN. Participation in MAGPIE does not change the main trial protocols and uses non-invasive sampling of stool and urine, along with any residual resected gut tissue if infants required surgery. Trial interventions may involve effects on gut microbes, metabolites (e.g., short-chain fatty acids), and aspects of host immune function. Current hypotheses suggest that NEC and/or LOS are due to a dysregulated immune system in the context of gut dysbiosis, but mechanisms have not been systematically studied within large RCTs. Microbiomic analysis will use next-generation sequencing, and metabolites will be assessed by mass spectrometry to detect volatile organic and other compounds produced by microbes or the host. We will explore differences between disease cases and controls, as well as exploring the actions of trial interventions. Impacts of this research are multiple: translation of knowledge of mechanisms promoting gut health may explain outcomes or suggest alternate strategies to improve health. Results may identify new non-invasive diagnostic or monitoring techniques, preventative or treatment strategies for NEC or LOS, or provide data useful for risk stratification in future studies. Mechanistic evaluation might be especially informative where there are not clear effects on the primary outcome (ISRCTN 12554594).

Modeling Seasonal and Spatiotemporal Variation: The Example of Respiratory Prescribing.

Many measures of chronic diseases, including respiratory disease, exhibit seasonal variation together with residual correlation between consecutive time periods and neighboring areas. We demonstrate a strategy for modeling data that exhibit both seasonal trend and spatiotemporal correlation, using an application to respiratory prescribing. We analyzed 55 months (2002-2006) of prescribing data from the northeast of England, in the United Kingdom. We estimated the seasonal pattern of prescribing by fitting a dynamic harmonic regression (DHR) model to salbutamol prescribing in relation to temperature. We compared the output of DHR models to static sinusoidal regression models. We used the DHR-fitted values as an offset in mixed-effects models that aimed to account for the remaining spatiotemporal variation in prescribing rates. As diagnostic checks, we assessed spatial and temporal correlation separately and jointly. Our application of a DHR model resulted in a better fit to the seasonal variation of prescribing than was obtained with a static model. After adjusting for the fitted values from the DHR model, we did not detect any remaining spatiotemporal correlation in the model's residuals. Using a DHR model and temperature data to account for the periodicity of prescribing proved to be an efficient way to capture its seasonal variation. The diagnostic procedures indicated that there was no need to model any remaining correlation explicitly.

Patterns of Coral-Reef Finfish Species Disappearances Inferred from Fishers' Knowledge in Global Epicentre of Marine Shorefish Diversity.

In the Philippines, very high fishing pressure coincides with the globally greatest number of shorefish species, yet no long-term fisheries data are available to explore species-level changes that may have occurred widely in the most species rich and vulnerable marine ecosystem, namely coral reefs. Through 2655 face-to-face interviews conducted between August 2012 and July 2014, we used fishers' recall of past catch rates of reef-associated finfish to infer species disappearances from catches in five marine key biodiversity areas (Lanuza Bay, Danajon Bank, Verde Island Passage, Polillo Islands and Honda Bay). We modeled temporal trends in perceived catch per unit effort (CPUE) based on fishers' reports of typical good days' catches using Generalized Linear Mixed Modelling. Fifty-nine different finfish disappeared from catches between the 1950s and 2014; 42 fish were identified to species level, two to genus, seven to family and eight to local name only. Five species occurring at all sites with the greatest number of fishers reporting zero catches were the green bumphead parrotfish (Bolbometopon muricatum), humphead wrasse (Cheilinus undulatus), African pompano (Alectis ciliaris), giant grouper (Epinephelus lanceolatus) and mangrove red snapper (Lutjanus argentimaculatus). Between the 1950s and 2014, the mean perceived CPUE of bumphead parrotfish declined by 88%, that of humphead wrasse by 82%, African pompano by 66%, giant grouper by 74% and mangrove red snapper by 64%. These declines were mainly associated with excess and uncontrolled fishing, fish life-history traits like maximum body size and socio-economic factors like access to market infrastructure and services, and overpopulation. The fishers' knowledge is indicative of extirpations where evidence for these losses was otherwise lacking. Our models provide information as basis for area-based conservation and regional resource management particularly for the more vulnerable, once common, large, yet wide-ranging reef finfish species.

Cytokine responses in birds challenged with the human food-borne pathogen Campylobacter jejuni implies a Th17 response.

Development of process orientated understanding of cytokine interactions within the gastrointestinal tract during an immune response to pathogens requires experimentation and statistical modelling. The immune response against pathogen challenge depends on the specific threat to the host. Here, we show that broiler chickens mount a breed-dependent immune response to Campylobacter jejuni infection in the caeca by analysing experimental data using frequentist and Bayesian structural equation models (SEM). SEM provides a framework by which cytokine interdependencies, based on prior knowledge, can be tested. In both breeds important cytokines including pro-inflammatory interleukin (IL)-1ß, , IL-4, IL-17A, interferon (IFN)-γ and anti-inflammatory IL-10 and transforming growth factor (TGF)-ß4 were expressed post-challenge. The SEM revealed a putative regulatory pathway illustrating a T helper (Th)17 response and regulation of IL-10, which is breed-dependent. The prominence of the Th17 pathway indicates the cytokine response aims to limit the invasion or colonization of an extracellular bacterial pathogen but the time-dependent nature of the response differs between breeds.

Ablative therapy for people with localised prostate cancer: a systematic review and economic evaluation.

BACKGROUND: For people with localised prostate cancer, active treatments are effective but have significant side effects. Minimally invasive treatments that destroy (or ablate) either the entire gland or the part of the prostate with cancer may be as effective and cause less side effects at an acceptable cost. Such therapies include cryotherapy, high-intensity focused ultrasound (HIFU) and brachytherapy, among others. OBJECTIVES: This study aimed to determine the relative clinical effectiveness and cost-effectiveness of ablative therapies compared with radical prostatectomy (RP), external beam radiotherapy (EBRT) and active surveillance (AS) for primary treatment of localised prostate cancer, and compared with RP for salvage treatment of localised prostate cancer which has recurred after initial treatment with EBRT. DATA SOURCES: MEDLINE (1946 to March week 3, 2013), MEDLINE In-Process & Other Non-Indexed Citations (29 March 2013), EMBASE (1974 to week 13, 2013), Bioscience Information Service (BIOSIS) (1956 to 1 April 2013), Science Citation Index (1970 to 1 April 2013), Cochrane Central Register of Controlled Trials (CENTRAL) (issue 3, 2013), Cochrane Database of Systematic Reviews (CDSR) (issue 3, 2013), Database of Abstracts of Reviews of Effects (DARE) (inception to March 2013) and Health Technology Assessment (HTA) (inception to March 2013) databases were searched. Costs were obtained from NHS sources. REVIEW METHODS: Evidence was drawn from randomised controlled trials (RCTs) and non-RCTs, and from case series for the ablative procedures only, in people with localised prostate cancer. For primary therapy, the ablative therapies were cryotherapy, HIFU, brachytherapy and other ablative therapies. The comparators were AS, RP and EBRT. For salvage therapy, the ablative therapies were cryotherapy and HIFU. The comparator was RP. Outcomes were cancer related, adverse effects (functional and procedural) and quality of life. Two reviewers extracted data and carried out quality assessment. Meta-analysis used a Bayesian indirect mixed-treatment comparison. Data were incorporated into an individual simulation Markov model to estimate cost-effectiveness. RESULTS: The searches identified 121 studies for inclusion in the review of patients undergoing primary treatment and nine studies for the review of salvage treatment. Cryotherapy [3995 patients; 14 case series, 1 RCT and 4 non-randomised comparative studies (NRCSs)], HIFU (4000 patients; 20 case series, 1 NRCS) and brachytherapy (26,129 patients; 2 RCTs, 38 NRCSs) studies provided limited data for meta-analyses. All studies were considered at high risk of bias. There was no robust evidence that mortality (4-year survival 93% for cryotherapy, 99% for HIFU, 91% for EBRT) or other cancer-specific outcomes differed between treatments. For functional and quality-of-life outcomes, the paucity of data prevented any definitive conclusions from being made, although data on incontinence rates and erectile dysfunction for all ablative procedures were generally numerically lower than for non-ablative procedures. The safety profiles were comparable with existing treatments. Studies reporting the use of focal cryotherapy suggested that incontinence rates may be better than for whole-gland treatment. Data on AS, salvage treatment and other ablative therapies were too limited. The cost-effectiveness analysis confirmed the uncertainty from the clinical review and that there is no technology which appears superior, on the basis of current evidence, in terms of average cost-effectiveness. The probabilistic sensitivity analyses suggest that a number of ablative techniques are worthy of further research. LIMITATIONS: The main limitations were the quantity and quality of the data available on cancer-related outcomes and dysfunction. CONCLUSIONS: The findings indicate that there is insufficient evidence to form any clear recommendations on the use of ablative therapies in order to influence current clinical practice. Research efforts in the use of ablative therapies in the management of prostate cancer should now be concentrated on the performance of RCTs and the generation of standardised outcomes. STUDY REGISTRATION: This study is registered as PROSPERO CRD42012002461. FUNDING: The National Institute for Health Research Health Technology Assessment programme.