P < 0.05) with two SNPs. During the follow‐up period, five SNPs were nominally associated with a poorer treatment response  and one with a more favorable response (rs6928813 [CNR1]). Within the fear‐based subset, the effect of rs806365 survived multiple testing corrections (P < 0.0016). We found very limited evidence for an association between variants in endocannabinoid system genes and treatment response once multiple testing corrections were applied. Larger, more homogenous cohorts are needed to allow the identification of variants of small but statistically significant effect and to estimate effect sizes for these variants with greater precision in order to determine their potential clinical utility. © 2016 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc.Extinction learning is an important mechanism in the successful psychological treatment of anxiety. Individual differences in response and relapse following Cognitive Behavior Therapy may in part be explained by variability in the ease with which fears are extinguished or the vulnerability of these fears to re‐emerge. Given the role of the endocannabinoid system in fear extinction, this study investigates whether genetic variation in the endocannabinoid system explains individual differences in response to CBT. Children  with a primary anxiety disorder diagnosis were recruited. We investigated the relationship between variation in the CNR1, CNR2, and FAAH genes and change in primary anxiety disorder severity between pre‐ and post‐treatment and during the follow‐up period in the full sample and a subset with fear‐based anxiety disorder diagnoses. Change in symptom severity during active treatment was nominally associated ( Childhood anxiety disorders are very common  and 2‐arachidonoylglycerol [2‐AG]), and the catabolic enzymes for endocannabinoid degradation (fatty acid amide hydrolase [FAAH] for AEA and monoacylglycerol lipase [MAGL] for 2‐AG). Considerable research supports the hypothesis that endogenous endocannabinoid signaling regulates anxiety. There is also suggestive evidence that targeting components of the ECB system via activation of CB1 receptors or by manipulating FAAH activity may produce anxiolytic effects [Kathuria et al., Animal research has shown that genetic deletion and pharmacological blockade of CB1 receptors impedes extinction [Marsicano et al., Recent research has investigated the effects of genetic variability in human endocannabinoid signaling for fear extinction. Numerous single nucleotide polymorphisms (SNPs) have been identified in CNR1 and CNR2, the genes that encode for cannabinoid receptor 1 and 2, respectively and in FAAH, the gene that encodes for the FAAH protein, the primary regulator of AEA signaling in the brain [Cravatt et al., Research in mice has shown that FAAH inhibitors facilitate extinction by augmenting AEA signaling in the amygdala. Similarly, healthy carriers of the low‐expressing A allele at rs324420, which leads to reduced expression of FAAH and elevated levels of AEA showed reduced amygdala activity [Hariri et al., In the current study, we tested the association between polymorphisms of the CNR1, CNR2, and FAAH genes and response to CBT in children and adolescents with an anxiety disorder diagnosis. To our knowledge, this is the first study to investigate genetic variation in the endocannabinoid system and response to a psychological treatment. We began by testing our hypotheses in a large sample of children  experiencing the full range of anxiety disorder diagnoses and who had received a course of CBT in order to maximize power to detect genetic effects. However, one possibility is that extinction learning may be implicated more or less in the mechanisms of treatments for different disorders. For example, extinction learning may be of greater relevance for the successful treatment of predominantly fear based disorders such as specific phobias and to a lesser extent for distress based disorders like generalized anxiety disorder [Borkovec and Ruscio, We tested two hypotheses. Firstly, that genetic variation in CNR1, CNR2, and FAAH would be significantly associated with change in symptom severity from baseline to post‐treatment reflecting the influence of genetic variation in the ECB system during the active treatment period. One possibility is that any effect of ECB genes on early symptom change may reflect the role of the ECB system in the extinction of fear. Second, we examined whether ECB genetic variation was associated with change in symptom severity from post‐treatment to follow‐up reflecting the influence of ECB genetic variation on maintenance of treatment gains. While for some, this will reflect a period in which they continue to consolidate the gains made during treatment, for others this may reflect a period in which they begin experiencing a relapse of symptoms. One possibility is that any effect of ECB genes on symptom change and specifically the continuance of treatment gains during the follow‐up period may reflect the role of the ECB system in the maintenance of extinction memories.Participants were recruited for the Genes for Treatment Study (G × T) study, a multi‐site international collaboration designed to identify clinical, demographic and genetic predictors of outcome following CBT for anxiety disorders in children and adolescents [Hudson et al., Diagnoses were made using the Anxiety Disorders Interview Schedule for DSM‐IV (ADIS‐IV‐C/P) [Silverman and Albano, DNA was collected using buccal swabs or Oragene saliva samples . Buccal swab DNA was extracted using established procedures designed to maximize the purity and yield of the sample [Freeman et al., Genotypes for seven CNR1 polymorphisms , one CNR2 polymorphism (rs2501431) and one FAAH polymorphism (rs324420) drawn from the candidate gene literature on fear extinction, emotional processing, and response to antidepressant treatment were genotyped by LGC Genomics  using validated arrays with KASP technology or were obtained from the Illumina Core Exome‐12v1.0 microarray. Four additional markers, which were genotyped using both platforms showed an average of 98% consensus on genotype calls.For the subset of the sample with array data (n = 980) additional genotypes were available for 123 CNR1 polymorphisms, 159 CNR2 polymorphisms, and 318 FAAH polymorphisms. Array data was included in all analyses to provide LD context for multiple testing corrections and to provide more accurate gene‐based tests of association.P‐value > 10−5). SNPs were included if they could be imputed to the December 2013 release of the 1000 Genomes Project reference [1000GenomesConsortium, 2 > 0.8) with at least one tagging SNP. This indicates good coverage of all linkage regions across the genes studied. To account for patterns of linkage disequilibrium (LD) between SNPs, LD based clumping was performed for each analysis to reduce the SNP set to a smaller number of clumps of correlated SNPs.Quality control and imputation procedures for those samples with microarray data are provided in full elsewhere [Coleman et al., Each site had trial‐specific Human Ethics and Biosafety Committee approval for the collection of biological samples with the research conducted in accordance with the Declaration of Helsinki. In all instances parents provided written informed consent, children assent. The storage and analysis of DNA was approved by the King's College London Psychiatry, Nursing and Midwifery Research Ethics Sub‐Committee.Two outcome measures were considered in our primary analyses. First, the change in severity (CSR score) of the primary anxiety diagnosis from baseline to post‐treatment, reflecting the active treatment period. Second, the change in severity of the primary anxiety diagnosis from post‐treatment to follow‐up time points, reflecting a period of consolidation or risk for relapse.Linear mixed effects models were performed to investigate the effect of ECB polymorphisms on change in severity (CSR score) of the primary anxiety disorder diagnosis. All genotypes were coded to reflect an additive model where −1, common homozygote; 0, heterozygote; and 1, rare homozygote. To make use of all available post baseline measurements and provide estimates in the presence of missing data, the effects of predictors of response were estimated using mixed models fitted with full maximum likelihood. All models included either the fixed effects of baseline severity  or post‐treatment severity , age (centred at the mean), and gender. Analyses investigating post to follow‐up change also included the linear and quadratic effects of time to account for the curvilinear slope of treatment response across this period. All models included the random effects of individual to account for correlations between repeated measures from the same individual. We also included a higher order random effect of trial to account for between trial differences in outcome. As each trial was conducted at a single site, this random effect also accounted for between‐site differences.In all analyses, the beta values of variables predicting a more favorable response to treatment or continued gains during the follow‐up period  are negative, while variables predicting a less favorable response are positive. Analyses were performed in STATA version 12.0.All analyses , gene‐based association tests) consider data from all available SNPs including both directly genotyped SNPs available on the entire sample  and the additional SNPs available for the subset of the sample with array data (n = 980). N's are given for each sentinel SNP in the corresponding table for each analysis.P‐value using PLINK [Purcell et al., P‐value in the clump), and contained all SNPs in linkage disequilibrium with the sentinel . To correct for multiple testing, revised significance thresholds were calculated based on the number of independent clumps identified for each analysis.Results from the initial association analyses were clumped based on patterns of LD according to Gene‐based tests for association with response were performed using VEGAS modified to use the hg19 genome build [Liu et al., Power calculations indicated that with a sample size of 980, we had 80% power to detect a variant with a minor allele frequency of 0.05 capturing 1.6% of variance with a corrected alpha level of 0.017. For variants explaining 0.1%, 0.5%, and 1% of the variance we had 1.6%, 18%, and 50% power, respectively.P < 0.0001) and post‐treatment and follow‐up time points  = 9.40, P < 0.0001). We initially explored the effects of clinical  and demographic factors  on change in symptom severity between baseline and post‐treatment. Findings were broadly similar to those reported for the full sample [Hudson et al., P < 0.0001; β = 0.11, P = 0.005, and β = 0.06, P = 0.044, respectively. Higher severity at baseline was associated with significantly poorer response to treatment . However, treatment response did not differ according to sex, age, or treatment type . For change in symptom severity between post‐treatment and follow‐up time points, individuals with Specific Phobias showed a significantly poorer treatment response compared to those with Generalized Anxiety Disorder . Higher severity at post‐treatment was also associated with significantly poorer response during the follow‐up period . Response during the follow‐up period did not differ according to sex, age, or treatment type . A highly similar pattern of results was observed when the sample was restricted to those with a fear‐based anxiety disorder diagnosis only.Clinical outcomes in the full sample were comparable to previously reported estimates [Hudson et al., P values for multiple testing corrections (P < 0.0017). Each independent clump was represented by a sentinel SNP , and contained all SNPs in linkage disequilibrium with the sentinel . Two independent clumps were nominally associated with response (P < 0.05). An increasing number of copies of the minor allele of rs12133557 was associated with a more favorable treatment response  across the treatment period. In contrast, the minor allele of the sentinel SNP rs6454676 (with this clump including the directly genotyped rs1535255) was associated with a poorer treatment response  are available in the supplementary materials. Gene based association tests were non‐significant .Thirty independent clumps were identified based on patterns of LD and were used to calculate adjusted P values for multiple testing corrections (p < 0.0017). Two independent clumps were nominally associated with response (P < 0.05) with an increasing number of copies of the minor allele of the sentinel SNP rs6454676 (with this clump including the directly genotyped rs1535255) associated with a poorer treatment response .Twenty‐nine independent clumps were identified based on patterns of LD and were used to calculate adjusted P values for multiple testing corrections (P < 0.0017). Of these, five independent clumps were associated with a poorer response  during the follow‐up period at a nominal P‐value of < 0.05  while one independent clump (sentinel SNP: rs6928813) predicted a more favorable response . All clumps with P < 0.05 are displayed in Table P < 0.0017) with rs806365 having the lowest P‐value at P = 0.004. Analyses restricted to a subset that identified as having four White European grandparents are available in the supplementary materials. Gene based association tests on the full sample were all non‐significant .Thirty independent clumps were identified and were used to calculate adjusted P values for multiple testing corrections (P < 0.0016). Of these, three independent clumps were associated with a poorer response  during the follow‐up period at a nominal P‐value of <0.05 . Gene based tests on this subset were non‐significant .Thirty‐one independent clumps were identified and were used to calculate adjusted P < 0.05) with change in symptom severity in both the entire sample and the subset with fear based diagnoses. An increasing number of copies of the minor allele of rs12133557 was associated with a more favorable response during the active treatment period. In contrast, an increasing number of copies of the minor allele of rs6454676 was associated with a poorer response during the active treatment period. However, these effects did not survive stringent multiple testing correction in either the entire sample or subset restricted to fear‐based diagnoses only. Furthermore, we hypothesized that individual differences in the continuation of treatment gains during the follow‐up period may be associated with genetic variation in ECB genes. Six independent clumps were nominally associated (P < 0.05) with change in symptom severity over the follow‐up period in the entire sample, five where an increasing number of copies of the minor allele was associated with a poorer response , and one with a more favorable response (sentinel SNP: rs6928813). Again, none of these effects survived multiple testing corrections. Three of these same sentinel SNPs were also nominally associated with response in the fear‐based subset . The effect size of these SNPs was larger in the fear‐based subset with the effect of rs806365 remaining significant after multiple testing corrections were applied. Gene based tests of association were all non‐significant. In summary, our findings suggest only very limited evidence for a role of genetic variation in the ECB system in predicting individual differences in response to CBT for anxiety disorders in children and adolescents. Where these effects do exist they are very small and appear to have greater predictive power when examined in a sample restricted to fear‐based anxiety diagnoses only.Given the potential role of the ECB system in fear extinction and the maintenance of extinction memories, this study investigated whether genetic variation in the CNR1, CNR2, and FAAH genes was associated with response to CBT in children and adolescents with an anxiety disorder. In our analyses, two SNPs (rs12133557 and rs6454676) were nominally associated (P = 0.004) and remained significantly associated after multiple testing correction in the fear‐based anxiety diagnosis subset (P = 0.0011). While not previously investigated with respect to anxiety linked traits or fear extinction, this locus has shown preliminary evidence of association with insulin resistance, risk for Type 2 diabetes and coronary heart disease [de Miguel‐Yanes et al., The strongest finding in our analyses was for SNP rs806365, which was nominally associated with a poorer response during the follow‐up period in the full sample . The change in symptom severity over the follow‐up period was smaller and less variable than that seen during the active treatment phase with 47% of participants showing no change in symptom severity from post‐treatment to follow‐up. Only a minority of participants (17%) showed any worsening of symptoms over the follow‐up period. Thus, analyses of the follow‐up period were limited by the reduced variance in response.A more general limitation of the present study is that it took a candidate gene approach. However, this limitation was mitigated by the inclusion of array data on a subset of the sample providing more comprehensive coverage of the genes under investigation and LD context for the calculation of multiple testing corrections. Nonetheless within psychiatric genetics broadly, and the therapygenetics literature to date, candidate gene studies have often failed to replicate, have typically reported very small effect sizes and are sensitive to publication bias [Duncan and Keller, Given the challenges of candidate gene studies, it will become increasingly important for the therapygenetics field to work collaboratively to assemble large datasets that can be used to both study the mechanisms underlying CBT response and which will allow us to exploit hypothesis‐free whole genome based approaches. These methods have the potential to identify novel and unexpected variants associated with treatment response [Coleman et al., In summary, this is the first study to investigate the role of genetic variation in the endocannabinoid system and response to psychological therapy for anxiety disorders. A small number of genetic variants were nominally associated with individual differences in treatment response during the active treatment and follow‐up period. Only one of these effects remained significant after multiple testing corrections and in a sample restricted to those with a fear‐based anxiety disorder diagnosis. The ECB system remains a plausible target for involvement in response to psychological therapies underpinned by the principles of extinction learning. However, the effect of any single variant is likely to be very small given the complexity and multitude of mechanisms underpinning response to psychological treatments. The use of larger samples with greater statistical power and more homogeneous samples which reduce noise in the data would allow us to estimate the effect size of any variant with greater precision. Notwithstanding this, there are potentially large benefits for patients and wider society in knowing more about what determines who responds well to psychological therapies, and why. Thus, therapygenetics remains an important area for further research.Additional supporting information may be found in the online version of this article.Supporting Information.Click here for additional data file.


Biosurfactants have not fulfilled the expectations generated when they were initially discovered. Heavy vacuum gas oil (HVGO) is conventionally treated with costly thermo‐chemical processes and cause environmental pollution. What if we could bio‐upgrade this HVGO at the same time that we produce a fine chemical? Because of their natural origin, in many cases, they show biocompatibility making them particularly relevant in the cosmetic, pharmaceutical and food industries ; this ambitious objective requires the transformation of the economy into more climate‐friendly and less energy‐consuming one. That means that new technologies have to be cleaner and more energy‐efficient. As in the EU, global trends advance towards a more sustainable economy. In this context, industrial biotechnologists have the responsibility to lead the way, transforming the old industries into cleaner and more efficient ones. This is precisely the type of contribution that Ismael and colleagues have reported in the paper published in this issue. They have taken a traditional industry (petroleum refinery) and have studied how they can transform one of the thermo‐chemical steps used to upgrade HVGO (energy intensive) into a biological process  at the same time that they add value to the process by the production of biosurfactants . Their approach is therefore ‘doubly green’; they intend to transform an energy intensive process into a less energy‐dependent one at the same time that they contribute to the reduction in the utilization of chemical surfactants by increasing the production of other more ‘environmentally friendly’ ones (rhamnolipids).The European Union has proposed an 80% cut in COPseudomonas putida AK6U  are produced. For the successful industrial production of these compounds from HVGO not only growth conditions but also industrial purification of the compounds remained to be explored. It is known that rhamnolipid production is tightly regulated at different levels, with catabolite repression being one of the factors that affect its production; however in mixtures such as HVGO the presence of easily degraded carbon sources is not anticipated. High carbon‐to‐nitrogen ratios favour biosurfactant production and this ratio is also favourable in HVGO; the rhamnolipid yield obtained in this carbon and sulfur source is similar to that reported for other bacteria (9.8 g l−1 in 18 days).Interestingly, only one strain, P. putida AK6U. HVGO is mainly composed of asphaltenes and maltenes. Asphaltenes represent the heavier compounds of crude oil and contain nitrogen, oxygen, sulfur, vanadium and nickel compounds as well as metal‐containing petroporphyrins and heterocycles; asphaltenes are formed of fused naphthenic and aromatic molecules with small aliphatic side‐chains and polar functional groups. Maltenes contain resins , aromatic compounds and linear and branches hydrocarbons . Pseudomonas putida AK6U is able to slightly decrease the boiling point of the heavy fuel‐oil fraction with the concomitant increase in the proportion of lighter distillate diesel fraction. FT‐ICR‐MS analysis indicated that biological treatment increased the number of hydrocarbon and sulfur compounds in the maltene fraction of HVGO and decreased the amount of heavy fuel oil, suggesting the mobilization of asphaltenes to the maltene fraction. As the authors point out, the compositional differences between the biotreated and original HVGO are not sufficient to induce significant changes in the distillation profiles of the biotreated HVGO but ‘on the industrial refining scale where huge volumes of the oil are processed, even small differences might lead to considerable increased yield, which further improves the revenue capture of the refining process’. Interestingly, the authors have previously identified that P. putida AK6U is able to use compounds such as dibenzothiophene, benzothiophene, 3‐methyldibenzothiophene, 4,6‐dimethyldibenzothiophene and dibenzylsufide as sole sulfur sources  barrels of heavy oil are available worldwide, therefore, together with vacuum residue (VR) this oil is considered as an alternative source for fuel  estimated that approximately 6 trillion (6 × 10None declared.


Rhodospirillium rubrum, stands out as an example of the synergistic contribution of chemical engineering and applied microbiology to sustainable biomaterial manufacturing, paving the way to similar applications for other syngas derived bioproducts.Successful merging of chemical and biotechnological operations is essential to achieve cost‐efficient industrialization of bio‐based processes. The demonstration of the use of syngas, derived from microwave assisted pyrolysis of municipal solid waste, for the improved growth and poly‐3‐hydroxybutyrate production in  Anaerobic growth also enables CO and CO2 assimilation, both in light and darkness. The ability of R. rubrum for producing PHB when grown on syngas has been described  bacteria.In conclusion, novel chemical and biotechnological processes are required to bring cost‐efficient bio‐based plants to industrial reality. The success of such hybrid biorefineries will stand on the synergistic contribution of both chemical and fermentative processes. Revelles et al.  demonstr


In healthy circumstances the immune system coordinates tissue repair responses in a tight balance that entails efficient inflammation for removal of potential threats, proper wound closure, and regeneration to regain tissue function. Pathological conditions, continuous exposure to noxious agents, and even ageing can dysregulate immune responses after injury. This dysregulation can lead to a chronic repair mechanism known as fibrosis. Alterations in wound healing can occur in many organs, but our focus lies with the lung as it requires highly regulated immune and repair responses with its continuous exposure to airborne threats. Dysregulated repair responses can lead to pulmonary fibrosis but the exact reason for its development is often not known. Here, we review the diversity of innate immune cells of myeloid origin that are involved in tissue repair and we illustrate how these cell types can contribute to the development of pulmonary fibrosis. Moreover, we briefly discuss the effect of age on innate immune responses and therefore on wound healing and we conclude with the implications of current knowledge on the avenues for future research. When a 22.1The events associated with acute injury involve the activity of the innate part of the immune system Fig. . InfiltrThe release of DAMPs and PAMPs occurs in parallel with activation of the coagulation cascade that is initiated by damage to blood vessels. This is the beginning of the clotting phase. Clotting prevents blood loss and protects the open wound from further exposure. Clotting also has a direct effect on resident tissue macrophages and leads to their activation through exposure to free heme from coagulation and through thrombin‐induced cleavage of protease‐activated receptors found on macrophages and other resident cells , and pulmonary fibrosis , but often its cause is unknown (IPF) Wynn, . The fibN‐acetylcysteine have been shown to be effective in reducing the functional decline and disease progression in pulmonary fibrosis fibroblasts, and subsequent production of ECM, and the dysregulated activity of macrophages  and ‐eides (likeness), refers to cells that resemble those in bone marrow. In a hematopoietic context, the myeloid line actually refers to those cells that in fact originate from bone marrow progenitors and form the granulocytic and monocytic lineages, but not the lymphoid lineage  . These Ly6Chi monocytes can migrate from bone marrow to blood after stimulation with CCL2 and CCL7, which is why they have high expression of the chemokine receptor CCR2  and CD16 (a low affinity immunoglobulin G receptor). With these two markers it is possible to identify three monocyte populations in human blood: CD14++CD16− , CD14+CD16+ (intermediate monocytes), and CD14+CD16++ , accounting for around 85%, 5% and 9% of all monocytes, respectively , this study was not able to prove that these macrophages originate from classical Ly6Chi monocytes. Another study using two mouse models of liver fibrosis showed that inhibiting the accumulation of classical Ly6Chi monocytes during the resolution phase of fibrosis accelerated scar resolution  induce the activation of cardiac fibroblasts towards myofibroblasts via direct cell‐to‐cell interaction, to a greater extent than the effect of TGF‐β on fibroblasts  can clarify this.Most studies on immune responses in fibrosis have focused on the influence of monocyte‐derived macrophages and not on monocytes per se, and it is therefore still unclear what the actual contributions of the classical Ly6C3.1.2Macrophages are tissue‐resident myeloid leukocytes belonging to the innate immune system that are key in maintaining tissue homeostasis. They have heterogeneous functions ranging from phagocytosis of microorganisms, ECM components, or dying cells to the production of cytokines for the modulation of other cells involved in immune responses  in fibrosis, particularly in the lung, still needs to be clarified.3.1.3DCs mature from myeloid progenitor cells after stimulation with granulocyte macrophage colony stimulating factor (GM‐CSF), IL‐4, tumor necrosis factor alpha (TNF‐α), and FMS‐like tyrosine kinase 3 ligand (FLT3L) Ardavín, . DCs arecDCs originate from hematopoietic stem cells in bone marrow that develop into lineage‐restricted macrophage‐DC progenitors, which in turn differentiate into common DC progenitors  , is currently being developed and tested as a potential treatment for pulmonary fibrosis fibroblast differentiation, and their regulation of other processes like angiogenesis. However, the lack of a standard technique for the accurate characterization of fibrocytes hampers the identification of their biological functions in pathological conditions. More studies are necessary to determine the exact functional and phenotypical overlap between the myofibroblasts originating from fibrocytes and from fibroblasts and the contribution of each type to fibrotic diseases.3.23.2.1Neutrophils are polymorphonuclear leukocytes that originate from bone marrow myeloid progenitors under the influence of granulocyte colony stimulating factor (G‐CSF)  are higher in pulmonary fibrosis patients in comparison to control individuals  and the c‐kit receptor. The former leads to mast cell activation by crosslinking of antigen‐specific IgE bound to FcεR1 receptors by antigens, while the latter results in stimulation after binding of its ligand SCF , which can lead to a prolongation and spreading of inflammation , middle‐aged (9 months), and old mice (24 months). They found that young mice were able to fully restore the lung volume and alveolar surface by day 21, while the middle‐aged mice showed a limited recovery in the same time and the old mice had a total lack of recovery , and mediators such as TGF‐β and IL‐4 are present in both conditions. However, while in tissue repair these traits are transitory, in fibrosis they persist. Even if these phenotypes can point to the development of fibrosis, other characteristics should be taken into consideration for the accurate assessment of fibrosis development. So, when is it accurate to call it fibrosis and when is it simply a repair response? In animal models and in patients with pulmonary fibrosis it is possible to identify fibrosis through physiological and histological characteristics, such as excess ECM deposition, alterations in lung architecture, the formation of fibroblast foci, and a poor or absent pro‐inflammatory aspect. However, some of these features are more difficult to reproduce during in vitro studies, as these models cannot represent all the possible variables found in vivo. It is therefore of importance to keep this in mind when interpreting in vitro experiments, since what one could consider as a fibrotic response could simply be the activation of a repair response. The use of patient samples, human and animal precision‐cut tissue slices, and animal models can provide more accurate information about the dynamics of fibrosis development.The inflammatory phase is not considered to play an important role in the pathogenesis of fibrosis, or at least not during advanced stages of the disease. This has been suggested by the observation that using corticosteroids for treating fibrosis can be detrimental for patients (Fujimoto, Kobayashi, & Azuma, The evidence supporting the essential role of innate immune cells in the development of fibrosis is currently leading to therapeutic developments targeting myeloid cells. For instance, an anti‐galectin‐3 drug called TD139 is going to enter a phase IIB trial (Hirani, Nicol, & MacKinnon, The study of smaller animals like salamanders may also help with finding alternative therapeutic strategies against the development of fibrosis, as these amphibians have the ability of scar‐free repair with full tissue regeneration after tissue damage. Interestingly, the study by Godwin and colleagues shows that, although many features of inflammation of the salamander resemble those of mammals, these amphibians present a more dynamic response to injury with a simultaneous induction of the inflammatory and the anti‐inflammatory phases in the first 24 h (Godwin et al., The authors have no conflict of interest to declare.


L/5 long‐range contact precision of 27%. MetaPSICOV method bases on a combination of classical contact prediction features, enhanced with three distinct covariation methods embedded in a two‐stage neural network predictor. Some unique features of our approach are (1) the tuning between the classical and covariation features depending on the depth of the input alignment and (2) a hybrid approach to generate deepest possible multiple‐sequence alignments by combining jackHMMer and HHblits. We discuss the CONSIP2 pipeline, our results and show that where the method underperformed, the major factor was relying on a fixed set of parameters for the initial sequence alignments and not attempting to perform domain splitting as a preprocessing step. Proteins 2016; 84(Suppl 1):145–151. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.Here we present the results of residue–residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effective sequences, our server achieved an average top‐ The highest precision for those methods and for methods evaluated in previous CASP experiments hovered around 20%  included 36,473,742 entries, that is, it had grown by 67% in the intervening period. In light of this, we attempted to supplement the sequence information for each query sequence. If the HHblits output alignment (A3M file) had <2000 sequences, we constructed an “on the fly” custom database for HHblits using jackHMMer to identify possible homologous sequences in an up‐to‐date release of the UniRef100 database . Then, the prebuilt custom database, along with the query sequence was used as an input for HHblits. Finally, we compared outputs of both runs—HHblits‐UniRef20 and HHblits‐jackHMMer, and selected the alignment with the most sequences as the input for MetaPSICOV. In this way, HHblits was always used to generate the alignments, but any additional sequences detected in new releases of UniRef100 could be incorporated.Crucial elements for contact predictions based on amino acid covariation are accurate large and diverse multiple sequence alignments. We developed a workflow to take advantage of as much public sequence data as possible Fig. . By defahttp://bioinf.cs.ucl.ac.uk/MetaPSICOV), mutual information measuresThe complete MetaPSICOV approach has already been described elsewhere.The covariation methods were selected to represent different approaches to solving the statistical decoupling problem inherent in residue covariation‐based contact predictions  and, therefore, produce only partially overlapping results. Aside from covariation methods, we used classical neural network‐based contact prediction features (for a full list of features used please refer to MetaPSICOV paperNeff) rather than raw sequence numbers to account for this redundancy. In our case, we cluster the protein sequences at a 62% identity threshold (which is the same clustering threshold used to compile the standard BLOSUM62 matrix used in BLAST) and then take the number of clusters as the Neff value.Large MSAs can contain many redundant sequences that do not contribute significant contact information. Therefore, like other authors,de novo structure prediction using MetaPSICOV contacts, we used our previously described approach.Z‐coordinate values within the lipid membrane.To perform SR‐RR, sequence separation < 23) and the other for the long‐range contacts (ELR‐RR). The potentials have the form of a square well with exponential decay above the contact distance threshold (8 Å Cβ‐Cβ distance) and are scaled according to the predicted contact probability for each pair of residues with PPV ≥0.5. In the original PSICOV, the contacts were predicted only for the residues where a covariational signal was observed. Therefore, it was suitable to use a single contact‐related function. In case of MetaPSICOV predictions, where contact probabilities for every pair of residues are reported, we found that separating short‐range and long‐range contact potentials yielded better results. Otherwise, the contributions from short‐range contacts (more abundant and easier to predict) outweigh the impact of long‐range contacts what results in lower long‐range contact satisfaction.We used two residue–residue contact potentials—one representing short‐range contacts  was adjacent to a TBM domain (not assessed here) and thus accumulated more sequences than would otherwise be included in the MSA for the FM domain alone. This would influence MetaPSICOV to overweight the contribution for covariation compared to other features. The other cause of worse than expected performance was anchoring of the alignments toward the more populated easier domain (TBM), resulting in a poor alignment quality for the FM region, but a good alignment for the remainder of the chain.Neff compared to the initial result for the whole protein sequence , and T0789 (PDB id: 4W4L). T0827‐D2 (FM domain) lost almost 250 sequences upon realignment, gaining 10% precision. T0789‐D2 lost 200 A different situation was observed for T0826. This target has 2 domains—D2 is a globular TBM domain (not considered here) and D1 is a transmembrane FM domain. When realigned, the number of sequences in D1 did not change substantially (422 vs. 424 effective sequences), but the contact prediction precision significantly increased. In this case, the improvement came about solely because the sequence alignment was no longer anchored to the C‐terminal (TBM) domain.Although we are focussing here on our contact prediction results, the utility of contact predictions can be put in better context by looking at our (group Jones‐UCL) free modeling predictions made using our predicted contact lists. In every FM case, CONSIP2 server predictions and alignments were manually inspected for domain boundaries, alignment errors, or transmembrane targets and rerun, if needed.L/5 precision = 44%) we were able to produce a model with TM‐score = 0.60  FM targets (including two transmembrane proteins) we were able to achieve GDT‐TS scores > 40 (TM‐score > 0.5).The analysis of outliers in our predictions clearly suggests that multi‐domain proteins should be processed per‐domain. The current CONSIP2 (and MetaPSICOV) server accepts the whole sequence and does not attempt to split the sequence into domains. This resulted in some subpar predictions. We hope to address this shortcoming before the next CASP experiment.Another aspect is setting the sequence coverage criteria appropriately. On one hand, a too stringent sequence coverage requirement might result in losing some sequence information for targets where the sequence data is already scarce. On the other hand, a too permissive sequence coverage requirement could result in finding partial matches for some targets and allowing for insufficient coverage in multi‐domain proteins. It is generally easy to spot and correct these issues when looking at the alignments by eye, but difficult to come up with a completely automated system that can deal with the wide variety of scenarios across the whole range of CASP targets.Our method was also designed to tackle the contact predictions for globular domains as the most general case. In the case of transmembrane domains, building too deep alignments could result in unrelated sequences or drifted domains being included and thus generating false positives in the predicted list of contacts. The notable case here is T0826‐D1, where we included over 400 sequences in the alignment but the contact prediction accuracy was very poor (precision below 10%). Thanks to manual tweaking in the FM category and rerunning the contact predictions on a new alignment, we were able to obtain a satisfactory model and a high contact prediction precision (above 60%).CONSIP2 was created to achieve the deepest achievable sequence alignments by constructing HHblits databases on the fly. It would, however, be more desirable to have a complete up to date HHblits database. We realize that clustering over 35 million sequences is a serious computational endeavour, particularly for a single research group, but perhaps this is a challenge best handled by a community‐wide distributed computing approach, as sequence alignments are required universally and public sequence data is growing at an ever increasing rate.In CASP11, we were able to improve the state‐of‐the‐art in residue–residue contact prediction by combining classical contact prediction features with three covariation‐based methods, within a neural network framework. In our approach, we put an emphasis on constructing the largest possible multiple‐sequence alignments. An important aspect of MetaPSICOV is its ability to modulate the relative impact of covariation‐based and classical features depending on the quality and depth of the MSA. If the alignment is shallow, then covariation features are downweighted, whereas for deep and diverse alignments the covariation features are dominant. It is possible that further improvements of the way this is currently handled could result in further increases in prediction accuracy for smaller numbers of sequences, and this is clearly a focus point for future research.de novo prediction problem for different sizes of MSAs. MetaPSICOV works very well at approximately 200 Neff and above, so although we were able to significantly decrease the required number of sequences in an alignment, there is still a gap between what is feasible for sequence family sizes as they currently are, in the majority case at least, and what is needed to exploit these modeling techniques for really challenging cases. It is clear, that with the current methods it is impossible to solve the protein structure prediction problem with the use of contact predictions alone unless we accumulate many more sequences or are better able to deal with alignments with fewer effective sequences.Overall, we were able to achieve a precision of 27% on the CASP11 contact prediction set which had a median of 44 effective sequences . Our CASP11 results probably show reasonably well what are the realistic expectations for what contact predictions can contribute to the Improvements in this area could come from two directions. One is the evolution of contact prediction algorithms. On the side of covariation, the major issues of indirect coupling and phylogenetic bias were ameliorated in recent years, but are still unresolved.The other issue is the availability of sequence data. We observe an increase in the median Pfam family size,


SVD).Microinfarcts, small ischaemic foci common in ageing brain, are associated with dementia and gait dysfunction. We determined their relationship with dementia, mobility and cerebrovascular disease in an older population‐representative brain donor cohort. These data on microinfarcts were evaluated in relation to pathological assessments of clinically significant cerebral small vessel disease (MRC Cognitive Function and Ageing Study (n = 331). Nine brain areas were staged according to the number of areas affected.Microinfarcts were assessed in the OR 1.41, 95% CI 1.02; 1.96, P = 0.038), whilst cortical and subcortical microinfarct stages were associated with impaired mobility  and falls . Adding data on microinfarcts to a definition of SVD, based on white matter lesions (WMLs), lacunes and significant arteriosclerosis, were assessed by comparing area under ROC curve (AUC) with and without microinfarcts. SVD was significantly related to dementia status with or without inclusion of microinfarcts. Modelling potential pathological definitions of SVD to predict dementia or impaired mobility indicated optimal prediction using combined assessment of WMLs, lacunes and microinfarcts.36% of brains showed at least 1 microinfarct. Higher cortical microinfarct stage was associated with dementia at death  and subcortical microinfarcts (impaired mobility) are related to diverse clinical outcomes. Optimal pathological assessment of significant  In neuropathological practice the term ‘microinfarct’ is used to describe CNS lesions of presumed ischaemic origin that are only detected by microscopic examination Microinfarcts are reported to be associated with a number of clinical and pathological observations in older people. Virtually all such studies to date are based on post‐mortem associations because microinfarcts, as defined above, are not demonstrated at magnetic field strengths (i.e. 3Tesla and below) used currently in routine clinical magnetic resonance imaging (MRI) MRC CFAS, a longitudinal, population‐representative cohort study of cognition and frailty in older people in the UK, has contributed substantially to the emerging consensus that vascular pathology is a major correlate of cognitive decline and dementia in old people In this study the brain donations to three of the six CFAS centres were re‐evaluated by a single neuropathologist (SBW) to record the location and number of microinfarcts in all the blocks used for CERAD evaluations. These new data have allowed us to address a number of important questions.How are microinfarcts associated, in this population representative cohort, with other types of small and large vessel ischaemia? Does the addition of complete data on microinfarcts alter previous conclusions about SVD published by CFAS, in particular by increasing the ascertainment of an SVD diagnosis, and in terms of the impact on pathological correlates of dementia? Do the findings and analyses offer useful insights into operationalizing the pathological evaluation of SVD?All brain donations n = 331) corresponding to CFAS data release 4.0 from 3 CFAS Centres  were examined for this study. These brains were prepared for archiving as previously described  correspoAn indication of the severity and anatomical dispersion of lesions was recorded as the number of regions in which microinfarcts and subcortical lesions were present in each case. For the analysis in this study, we have used the word ‘stage’ to encompass the number of regions affected although we do not imply any hierarchic element to the anatomical dispersion or severity of microinfarcts.Existing CFAS data were used to define SVD in the absence of either microinfarcts/subcortical lesions detected in the review conducted for this analysis as described above, or any previous microinfarct data that had been recorded. Details of the definitions and techniques used to detect these lesions are described previously. Briefly, severe or moderate arteriosclerosis was evaluated by microscopy in H&E sections as thickened vessel profiles with variable hyalinization of the muscle media and loss of smooth muscle nuclei. Lacunes were cystic lesions measuring less than 1 cm in diameter that were observed at brain dissection by macroscopic inspection. WMLs were detected by MRI scanning of 3 formalin fixed, 1 cm thick, coronal cerebral hemisphere slices as previously described. Significant WML, in terms of a CFAS diagnosis of SVD, corresponds to the presence of WML at modified Schelten's scale scores of 5 or 6 in any of this sample. Scheltens’ score 5 implies the presence of at least one area of deep hemispheric white matter T2 signal attenuation greater than 11 mm in any diameter. Scheltens’ score 6 refers to the presence of larger and more confluent areas of MRI white matter attenuation. Previous work in CFAS including this cohort of brain donors has shown that scores of 5 and 6 are significantly associated with risk of dementia Data for CAA were available from existing CFAS data collected by neuropathologists blind to clinical data using immunohistochemical or tinctorial methods. The severity of meningeal and parenchymal CAA was scored semi‐quantitatively according to the CERAD protocol, as either ‘none’, ‘mild’, ‘moderate’ or ‘severe’, in the hippocampal, entorhinal and neocortical regions. A final semi‐quantitative score was obtained by calculating the maximum score across these areas. These scores were simplified for analysis: ‘severe’ was merged with ‘moderate’, and ‘none’ was merged with ‘mild’.All CFAS brain donors underwent longitudinal assessments in life using a standard interview battery. Existing data relating to clinical diagnoses and self‐reported risk factors were available including dementia status at death (based on data from the last assessment before death and a Retrospective Informant Interview [RINI]), and any self‐reported medical history of angina, heart attack, stroke, systemic hypertension or diabetes mellitus (DM). The ApoEε4 status for each brain donor was known from previous genetic analyses. In the absence of formal gait‐analysis data, a mobility score was created by combining CFAS interview questions regarding mobility and tendency to fall, and based on the last interview before death. A semi‐quantitative score of 0 was assigned if the participant was ambulant, score 1 if there were recent falls , and score 3 if the participant was chair or bed bound.P‐value of less than 0.05 indicated statistical significance. Statistical analyses were performed using statistical package STATA, version 12.Logistic regression analyses were used to verify the relationship between the presence of dementia and vascular lesions. To study the relationship between mobility scores and microinfarct stages, and between microinfarct stages and WML scores, ordinal logistic regression analyses were used. Because microinfarct stages are counts of regions containing lesions, and were over‐dispersed, negative binomial regression was used when assessing risk factors for microinfarct stages. The effect of adding data on microinfarcts into the definition of SVD was assessed by comparing the logistic regression models with and without microinfarcts based on area under receiver‐operating characteristic curve (AUC). All tests were two‐tailed. Confidence intervals (95% CI) were calculated for the odds ratio (OR), incidence rate ratio (IRR), β and AUC. A The demographic and pathological details of the cohort are presented in Table Overall 36% of brains contained at least one microinfarct. The frequency of microinfarcts in cortical and subcortical regions according to dementia status is shown in Table Using the mobility scores generated from the interview data as the dependent variable in ordinal logistic regression analysis, and microinfarct stages as independent variables, higher microinfarct stages in cortical, subcortical and total regions were significantly related to impaired mobility and falls. The analysis was controlled by age of death, sex, education and gap between last mobility assessment and death Table .The prevalence of self‐reported hypertension (HTN) was 39%, Diabetes mellitus (DM) 11%, angina 19%, myocardial infarct (MI) 12% and cerebrovascular accident (CVA) 15% in this cohort of CFAS respondents. Twenty‐three percent of the respondents had at least one APOEε4 allele. Moderate or severe CAA was present in 22% of the brains. Negative binomial regression was used to investigate possible risk factors for microinfarction. Microinfarcts stages were selected as dependent variables and angina, CVA, DM, HTN, MI, presence of at least one APOEε4 allele, and moderate or severe CAA, were selected as independent variables. All analyses were controlled by age at death and sex  and a periventricular (PV) WML median score of 2 (range 0–3). To explore a relationship between MRI WML and microinfarcts ordinal logistic regression analyses were used with deep WML and PVWML scores as dependent variables. Microinfarct stages were selected as independent variable, and all analyses were controlled by age of death and sex Table .Cortical microinfarcts in more regions was significantly related to higher deep WML scores.Among the 300 participants in whom clinical dementia status was established, SVD was present in 55 participants without dementia and 109 with dementia. The addition of microinfarcts into the operational definition of SVD identified 11 additional respondents with SVD: seven of these had clinical dementia and four did not. To investigate the effect of adding data on microinfarcts into the definition of SVD in relation to clinical dementia status, we compared the area under ROC curve (AUC) for two logistic regression models: Model 1 used the previously defined CFAS SVD status without microinfarct data; Model 2 incorporated microinfarct data into the previously defined CFAS SVD status. Both models used clinical dementia status as dependent variable and SVD as independent variable, and were controlled for age of death and sex. SVD was significantly related to dementia status in both models but the two AUC were not significantly different.Since the effect of microinfarcts on dementia status was modest we additionally explored the contribution of each component used in the operational definition of significant SVD and both dementia status and mobility. The contribution of the presence of each SVD component  and their relationship with dementia and mobility status, controlled by sex and age, is demonstrated in Table The analysis confirms that microinfarction is a common finding in an unselected, population‐representative, cohort of older brain donors in the UK among whom more than 75% were aged over 80 years at death. More than one‐third of the cohort had at least one lesion. Our data analysis supports the hypothesis that such lesions are clinically relevant in terms of the risk of dementia and of impaired mobility and falling in old age, and thus we conclude that microinfarcts significantly contribute to physical and mental frailty in the elderly. These data are very similar to those reported in a large community‐based sample (Religious Orders Study) in which 30% of brain donors had microinfarcts among whom 45% did not have any macroscopic infarction The burden of microinfarcts is associated with other manifestations of cerebrovascular pathology Our working definition of SVD conflates a measure of blood vessel damage (severity of arteriosclerosis) with several pathologies assumed to represent parenchymal sequelae of presumed acute  and chronic (WMLs) ischaemia. We have used multivariate analysis to try and tease apart the impact of these various types of lesion on clinical outcomes and the association with risk factors but acknowledge that there are likely to be major common underlying mechanisms so that they are not entirely independent.2 in surface area and 4–8 μm thick, i.e. up to 0.5 mm3 in volume) this likely corresponds to around 550–1100 such lesions throughout the whole brain There is no established consensus on the evaluation of lesions that fall within the spectrum of SVD In view of the above considerations, we have examined our data to see if the assertion arising from the Honolulu Asian Ageing Study, that microinfarcts are of particular significance as predictors of clinically expressed SVD, is justified in this cohort We therefore propose that a pathological concept of SVD based on a constellation of lesion types remains the most valid approach to capturing this pathological state for clinicopathological correlation and to study disease mechanisms in post‐mortem brain samples. Because WML remain an important lesion type in this analysis, and it is necessary to stratify cases by severity and lesion burden, it is reasonable to assert that neuropathological protocols that do not adequately assess WML are incomplete in terms of assessing SVD brain pathology in older people. This is most conveniently and efficiently achieved using post‐mortem MRI which is presently not widely available to neuropathology laboratories


This review considers, in the context of British Skin Foundation (BSF)‐funded translational research into atopic eczema conducted in Newcastle, the complex interactions between clinical and non‐clinical scientists in both academia and industry and how this may have impacted on clinical care. However, research in individual centres does not occur in isolation and clinically relevant outcomes from collaborative research are increasingly supported through regional and national networks. This is illustrated by our trial of azathioprine in adults with atopic eczema conducted across centres in the North East of England that employed pharmacogenetic dosimetry. Correspondingly the formation of a UK Translational Network for Translational Research in Dermatology (UK TREND) has facilitated the development of a UK‐wide network to support atopic eczema projects based on an e‐Delphi prioritisation exercise. What's already known about this topic?Atopic eczema is a disabling long‐term skin condition that profoundly impacts on patients and their families.Ciclosporin remains the only licenced systemic treatment for moderate‐to‐severe atopic eczema in adults.What does this study add?Translational research is not linear but represents a complex multi‐disciplinary reciprocal interaction across the clinical/non‐clinical science interface.Investigator‐initiated clinical trials in atopic eczema funded by the BSF have influenced national/international guidelines and clinical practice and for the benefit of patients.Pharmacogenetic dosimetry for azathioprine is now embedded in dermatological clinical practice. The Dermatology Research Group in Newcastle places the highest possible priority on the translation of discovery science for the benefit of all users  which is in close alignment with the British Skin Foundation's (BSF) strategic aims to further understand the different types of skin disease and to identify better and more effective treatments. We are also strongly committed to increasing public and patient awareness about the impact of disabling skin disease and promoting interaction and education outside of the routine clinical care setting.In this review, we will consider the outcomes from some of the BSF‐funded research related to atopic eczema conducted in Newcastle and the impact on patient care and future research.Atopic eczema is a disabling long‐term skin condition that has a profound negative impact on patients and their families and therapeutic options for moderate‐to‐severe disease remain limited. Although onset is usually in early childhood, atopic eczema may persist (particularly in more severe cases) or recur during adulthood where a prevalence of ~3–10%Following an open pilot study in 2001,The evidence from this studyBased on the reported numbers of patients treated by the consultant dermatologists in the survey, we can estimate that about 4900 patients begin treatment with azathioprine each year in the UK. This compares to ~4450 commencing ciclosporin and ~3950 commencing methotrexate and 7850 being referred for narrow‐band UVB phototherapy. Together this represents a large proportion of the patient pool of adult patients with refractory atopic eczema seen by consultant‐level dermatologists in the UK.In a previous study in which we compared narrowband UVB phototherapy to UVA phototherapy to placebo,A full entry on azathioprine appeared for the first time in the skin section of the British National Formulary (a standard resource consulted by UK clinicians when deciding which drug to prescribe) in March 2010. This entry provides further evidence of research impact and states that azathioprine should be considered for severe refractory eczema.TPMTLL) may result in high toxic levels of 6‐TGNs and is a contraindication to azathioprine therapy. Further, evidence supports a lower starting dose of azathioprine in patients with intermediate TPMT activity (TPMTHL). The dosing guidance within the BNF–1–3 mg/kg/day for normal/high TPMT activity (TPMTHH), 0.5–1 mg/kg/day for low/intermediate TPMT activity (TPMTHL). –reflects the doses used in our published trial (2.5 and 1 mg/kg/day respectively).As illustrated in Figure In line with the concept of pharmacogenetic dosing, almost 95% of respondents from our 2013 survey8 red blood cells has been proposed8 red blood cells.8 red blood cells. Consequently during a second course, the lower dose initiation phase was omitted and TGN levels within the nominal therapeutic range were achieved. This correlated with an improved clinical response  of action in atopic eczema may identify novel therapeutic targets. This would have clinical relevance as ciclosporin usage for atopic eczema is generally limited to short courses due to its potential side‐effects.Given that the pathogenesis of atopic eczema involves a complex interplay between barrier dysfunction and immune activation and that filaggrin mutations remain the most common genetic risk factor for atopic eczema, we were interested to explore direct effects of ciclosporin and epidermal keratinocytes. The highly conserved family of cyclophilin proteins, characterized by peptidyl‐prolyl cis‐trans isomerase activity, were first identified as binding partners for ciclosporin. Although the interaction between the ciclosporin/cyclophilin A complex, calcineurin and NFAT transcription factors is crucial to inhibition of T cell activation, cyclophilins are ubiquitously expressed. In an earlier study, supported by the BSF, we showed that cyclophilin B (CypB), an endoplasmic reticulum (ER)‐resident protein, is secreted by keratinocytes in response to pharmacologically relevant concentrations of ciclosporin.WT) and a mutant protein that is effectively unable to bind ciclosporin (CypBW128A). Interestingly, we showed that both CypB WT and CypBW128A increased the proliferative capacity of keratinocytes in both monolayer and in 3‐D skin equivalents.To further understand the physiological role of CypB in human keratinocytes, we overexpressed wild type CypB  identified a number of differentially expressed proteins that included cyclophilin A, further underscoring a potential role for cyclophilins in atopic eczema pathogenesis.Taking advantage of the collaborative nature of UK dermatology, and building on the success of established networks including BADBIR and the UK DCTN, we have recently established UK TREND. Based on an e‐Delphi prioritisation exerciseIn summary, BSF‐funded research in Newcastle has provided insight into pathophysiological mechanisms in atopic eczema, as well as the pharmacology and pharmacogenetics of systemic therapeutic agents. These findings have been translated into improved patient care. In part through the support of individual research careers and support nationally for organisations such as UK TREND, we are now poised to further advance understanding of atopic eczema with the real prospect of personalized therapeutics in this disabling long‐term condition.


The aim of this study was to identify factors associated with independent living of older people from the point of view of health and functional capacity.Living independently at home is major wish for older people but is depending on health and functional capacity among others. Objective and subjective assessments have been considered important in determining threats for independent living but both of these views have rarely included in the same study.Descriptive, cross‐sectional register‐based study was conducted.N = 292) of 75‐year old's, born in 1936 (N = 388), in one Finnish medium‐sized municipality in 2011. This study is part of the Functional Ageing project Kaste 2013. The data were analysed statistically by using descriptive analysis, cross‐tabulation and logistic regression.Data were collected using the Health and Functional Capacity survey by identifying the factors of health examinations of a cohort (Partly, different factors were associated with subjective and objective health and functional capacity showing wide range of individuality. Worsening subjective health was associated with worsened self‐assessment of life situation. Worsening subjective health threatens independent living. Factors statistically significantly associated with worsening subjective health were low physical activity, falls during the last 6 months, not managing heavy housework, being sometimes lonely or dejected, having diagnosed diseases or health problems and polypharmacy. Living independently at home is considered the main wish of the majority of older people in European countries  , physical activity (2), way of travelling from one place to another (2), how they are able to perform their daily activities (4) and about falls and cause of possible falls (1) activity , way of Concerning health (three questions), participants were asked how they would rate their health and life situation and compare it to the previous year. For example, they were asked how do they feel about their health situation and the answering scale was very good, good, moderate and poor. In addition, there were questions using a dichotomous scale yes and no concerning sleeping, nutrition, sexuality, smoking and alcohol use, one of each. With an open‐ended question participants were asked if they had any chronic diseases , or regular medicine use. In discussion they were also asked about sensory function (eyesight and hearing) and cognitive/memory status. Cognitive status was assessed during the discussion with the public health nurse and MMSE was used for those having some difficulties in communicating their health in the encounter.Second, the public health nurse made physical measurements of blood pressure and body mass index (BMI). Based on the results of health examination the public health nurse assessed if the older people were healthy or at risk of decline in functional capacity forming the objective view of health and functional capacity (two assessments).We studied relationships with factors which, based on previous studies, were associated with independent living. The dependent variables were public nurse's assessment of functional capacity variable 21), self‐assessed life situation (22), subjective health (23) and public nurse's assessment of the results of health examination (42). We selected these variables as dependent because they best describe subjective  and objective  functional capacity and health in this data set . Descriptive statistics, cross‐tabulation and logistic regression were used. First, a description of the 75‐year‐old people who participated in health examinations was computed by using descriptive statistics, such as frequencies, means and standard deviations. Second, relationships between the dependent and independent variables were examined using cross‐tabulation and logistic regression. Those independent variables which correlated statistically significantly with dependent variables in cross‐tabulation were entered into the logistic regression. A dichotomous logistic regression was used with variables having only two categories, while cumulative logistic regression was used with variables with three or more categories. We wanted to explain dependent variables with several independent variables. To succeed we need to capsulize some variable categories because of the frequency rate. To interpret logistic regression we used odds ratios with 95% confidence intervals. If the confidence intervals of the odds ratio included 1 there were no statistically significant relationships among the variables. A value of Based on the Finnish Personal Data Act  informedn = 292) was not possible afterwards. Although the older people did not know that their registration was used as study data, their privacy was extremely important and anonymity was maintained throughout the study. The public health nurse removed all identification information from the data and it was handed over to the research group without revealing the identity of the older people  assessment about using registration in this study enacted in the Finnish legislation (Act on the Openness of Government Activities n = 292) of the cohort participated in the health examination and their register data were used in this study. Most of them were women (57%), married or in a relationship (73%) and living with a spouse (72%) in a townhouse  or moderate (15%). The 75‐year‐olds’ self‐assessed life situation (90%) and subjective (95%) health were also mostly good or satisfying although nearly all (92%) had some chronic diseases or health problems. Most of the respondents were physically active (67%) and did not feel lonely or dejected (63%). The majority had hobbies (91%) or participated in activities outside the home (64%). For the majority, type of accommodation was suitable for their functional capacity (91%). The 75‐year olds mostly managed light (92%) and heavy (67%) housework, home repairs (76%), banking and shopping (93%) independently.When assessing capability to live independently, it is important to understand what factors are associated with independent living. In this study, we viewed independent living from the perspective of subjective and objective health and functional capacity and studied factors associated to them.Subjectively assessed health and functional capacity were associated with partly the same factors as objectively assessed health and functional capacity, such as chronic diseases, number of medicines used, BMI and systolic blood pressure. The quality of disease played a role. For example, objective health and functional capacity were associated with having cancer and mental disorders, but not with subjective assessment of health and functional capacity. Smoking was associated with objective view, but not when assessing health and functional capacity subjectively. Participating in activities outside the home and physical activity were associated with subjective and objective health and functional capacity and therefore with independent living. The ability to perform ADL had a similar association with both. According to the results, memory status was statistically significantly associated with subjective health.To identify factors that are associated and can threaten 75‐year‐olds’ independent living, we studied, using logistic regression, why the participants self‐assessed their life situation or subjective health as poor, as well as why they assessed their functional capacity as impaired, or why they were assessed as being at risk of decline in functional capacity Table .Experiencing subjective health as worsening during the last year explained statistically significantly why the 75‐year olds assessed their life situation as poor. Low physical activity, falls during the last 6 months, not managing heavy housework, being sometimes lonely or dejected, having diagnosed diseases/health problems and polypharmacy explained statistically significantly why the 75‐year olds assessed their subjective health as poor.Type of accommodation not being suitable, not managing heavy housework, experiencing subjective health worsening during last year, having polypharmacy, being obese or being smoker explained statistically significantly why public health nurse assessed functional capacity of the 75‐year olds as impaired. Not managing heavy housework, being sometimes lonely or dejected, experiencing subjective health worsening during last year, having polypharmacy or being obese explained statistically significantly why public health nurse assessed the 75‐year olds as being at risk of decline in functional capacity.et al. et al. The main aim of this study was to identify factors associated with independent living from the point of view of health and functional capacity. The results revealed that most of the 75‐year olds were in good condition from a subjective and objective point of views and capable of continuing independent living. It is noticeable that partly different factors were associated with subjective and objective health and functional capacity. This means that healthcare professionals may have different views of the factors that are associated with and can threaten independent living of older people than the older people themselves. This study highlights that healthcare professionals should take into account older persons’ subjective views on their life situation, health and functional capacity. This is very important when assessing the capability of living at home or trying to support it. In previous studies older persons’ personal point of view has been found to be more important from the perspective of independent living than objective view ]:substantial contributions to conception and design, acquisition of data or analysis and interpretation of data;drafting the article or revising it critically for important intellectual content.All authors have agreed on the final version and meet at least one of the following criteria [recommended by the ICMJE (


SDMs), although many taxa may be only georeferenced to county. It is tacitly assumed that SDMs built from county‐scale data should be less precise than those built with more accurate localities, but the extent of the bias is currently unknown. Our aims in this study were to illustrate the effects of using county‐scale data on the spatial extent and accuracy of SDMs relative to true locality data and to compare potential compensatory methods . To do so, we developed SDMs in maxent with PRISM‐derived BIOCLIM parameters for 283 and 230 species of odonates (dragonflies and damselflies) and butterflies, respectively, for five subsets from the OdonataCentral and Butterflies and Moths of North America citizen‐science databases: (1) a true locality dataset, (2) a corresponding sister dataset of county‐centroid coordinates, (3) a dataset where the average environmental conditions within each county were assigned to each record, (4) a 50/50% mix of true localities and county‐centroid coordinates, and (5) a 50/50% mix of true localities and records assigned the average environmental conditions within each county. These mixtures allowed us to quantify the degree of bias from county‐scale data. Models developed with county centroids overpredicted the extent of suitable habitat by 15% on average compared to true locality models, although larger sample sizes  reduced this disparity. Assigning county‐averaged environmental conditions did not offer consistent improvement, however. Because county‐level data are of limited value for developing SDMs except for species that are widespread and well collected or that inhabit regions where small, climatically uniform counties predominate, three means of encouraging more accurate georeferencing in citizen‐science databases are provided.Citizen‐science databases have been used to develop species distribution models ( Given the value of vouchered data collected by citizen scientists that is now being realized and utilized , but many others use only anthropogenic designations such as country, state, province, or county . Within the USA, many citizen‐science databases focus at the level of county for recording species localities . The environmental conditions at county centroids may be outside the range of suitable conditions for a species, so using centroid data for SDM development may inflate the empirically derived niche, or environmental envelope, and consequently inflate the geographic range of suitable conditions for the species. This study therefore predicts that SDMs developed with US county centroids will overpredict the geographic range of suitable conditions as compared to models developed with true localities and that geographic overprediction will be highest in species that occur in the western USA where large counties include a larger range of environmental conditions compared to smaller eastern US counties Figure .An ideal test case would be to use a large database of precise species localities from which precise species distribution models can be built and then rescale these localities to a coarser (county) resolution; with these two sets of localities, various approaches to treating background environmental data can then be compared . Some citizen‐science databases for butterflies and odonates (dragonflies and damselflies) provide such test cases, so our objectives were to determine how species distribution models built using only county‐scale data compared to using true localities. We then asked whether any techniques could be employed that would allow county‐scale data to generate species distribution models that were of comparable accuracy to those built with true localities; specifically, we examined whether using more samples or using county‐scale environmental averages improved model performance.22.1http://www.OdonataCentral.org) and the Butterflies and Moths of North America  include vouchered records of odonates and butterflies, respectively, from personal and museum collections and photo‐records submitted by professional and citizen scientists that are vetted by experts . These 19 metrics are considered more biologically meaningful than the 36 raw monthly values  variables were derived from monthly values of maximum and minimum temperature and precipitation from the PRISM 30‐arcsec climatology normals (1971–2000) gridded dataset  was performed so that a subset of uncorrelated layers describing climate could be used for model development. Using PCA for this purpose is recommended over using full sets of potentially correlated variables, such as bioclim data  values were also compared between models for each species with Wilcoxon signed‐rank tests. AUC is a threshold‐independent measure of model performance . The AUC of county‐centroid SDMs was still fairly high . Developing niche models with county data led to overprediction, on average, of the geographic representation of the environmental niche . The mean predicted areas were larger regardless of how the county‐scale data were treated (Table n = 288) showed greater than a 1.0% increase in the predicted range when county centroids were substituted for true localities, although 201 species showed a reduction in range by more than 1.0%, and 24 species showed less than 1.0% change , and for the odonate models, the county‐centroid models outperformed the county‐average models as assessed by the I, D, and RR metrics .Species distribution models for 283 species of odonates and 230 species of butterflies in the continental USA based on true locality data outperformed corresponding SDMs based on county centroids, with a mean AUC reduction of 0.007 for the latter models (Wilcoxon signed‐rank test Appendix . Considep = 0.008).Misrepresentation of the geographic distribution of a species, an effect of modeling with county centroids, was reduced in more widespread species, which had records in many US counties  level. With these species localities, distribution models built by taking county‐wide environmental averages were compared to those built with county‐centroid environmental values, and combinations of these (compared to models built with the same data but from specified coordinates). We show that none of these compromises is particularly effective for large, heterogeneous counties of the western USA, although large sample sizes can reduce the possibility of overpredicting species distributions. Using county‐scale data somewhat compromises species distributional predictions, although this effect is more pronounced in the large and environmentally heterogeneous western US counties. Our attempts to compensate for this bias  had mixed success. There was not a consistent performance benefit to using county‐average environmental conditions compared to county centroids. The predicted range sizes of models built with county‐average environmental conditions were closer to models built with true locality data for both butterflies and odonates Table , but comFor widespread species with many county‐scale data points, the risk of inflating the predicted range of a species is small. It is already known that model accuracy declines with reduced sample size, with model performance declining by as much as 19% when using 10 samples instead of 100 , although boosting sample size of species locality data showed some model improvement. Instead, some alternative approaches may be taken to improve model reliability. For example, background samples could be limited to locations where there are species records, which would control for sampling bias. Furthermore, rather than compare the AUC of models built from different types of data as we did , models could be built with k‐fold partitioning to evaluate all models on the same withheld fold of true locality data. However, withholding a test dataset for comparing the AUC of the true locality and county‐data models would have further reduced the number of species that could be modeled. Moreover, species with few locality records could not be modeled in that manner, which would limit understanding how the different modeling approaches affected species with few records (species with few records could be disproportionately affected if county data were substituted). Additionally, comparing predicted areas and niche similarity indices makes reporting AUC secondary.www.birdseyebirding.com). Both of these improvements could have the added effect of improving record accuracy. Finally, incorporating more user‐centric tools would motivate many contributors. For example, these databases could keep track of user “life‐lists” based on submitted records and list the top contributors by county, state, or country. Though “life‐list” tools would be expected to have only limited scientific value, they would increase the record submission rate. Providing such incentives is important (Wood et al., There is value to county‐scale data in that it provides at least some evidence of the occurrence of a species, though including it may provide an overly optimistic view of the completeness and extent of data coverage. It is important to understand biases that may be present in citizen‐science databases. Citizen‐science databases are likely biased toward the locations of active users, because there are seldom going to be attempts to randomize localities or search beyond what is convenient for users. The data may suggest some areas to be biodiversity hot spots and others depauperate simply because of differences in effort. For the two databases used in this study, this was a bias in user‐submitted records: contributors are more likely to submit records with actual coordinates if no record existed in a county previously regardless of the precision of that previous record Table . Table 1None declared. Click here for additional data file.


Management of intraductal papillary mucinous neoplasm is controversial, and several guidelines have aimed to establish an adequate strategy for surgical resection and surveillance. We compared various intraductal papillary mucinous neoplasm guidelines and considered new matters that are pivotal for improved treatment of intraductal papillary mucinous neoplasm. We identified and compared 11 published guidelines, three of which were major guidelines that mainly referred to the diagnosis and treatment of intraductal papillary mucinous neoplasm . The main concerns of these three guidelines were indication for surgery and follow up of non‐resected lesions. Among the differences between the three guidelines, the period of surveillance recommended was the most controversial matter. Meanwhile, several nomograms have been proposed to improve the diagnosis of intraductal papillary mucinous neoplasm from the level of experts' experiences to that of rational systems. We discuss the adequate strategy of surveillance for intraductal papillary mucinous neoplasm with and without pancreatectomy and nomograms aiming to predict the risk of malignancy in patients with intraductal papillary mucinous neoplasm. In this review, we summarize current available guidelines for IPMN, and discuss concerns that are pivotal for improvement of the guidelines. IPMN may progress to colloid carcinoma and tubular carcinoma and accounts for 20% to 30% of pancreatic cancer.2Table The American Society for Gastrointestinal Endoscopy guideline (#2) discussed the use of endoscopic modalities, such as endoscopic ultrasonography (EUS), EUS‐guided fine‐needle aspiration (EUS‐FNA), and endoscopic retrograde cholangiopancreatography (ERCP), in differentiating IPMN from other cystic pancreatic lesions.The remaining three guidelines  are the current comprehensive guidelines citing diagnostic work‐up, indications for surgery, surveillance after surgery, and surveillance of non‐resected IPMN.Comparison of these three guidelines shows that the main concerns are indications for surgery and follow up of non‐resected lesions. Because IPMN varies from low‐grade dysplasia to invasive cancer, it is important to establish a reliable indication that can predict malignant lesions. In the IAP2012 guidelines, high‐risk stigmata  of ≥10 mm) are absolute indications for surgery. If worrisome features are recognized , EUS is recommended. Surgery should be considered if a definite nodule, MPD involvement, or positive cytology is seen on EUS. In the EURO guidelines, absolute indications for surgery include a cyst diameter ≥4 cm, pancreas‐related symptoms , mural nodules, and MPD >6 mm; relative indications are a rapid increase in size and an elevated serum CA19‐9 concentration. In the AGA guidelines, indications for surgery are positive cytology on EUS‐FNA which is carried out if at least two of three high‐risk features are present . Threshold of the AGA guidelines was set at a high level from the viewpoint of medical economics. Therefore, the AGA guidelines carry a higher risk of excluding resection of malignant lesions than the other two guidelines. Lekkerkerker et al.In the IAP2012 guidelines, surveillance of non‐resected IPMN depends on the size of the cyst . The IAP2012 guidelines do not indicate a definite period of surveillance, although they state that “there are no good long‐term data to indicate whether surveillance can be safely discontinued after long‐term stability.” In the EURO guidelines, surveillance of non‐resected IPMN should be carried out every 6 months in the first year, and annual surveillance with MRI (or EUS) is recommended for the following 5 years. After the fifth year, surveillance is recommended every 6 months. The EURO guidelines also state that surveillance should be continued as long as the patient is fit for surgery. The AGA guidelines suggest that patients with non‐resected IPMN should undergo surveillance with MRI at 1, 3, and 5 years and that surveillance can be discontinued if no significant change is recognized. The matter of termination of surveillance of non‐resected IPMN will be discussed in another section.The IAP2012 and EURO guidelines mention the method of IPMN resection. Both guidelines agree that oncological resection should be carried out if malignancy is suspected and that partial resection is preferred to total pancreatectomy in the treatment of multiple BD‐IPMN. However, the guidelines disagree regarding the management of dysplasia at the margin of intraoperative frozen sections. In the IAP2012 guidelines, additional resection is recommended if high‐grade dysplasia or invasive carcinoma is recognized at the margin, and the presence of low‐/moderate‐grade dysplasia does not require further treatment. The EURO guidelines recommend additional resection even if moderate‐grade dysplasia is recognized at the margin.Another point is surveillance after IPMN resection. For invasive IPMN, the IAP2012 and EURO guidelines recommend the same surveillance as carried out for pancreatic cancer. In contrast, the AGA guidelines suggest MRI surveillance every 2 years even after invasive IPMN. For noninvasive IPMN, the IAP2012 guidelines recommend repeat examinations at 2 and 5 years for new recurrences after resection, whereas they also suggest a 6‐month interval, which is appropriate for surveillance considering the risk of PDAC development. The EURO guidelines recommend annual follow up for noninvasive IPMN. The AGA guidelines suggest MRI surveillance every 2 years after resection of high‐grade IPMN, but they do not recommend routine surveillance after resection of pancreatic cysts without high‐grade dysplasia or invasive malignancy. This matter will also be discussed later.3Besides expert opinion‐based guidelines, several efforts have been made to establish a nomogram as a more rational system with which to predict malignant IPMN, as listed in Table These nomograms were validated by two methods: internal validation and external validation Table . ExternaA nomogram that simultaneously covers both BD‐IPMN and MD‐IPMN is feasible and versatile because morphological classification is sometimes vague. However, validation results have demonstrated that nomograms limited to BD‐IPMN are precise with good discrimination. The nomogram discrimination power depends on patient volume and accurate patient data. Therefore, in the near future, establishment of a more convenient and reliable nomogram with which to predict malignant IPMN with greater accumulation of clinical data is expected.4The aim of surveillance after resection of IPMN is early detection of recurrence. “Recurrence” after resection of IPMN includes several situations: recurrence of associated carcinoma, development of a new IPMN lesion, and progression of unresected IPMN in the remnant pancreas. Besides these types of IPMN recurrence, PDAC distinct from IPMN may also develop in the remnant pancreas. In this section, recurrence of carcinoma derived from a resected IPMN is designated as a recurrent lesion, and newly developing or progressing IPMN and newly developing PDAC in the remnant pancreas are designated as remnant pancreatic lesions.Recurrent lesions frequently develop and influence patient survival after resection of invasive IPMN. Disease‐specific survival of patients with recurrent lesions remains low.Several follow‐up studies have revealed frequent development of remnant pancreatic lesions after resection of IPMNHirono et al.5Although several guidelines have provided recommendations regarding management of IPMN without pancreatectomy,Another important issue is how long the surveillance should be continued in terms of detecting PDAC concomitant with IPMN. The AGA guidelines suggest that patients without significant changes in their pancreatic cyst for 5 years can discontinue surveillance. However, in their long‐term surveillance of BD‐IPMN without pancreatectomy, Tanno et al.P=.02). Meanwhile, Mandai et al.Considering the high incidence of IPMN, the estimated prevalence of which is approximately 26/100 000 and increases three‐ to fourfold in individuals older than 60 years,Although several Japanese investigatorsIn summary, it might be important to carry out long‐term surveillance at short intervals for more than 5 years as long as the patient is fit for surgery. A common protocol for IPMN with and without resection is alternate CT and MRCP (EUS) twice a year in Japan;Conflict of Interest: Authors declare no conflicts of interest for this article.


The ENhanced Control of Hypertension And Thrombolysis strokE stuDy trial is a 2 × 2 quasi‐factorial active‐comparison, prospective, randomized, open, blinded endpoint clinical trial that is evaluating in thrombolysis‐eligible acute ischemic stroke patients whether: (1) low‐dose (0·6 mg/kg body weight) intravenous alteplase has noninferior efficacy and lower risk of symptomatic intracerebral hemorrhage compared with standard‐dose (0·9 mg/kg body weight) intravenous alteplase; and (2) early intensive blood pressure lowering (systolic target 130–140 mmHg) has superior efficacy and lower risk of any intracerebral hemorrhage compared with guideline‐recommended blood pressure control (systolic target <180 mmHg).To outline in detail the predetermined statistical analysis plan for the ‘alteplase dose arm’ of the study.All data collected by participating researchers will be reviewed and formally assessed. Information pertaining to the baseline characteristics of patients, their process of care, and the delivery of treatments will be classified, and for each item, appropriate descriptive statistical analyses are planned with appropriate comparisons made between randomized groups. For the trial outcomes, the most appropriate statistical comparisons to be made between groups are planned and described.A statistical analysis plan was developed for the results of the alteplase dose arm of the study that is transparent, available to the public, verifiable, and predetermined before completion of data collection.We have developed a predetermined statistical analysis plan for the ENhanced Control of Hypertension And Thrombolysis strokE stuDy alteplase dose arm which is to be followed to avoid analysis bias arising from prior knowledge of the study findings. Alteplase is the recombinant form of the naturally occurring tissue plasminogen activator (t‐PA) that is produced by endothelial and other vascular cells. It was the first recombinant tissue plasminogen activator (rt‐PA) to be licensed for the management of various thromboembolic diseases including acute myocardial infarction in 1987, massive pulmonary embolism in 1990, and acute ischemic stroke (AIS) in 1996. The basis of the latter license was the pivotal National Institutes of Neurological Diseases and Stroke (NINDS) trial Compared with the cardiology literature, it is surprising that there has been so little research into the optimal dose of alteplase in AIS, or of the importance of ancillary treatments such as early intensive control of blood pressure (BP), to further improve outcome of such patients. The standard 0·9 mg/kg dose of alteplase was chosen for the NINDS trial on the basis of small pilot dose escalation studies which showed that higher doses were related to the risk of sICH, but no clear correlation was found between treatment and early neurological improvement Uncertainty over the most efficacious dose and safety of alteplase has resulted in variations in dose regimes and proposed therapeutic response and risks of sICH in the treatment of AIS patients in Asia There is strong rationale to expect the effects of alteplase to vary across different AIS patient groups and for interaction between dose and hemostatic and cerebrovascular factors. In particular, Asians are more likely to have AIS with lower ‘clot volume’ due to the greater frequency of small vessel or ‘lacunar’ forms of AIS as compared with more large vessel and cardio‐embolic strokes in non‐Asians As the largest randomized evaluation of alteplase in AIS, the ENhanced Control of Hypertension And Thrombolysis strokE stuDy (ENCHANTED) has been designed as a comparative effectiveness trial to resolve uncertainty over the most efficacious dose of alteplase as well as the most appropriate level of control of elevated BP in the context of AIS. Planning for the study began in 2010 after completion of the pilot phase Intensive Blood Pressure Reduction in Acute Cerebral Hemorrhage Trial (INTERACT1) The study protocol for ENCHANTED has been outlined elsewhere Herein we describe the statistical analysis plan (SAP) for the ENCHANTED ‘alteplase dose’ arm, where patient recruitment has been more rapid and the required sample size will be achieved sooner than for the BP control arm. This SAP was completed prior to completion of the data collection, and is what investigators will adhere to in analyzing the results of the study pertaining to the dose of alteplase in AIS. The SAP was approved and signed off by the study Steering Committee in May 2015. Participant recruitment to the alteplase dose arm was completed in August 2015, and final patient follow‐up occurred in November 2015. The statistical analyses specified in the SAP occurred in January 2016, and the main results announced at the European Stroke Organisation conference in Barcelona in May 2016.Critical appraisal of the noninferiority results of ENCHANTED should follow the principles and criteria used in assessing any study of novel management strategies Appendix S1. Statistical analysis plan.Click here for additional data file.