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1.
Proc Natl Acad Sci U S A ; 119(30): e2114100119, 2022 07 26.
Article in English | MEDLINE | ID: mdl-35858401

ABSTRACT

Salamanders are an important group of living amphibians and model organisms for understanding locomotion, development, regeneration, feeding, and toxicity in tetrapods. However, their origin and early radiation remain poorly understood, with early fossil stem-salamanders so far represented by larval or incompletely known taxa. This poor record also limits understanding of the origin of Lissamphibia (i.e., frogs, salamanders, and caecilians). We report fossils from the Middle Jurassic of Scotland representing almost the entire skeleton of the enigmatic stem-salamander Marmorerpeton. We use computed tomography to visualize high-resolution three-dimensional anatomy, describing morphologies that were poorly characterized in early salamanders, including the braincase, scapulocoracoid, and lower jaw. We use these data in the context of a phylogenetic analysis intended to resolve the relationships of early and stem-salamanders, including representation of important outgroups alongside data from high-resolution imaging of extant species. Marmorerpeton is united with Karaurus, Kokartus, and others from the Middle Jurassic-Lower Cretaceous of Asia, providing evidence for an early radiation of robustly built neotenous stem-salamanders. These taxa display morphological specializations similar to the extant cryptobranchid "giant" salamanders. Our analysis also demonstrates stem-group affinities for a larger sample of Jurassic species than previously recognized, highlighting an unappreciated diversity of stem-salamanders and cautioning against the use of single species (e.g., Karaurus) as exemplars for stem-salamander anatomy. These phylogenetic findings, combined with knowledge of the near-complete skeletal anatomy of Mamorerpeton, advance our understanding of evolutionary changes on the salamander stem-lineage and provide important data on early salamanders and the origins of Batrachia and Lissamphibia.


Subject(s)
Biological Evolution , Fossils , Urodela , Animals , Phylogeny , Skull/anatomy & histology , Urodela/anatomy & histology , Urodela/classification
2.
Int Arch Occup Environ Health ; 96(7): 1015-1027, 2023 09.
Article in English | MEDLINE | ID: mdl-37269341

ABSTRACT

OBJECTIVE: Taking regular rest breaks while working positively impacts productivity and wellbeing. While home and hybrid working styles have become a popular choice for employees, the impact of, and perceptions towards, taking breaks while working at home is poorly understood. The current research aimed to explore attitudes towards taking rest breaks while working from home and capture levels of breaks taken, wellbeing and productivity in a sample of UK white-collar workers. METHODS: A mixed method approach was applied where self-report data from an online survey were gathered from individuals (N = 140) from one organisation. Open-ended questions regarding attitudes and perceptions towards rest break behaviours were obtained. Further quantitative measures included the number of breaks taken while working from home, levels of productivity (measured by the Health and performance Presenteeism subscale) and mental wellbeing (measured by the Short Warwick-Edinburgh Mental wellbeing scale). Both quantitative and qualitative analysis approaches were applied. RESULTS: Qualitative responses indicated two overarching themes (1) Personal and (2) Organisational sat above four further themes including Movement outside, Structure of home working, Home environment and Digital presence. Additionally, quantitative findings indicated that the number of breaks taken outside was associated with positive changes in wellbeing. CONCLUSION: Employers could aim to support employees working from home in taking outside breaks through flexible working patterns, authentic leadership, and a change in company social norms around break behaviours. Such organisational changes could help to improve workforce productivity and wellbeing.


Subject(s)
Attitude , Humans , Surveys and Questionnaires , Self Report
3.
Article in English | MEDLINE | ID: mdl-38016487

ABSTRACT

OBJECTIVE: The development of serious games for mental wellbeing is a topic of growing interest. The increase in acceptance of games as a mainstream entertainment medium combined with the immersive qualities of games provides opportunities for meaningful support and intervention in mental wellbeing. METHOD: We conducted a systematic review and exploratory meta-analysis to examine if aspects of the interventions influenced outcomes as measured via overall effect sizes. We employed a multilevel meta-analytic approach to accommodate the interdependency of effect sizes (18 effect sizes from 14 studies, with 2027 participants). RESULTS: Overall, the main effect for gaming interventions on any outcome variable was small to medium sized, d = .35 (confidence interval [.23, 47], p < .001). Results revealed that the only significant moderator was the nature of the intervention. Specifically, only interventions that included a rational emotional behavioural focus significantly predicted an improvement in depression and/or anxiety in participants. CONCLUSION: The findings reveal promising effects for therapeutic games for mental health, but replications are needed, alongside the addressing of methodological and procedural concerns.

4.
Mil Psychol ; : 1-13, 2023 Nov 03.
Article in English | MEDLINE | ID: mdl-37921638

ABSTRACT

Defense and Security Personnel (DSP) often have to operate in the presence of stressful demands. Prior research has identified factors and processes associated with DSP being able to perform resiliently in demanding situations and settings. The aim of the present study was to develop a resilient performance training programme for UK defense and security operators. An intervention mapping (IM) method was used to guide the development of the programme. Typically, IM follows six sequential phases. In the present work, these phases were shaped by insights from prior research (e.g. systematic review and end user interviews), the input of a dedicated working group (N = 13) and from practitioner focus groups. During the IM process, the importance of programme flexibility was emphasized by practitioners. As such, the enAbling REsilieNt performAnce (ARENA) training programme was designed to be agile and include both face-to-face training and online learning modules. Theoretical behavior change principles, closely aligned to findings of earlier work on resilient defense and security performance, were used to underpin programme content and delivery. Future research should seek to gather data on the impact of the ARENA programme, in the targeted biological, psychological and social factors that previously been associated with resilient performances.

5.
Gastroenterology ; 160(1): 362-377.e13, 2021 01.
Article in English | MEDLINE | ID: mdl-33039466

ABSTRACT

BACKGROUND & AIMS: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC. METHODS: We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids. RESULTS: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P < .001) and PARP inhibitor therapy (P < .001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P < .018) and WEE1 inhibitor (P < .029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < .001) but was not associated with DDR deficiency. CONCLUSIONS: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.


Subject(s)
Adenocarcinoma/pathology , DNA Damage/genetics , DNA Repair/genetics , DNA Replication/genetics , Pancreatic Neoplasms/pathology , Adenocarcinoma/genetics , Adenocarcinoma/therapy , Biomarkers , Cell Culture Techniques , Cell Line, Tumor , Humans , Molecular Targeted Therapy , Organoids , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/therapy , Xenograft Model Antitumor Assays
6.
Proc Biol Sci ; 289(1969): 20212493, 2022 02 23.
Article in English | MEDLINE | ID: mdl-35193399

ABSTRACT

Performance traits are tightly linked to the fitness of organisms. However, because studies of variation in performance traits generally focus on just one or several closely related species, we are unable to draw broader conclusions about how and why these traits vary across clades. One important performance trait related to many aspects of an animal's life history is bite-force. Here, we use a clade-wide phylogenetic comparative approach to investigate relationships between size, head dimensions and bite-force among lizards and tuatara (lepidosaurs), using the largest bite-force dataset collated to date for any taxonomic group. We test four predictions: that bite-force will be greater in larger species, and for a given body size, bite-force will be greatest in species with acrodont tooth attachment, herbivorous diets, and non-burrowing habits. We show that bite-force is strongly related to body and head size across lepidosaurs and, as predicted, larger species have the greatest bite-forces. Contrary to our other predictions, tooth attachment, diet and habit have little predictive power when accounting for size. Herbivores bite more forcefully simply because they are larger. Our results also highlight priorities for future sampling to further enhance our understanding of broader evolutionary patterns.


Subject(s)
Bite Force , Lizards , Animals , Biological Evolution , Ecology , Phylogeny
7.
Nature ; 531(7592): 47-52, 2016 Mar 03.
Article in English | MEDLINE | ID: mdl-26909576

ABSTRACT

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-ß, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.


Subject(s)
Genes, Neoplasm/genetics , Genome, Human/genetics , Genomics , Mutation/genetics , Pancreatic Neoplasms/classification , Pancreatic Neoplasms/genetics , Animals , Basic Helix-Loop-Helix Transcription Factors/genetics , Carcinoma, Pancreatic Ductal/classification , Carcinoma, Pancreatic Ductal/genetics , Carcinoma, Pancreatic Ductal/immunology , Carcinoma, Pancreatic Ductal/metabolism , Carcinoma, Pancreatic Ductal/pathology , Cell Line, Tumor , DNA Methylation , DNA-Binding Proteins/genetics , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Hepatocyte Nuclear Factor 3-beta/genetics , Hepatocyte Nuclear Factor 3-gamma/genetics , Histone Demethylases/genetics , Homeobox Protein Nkx-2.2 , Homeodomain Proteins/genetics , Humans , Mice , Nuclear Proteins/genetics , Pancreatic Neoplasms/immunology , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/pathology , Prognosis , Receptors, Cytoplasmic and Nuclear/genetics , Survival Analysis , Trans-Activators/genetics , Transcription Factors/genetics , Transcription, Genetic , Transcriptome , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Proteins/genetics , Zebrafish Proteins
8.
J Exp Biol ; 224(Pt 5)2021 03 11.
Article in English | MEDLINE | ID: mdl-33504585

ABSTRACT

Cranial morphology in lepidosaurs is highly disparate and characterised by the frequent loss or reduction of bony elements. In varanids and geckos, the loss of the postorbital bar is associated with changes in skull shape, but the mechanical principles underlying this variation remain poorly understood. Here, we sought to determine how the overall cranial architecture and the presence of the postorbital bar relate to the loading and deformation of the cranial bones during biting in lepidosaurs. Using computer-based simulation techniques, we compared cranial biomechanics in the varanid Varanus niloticus and the teiid Salvator merianae, two large, active foragers. The overall strain magnitude and distribution across the cranium were similar in the two species, despite lower strain gradients in V. niloticus In S. merianae, the postorbital bar is important for resistance of the cranium to feeding loads. The postorbital ligament, which in varanids partially replaces the postorbital bar, does not affect bone strain. Our results suggest that the reduction of the postorbital bar impaired neither biting performance nor the structural resistance of the cranium to feeding loads in V. niloticus Differences in bone strain between the two species might reflect demands imposed by feeding and non-feeding functions on cranial shape. Beyond variation in cranial bone strain related to species-specific morphological differences, our results reveal that similar mechanical behaviour is shared by lizards with distinct cranial shapes. Contrary to the situation in mammals, the morphology of the circumorbital region, calvaria and palate appears to be important for withstanding high feeding loads in these lizards.


Subject(s)
Lizards , Animals , Biomechanical Phenomena , Computer Simulation , Skull/anatomy & histology , Species Specificity
9.
Nature ; 518(7540): 495-501, 2015 Feb 26.
Article in English | MEDLINE | ID: mdl-25719666

ABSTRACT

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.


Subject(s)
DNA Mutational Analysis , Genome, Human/genetics , Genomics , Mutation/genetics , Pancreatic Neoplasms/genetics , Adenocarcinoma/drug therapy , Adenocarcinoma/genetics , Animals , Carcinoma, Pancreatic Ductal/drug therapy , Carcinoma, Pancreatic Ductal/genetics , DNA Repair/genetics , Female , Genes, BRCA1 , Genes, BRCA2 , Genetic Markers/genetics , Genomic Instability/genetics , Genotype , Humans , Mice , Pancreatic Neoplasms/classification , Pancreatic Neoplasms/drug therapy , Platinum/pharmacology , Point Mutation/genetics , Poly(ADP-ribose) Polymerase Inhibitors , Xenograft Model Antitumor Assays
10.
Ann Surg ; 272(2): 366-376, 2020 08.
Article in English | MEDLINE | ID: mdl-32675551

ABSTRACT

OBJECTIVE: We aimed to define preoperative clinical and molecular characteristics that would allow better patient selection for operative resection. BACKGROUND: Although we use molecular selection methods for systemic targeted therapies, these principles are not applied to surgical oncology. Improving patient selection is of vital importance for the operative treatment of pancreatic cancer (pancreatic ductal adenocarcinoma). Although surgery is the only chance of long-term survival, 80% still succumb to the disease and approximately 30% die within 1 year, often sooner than those that have unresected local disease. METHOD: In 3 independent pancreatic ductal adenocarcinoma cohorts (total participants = 1184) the relationship between aberrant expression of prometastatic proteins S100A2 and S100A4 and survival was assessed. A preoperative nomogram based on clinical variables available before surgery and expression of these proteins was constructed and compared to traditional measures, and a postoperative nomogram. RESULTS: High expression of either S100A2 or S100A4 was independent poor prognostic factors in a training cohort of 518 participants. These results were validated in 2 independent patient cohorts (Glasgow, n = 198; Germany, n = 468). Aberrant biomarker expression stratified the cohorts into 3 distinct prognostic groups. A preoperative nomogram incorporating S100A2 and S100A4 expression predicted survival and nomograms derived using postoperative clinicopathological variables. CONCLUSIONS: Of those patients with a poor preoperative nomogram score, approximately 50% of patients died within a year of resection. Nomograms have the potential to improve selection for surgery and neoadjuvant therapy, avoiding surgery in aggressive disease, and justifying more extensive resections in biologically favorable disease.


Subject(s)
Carcinoma, Pancreatic Ductal/genetics , Carcinoma, Pancreatic Ductal/mortality , Chemotactic Factors/genetics , Pancreatectomy/methods , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/mortality , S100 Proteins/genetics , Aged , Carcinoma, Pancreatic Ductal/surgery , Cause of Death , Cohort Studies , Disease-Free Survival , Female , Gene Expression Regulation, Neoplastic , Humans , Male , Middle Aged , Nomograms , Pancreatectomy/mortality , Pancreatic Neoplasms/surgery , Patient Selection , Prognosis , Proportional Hazards Models , Retrospective Studies , Risk Assessment , Survival Analysis
11.
Biol Lett ; 16(7): 20200199, 2020 07.
Article in English | MEDLINE | ID: mdl-32603646

ABSTRACT

Analyses of morphological disparity have been used to characterize and investigate the evolution of variation in the anatomy, function and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear whether they provide equivalent insights. Here, we review the most commonly used approaches for characterizing and analysing morphological disparity, all of which have associated limitations that, if ignored, can lead to misinterpretation. We propose best practice guidelines for disparity analyses, while noting that there can be no 'one-size-fits-all' approach. The available tools should always be used in the context of a specific biological question that will determine data and method selection at every stage of the analysis.


Subject(s)
Biological Evolution , Ecology
12.
Med Educ ; 54(3): 254-263, 2020 03.
Article in English | MEDLINE | ID: mdl-32034800

ABSTRACT

OBJECTIVES: The present study explored how challenge and threat responses to stress relate to performance, anxiety, confidence, team identity and team characteristics (time spent in training and postgraduate experience) in a medical simulation-based team competition. METHODS: The study was conducted during a national simulation-based training event for residents, the SIMCUP Italia 2018. The SIMCUP is a simulation competition in which teams of four compete in simulated medical emergency scenarios. Cross-sectional data were collected prior to the 3 days of the competition. Subjects included 95 participants on 24 teams. Before the competition on each day, participants completed brief self-report measures that assessed demands and resources (which underpin challenge and threat responses to stress), cognitive and somatic anxiety, self-confidence and team identification. Participants also reported time (hours) spent practising as a team and years of postgraduate experience. A team of referees judged each scenario for performance and assigned a score. A linear mixed model using demands and resources was built to model performance. RESULTS: The data showed that both demands and resources have positive effects on performance (31 [11-50.3] [P < .01] and 54 [25-83.3] [P < .01] percentage points increase for unitary increases in demands and resources, respectively); however, this is balanced by a negative interaction between the two (demands * resources interaction coefficient = -10 [-16 to -4.2]). A high level of resources is associated with better performance until demands become very high. Cognitive and somatic anxieties were found to be correlated with demands (Pearson's r = .51 [P < .01] and Pearson's r = .48 [P < .01], respectively). Time spent training was associated with greater perceptions of resources (Pearson's r = .36 [P < .01]). CONCLUSIONS: We describe a model of challenge and threat that allows for the estimation of performance according to perceived demands and resources, and the interaction between the two. Higher levels of resources and lower demands were associated with better performance.


Subject(s)
Clinical Competence/standards , Cognition , Patient Care Team/standards , Simulation Training , Stress, Psychological/psychology , Adult , Cross-Sectional Studies , Emergency Service, Hospital , Female , Humans , Internship and Residency , Italy , Male
13.
BMC Evol Biol ; 19(1): 7, 2019 01 08.
Article in English | MEDLINE | ID: mdl-30621580

ABSTRACT

BACKGROUND: Morphological diversity among closely related animals can be the result of differing growth patterns. The Australian radiation of agamid lizards (Amphibolurinae) exhibits great ecological and morphological diversity, which they have achieved on a continent-wide scale, in a relatively short period of time (30 million years). Amphibolurines therefore make an ideal study group for examining ontogenetic allometry. We used two-dimensional landmark-based geometric morphometric methods to characterise the postnatal growth patterns in cranial shape of 18 species of amphibolurine lizards and investigate the associations between cranial morphology, and life habit and phylogeny. RESULTS: For most amphibolurine species, juveniles share a similar cranial phenotype, but by adulthood crania are more disparate in shape and occupy different sub-spaces of the total shape space. To achieve this disparity, crania do not follow a common post-natal growth pattern; there are differences among species in both the direction and magnitude of change in morphospace. We found that these growth patterns among the amphibolurines are significantly associated with ecological life habits. The clade Ctenophorus includes species that undergo small magnitudes of shape change during growth. They have dorsoventrally deep, blunt-snouted skulls (associated with terrestrial lifestyles), and also dorsoventrally shallow skulls (associated with saxicolous lifestyles). The sister clade to Ctenophorus, which includes the bearded dragon (Pogona), frill-neck lizard (Chlamydosaurus), and long-nosed dragon (Gowidon), exhibit broad and robust post-orbital regions and differing snout lengths (mainly associated with scansorial lifestyles). CONCLUSIONS: Australian agamids show great variability in the timing of development and divergence of growth trajectories which results in a diversity of adult cranial shapes. Phylogenetic signal in cranial morphology appears to be largely overwritten by signals that reflect life habit. This knowledge about growth patterns and skull shape diversity in agamid lizards will be valuable for placing phylogenetic, functional and ecological studies in a morphological context.


Subject(s)
Biodiversity , Lizards/anatomy & histology , Skull/anatomy & histology , Animals , Australia , Lizards/genetics , Phenotype , Phylogeny , Principal Component Analysis , Species Specificity
14.
Ophthalmology ; 126(8): 1076-1083, 2019 08.
Article in English | MEDLINE | ID: mdl-30790587

ABSTRACT

PURPOSE: To determine whether preoperative endothelial cell density (ECD) and postoperative ECD after Descemet stripping automated endothelial keratoplasty (DSAEK) are associated with late endothelial graft failure (LEGF) in the Cornea Preservation Time Study (CPTS). DESIGN: Cohort study within a multicenter, randomized clinical trial. PARTICIPANTS: A total of 1007 individuals (1223 study eyes), mean age 70 years, undergoing DSAEK for Fuchs' dystrophy (94% of eyes) or pseudophakic or aphakic corneal edema (PACE) (6% of eyes) and followed for up to 5 years. METHODS: Central ECD was determined by a central image analysis reading center. Preoperative ECD was determined for 1209 eyes that did not fail and 14 eyes that experienced LEGF. The ECD at 6 and 12 months after DSAEK, the change in ECD from preoperative to 6 and 12 months, surgeon-reported operative complications, and postoperative graft dislocation were investigated for an association with LEGFs unrelated to other postoperative events. Univariable and multivariable Cox proportional hazards regression models were used to assess associations. MAIN OUTCOME MEASURES: Late endothelial graft failure and its associations with pre- and postoperative ECD and operative complications. RESULTS: The cumulative probability of LEGF was 1.3% (95% confidence interval [CI], 0.8%-2.4%). Median (interquartile range [IQR]) preoperative ECDs were similar for eyes with LEGF (2523; 2367-3161) cells/mm2) and eyes without failure (2727; 2508-2973) cells/mm2) (P = 0.34). The ECD at 6 months was associated with LEGF (P < 0.001) in time-to-event analyses, whereas preoperative ECD was not (P = 0.55). The cumulative incidence (95% CI) of LEGF was 6.5% (3.0%, 14.0%) for 97 grafts with a 6-month ECD less than 1200 cells/mm2, 0.3% (0.0%, 2.4%) for 310 grafts with a 6-month ECD between 1200 and 2000 cells/mm2, and 0.6% (0.1%, 2.7%) for 589 grafts with a 6-month ECD greater than 2000 cells/mm2. In multivariable analyses, ECD at 6 months and operative complications were both associated with LEGF (P = 0.002 and P = 0.01, respectively), whereas graft dislocation was not (P = 0.61). CONCLUSIONS: In eyes undergoing DSAEK, preoperative ECD is unrelated to LEGF, whereas lower ECD at 6 months is associated with LEGF. Early endothelial cell loss after DSAEK and intraoperative complications should be minimized to improve graft survival.


Subject(s)
Corneal Edema/surgery , Corneal Endothelial Cell Loss/pathology , Descemet Stripping Endothelial Keratoplasty/adverse effects , Fuchs' Endothelial Dystrophy/surgery , Graft Rejection/pathology , Pseudophakia/surgery , Adult , Aged , Aged, 80 and over , Cohort Studies , Corneal Endothelial Cell Loss/etiology , Descemet Stripping Endothelial Keratoplasty/methods , Endothelium, Corneal/pathology , Female , Humans , Male , Middle Aged , Proportional Hazards Models
15.
Gastroenterology ; 152(1): 68-74.e2, 2017 01.
Article in English | MEDLINE | ID: mdl-27856273

ABSTRACT

Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched in those with the highest mutation burdens. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers and the optimal assay for patient selection may inform clinical trial design for immunotherapy in pancreatic cancer.


Subject(s)
Carcinoma, Pancreatic Ductal/genetics , DNA Mismatch Repair/genetics , Mutation , Pancreatic Neoplasms/genetics , Transcriptome , Adult , Aged , Aged, 80 and over , DNA Mutational Analysis , Female , Genome , Humans , Male , Middle Aged , MutL Protein Homolog 1/genetics , MutS Homolog 2 Protein/genetics , Proto-Oncogene Proteins p21(ras)/genetics
17.
Nature ; 491(7424): 399-405, 2012 Nov 15.
Article in English | MEDLINE | ID: mdl-23103869

ABSTRACT

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.


Subject(s)
Axons/metabolism , Carcinoma, Pancreatic Ductal/genetics , Carcinoma, Pancreatic Ductal/pathology , Genome/genetics , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Animals , Gene Dosage , Gene Expression Regulation, Neoplastic , Humans , Kaplan-Meier Estimate , Mice , Mutation , Proteins/genetics , Signal Transduction
18.
J Pathol ; 238(4): 562-70, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26690310

ABSTRACT

HER2 overexpression/amplification is linked to trastuzumab response in breast/gastric cancers. One suggested anti-EGFR resistance mechanism in colorectal cancer (CRC) is aberrant MEK-AKT pathway activation through HER2 up-regulation. We assessed HER2-amplification/overexpression in stage II-III and IV CRC patients, assessing relationships to KRAS/BRAF and outcome. Pathological material was obtained from 1914 patients in the QUASAR stage II-III trial and 1342 patients in stage IV trials (FOCUS and PICCOLO). Tissue microarrays were created for HER2 immunohistochemistry. HER2-amplification was assessed using FISH and copy number variation. KRAS/BRAF mutation status was assessed by pyrosequencing. Progression-free survival (PFS) and overall survival (OS) data were obtained for FOCUS/PICCOLO and recurrence and mortality for QUASAR; 29/1342 (2.2%) stage IV and 25/1914 (1.3%) stage II-III tumours showed HER2 protein overexpression. Of the HER2-overexpressing cases, 27/28 (96.4%) stage IV tumours and 20/24 (83.3%) stage II-III tumours demonstrated HER2 amplification by FISH; 41/47 (87.2%) also showed copy number gains. HER2-overexpression was associated with KRAS/BRAF wild-type (WT) status at all stages: in 5.2% WT versus 1.0% mutated tumours (p < 0.0001) in stage IV and 2.1% versus 0.2% in stage II-III tumours (p = 0.01), respectively. HER2 was not associated with OS or PFS. At stage II-III, there was no significant correlation between HER2 overexpression and 5FU/FA response. A higher proportion of HER2-overexpressing cases experienced recurrence, but the difference was not significant. HER2-amplification/overexpression is identifiable by immunohistochemistry, occurring infrequently in stage II-III CRC, rising in stage IV and further in KRAS/BRAF WT tumours. The value of HER2-targeted therapy in patients with HER2-amplified CRC must be tested in a clinical trial. © 2015 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.


Subject(s)
Colorectal Neoplasms/genetics , DNA Copy Number Variations/genetics , Gene Expression Regulation, Neoplastic/genetics , Mutation/genetics , Neoplasm Recurrence, Local/genetics , Receptor, ErbB-2/genetics , Receptor, ErbB-2/metabolism , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Clinical Trials as Topic , Female , Humans , Immunohistochemistry , Male , Neoplasm Staging
19.
Environ Res ; 155: 268-275, 2017 05.
Article in English | MEDLINE | ID: mdl-28254708

ABSTRACT

BACKGROUND: Urban residents may experience cognitive fatigue and little opportunity for mental restoration due to a lack of access to nature. Natural outdoor environments (NOE) are thought to be beneficial for cognitive functioning, but underlying mechanisms are not clear. OBJECTIVES: To investigate the long-term association between NOE and cognitive function, and its potential mediators. METHODS: This cross-sectional study was based on adult participants of the Positive Health Effects of the Natural Outdoor Environment in Typical Populations in Different Regions in Europe (PHENOTYPE) project. Data were collected in Barcelona, Spain; Doetinchem, the Netherlands; and Stoke-on-Trent, United Kingdom. We assessed residential distance to NOE, residential surrounding greenness, perceived amount of neighborhood NOE, and engagement with NOE. Cognitive function was assessed with the Color Trails Test (CTT). Mediation analysis was undertaken following Baron and Kenny. RESULTS: Each 100m increase in residential distance to NOE was associated with a longer CTT completion time of 1.50% (95% CI 0.13, 2.89). No associations were found for other NOE indicators and cognitive function. Neighborhood social cohesion was (marginally) significantly associated with both residential distance to NOE and CTT completion time, but no evidence for mediation was found. Nor were there indications for mediation by physical activity, social interaction with neighbors, loneliness, mental health, air pollution worries, or noise annoyance. CONCLUSIONS: Our findings provide some indication that proximity to nature may benefit cognitive function. We could not establish which mechanisms may explain this relationship.


Subject(s)
Cognition , Environment , Adult , Aged , Air Pollution , Cities , Exercise , Female , Humans , Interpersonal Relations , Loneliness , Male , Mental Health , Middle Aged , Netherlands , Noise , Spain , United Kingdom , Young Adult
20.
J Anat ; 228(5): 864-76, 2016 May.
Article in English | MEDLINE | ID: mdl-26740056

ABSTRACT

The patella (kneecap) is the largest and best-known of the sesamoid bones, postulated to confer biomechanical advantages including increasing joint leverage and reinforcing the tendon against compression. It has evolved several times independently in amniotes, but despite apparently widespread occurrence in lizards, the patella remains poorly characterised in this group and is, as yet, completely undescribed in their nearest extant relative Sphenodon (Rhynchocephalia). Through radiography, osteological and fossil studies we examined patellar presence in diverse lizard and lepidosauromorph taxa, and using computed tomography, dissection and histology we investigated in greater depth the anatomy and morphology of the patella in 16 lizard species and 19 Sphenodon specimens. We have found the first unambiguous evidence of a mineralised patella in Sphenodon, which appears similar to the patella of lizards and shares several gross and microscopic anatomical features. Although there may be a common mature morphology, the squamate patella exhibits a great deal of variability in development (whether from a cartilage anlage or not, and in the number of mineralised centres) and composition (bone, mineralised cartilage or fibrotendinous tissue). Unlike in mammals and birds, the patella in certain lizards and Sphenodon appears to be a polymorphic trait. We have also explored the evolution of the patella through ancestral state reconstruction, finding that the patella is ancestral for lizards and possibly Lepidosauria as a whole. Clear evidence of the patella in rhynchocephalian or stem lepidosaurian fossil taxa would clarify the evolutionary origin(s) of the patella, but due to the small size of this bone and the opportunity for degradation or loss we could not definitively conclude presence or absence in the fossils examined. The pattern of evolution in lepidosaurs is unclear but our data suggest that the emergence of this sesamoid may be related to the evolution of secondary ossification centres and/or changes in knee joint conformation, where enhancement of extensor muscle leverage would be more beneficial.


Subject(s)
Biological Evolution , Lizards/anatomy & histology , Patella/anatomy & histology , Animals , Fossils , Phylogeny
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