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With the aim of producing a 3D representation of tumors, imaging and molecular annotation of xenografts and tumors (IMAXT) uses a large variety of modalities in order to acquire tumor samples and produce a map of every cell in the tumor and its host environment. With the large volume and variety of data produced in the project, we developed automatic data workflows and analysis pipelines. We introduce a research methodology where scientists connect to a cloud environment to perform analysis close to where data are located, instead of bringing data to their local computers. Here, we present the data and analysis infrastructure, discuss the unique computational challenges and describe the analysis chains developed and deployed to generate molecularly annotated tumor models. Registration is achieved by use of a novel technique involving spherical fiducial marks that are visible in all imaging modalities used within IMAXT. The automatic pipelines are highly optimized and allow to obtain processed datasets several times quicker than current solutions narrowing the gap between data acquisition and scientific exploitation.
Current psychiatric diagnoses, although heritable, have not been clearly mapped onto distinct underlying pathogenic processes. The same symptoms often occur in multiple disorders, and a substantial proportion of both genetic and environmental risk factors are shared across disorders. However, the relationship between shared symptoms and shared genetic liability is still poorly understood.
Well-characterised, cross-disorder samples are needed to investigate this matter, but few currently exist. Our aim is to develop procedures to purposely curate and aggregate genotypic and phenotypic data in psychiatric research.
As part of the Cardiff MRC Mental Health Data Pathfinder initiative, we have curated and harmonised phenotypic and genetic information from 15 studies to create a new data repository, DRAGON-Data. To date, DRAGON-Data includes over 45 000 individuals: adults and children with neurodevelopmental or psychiatric diagnoses, affected probands within collected families and individuals who carry a known neurodevelopmental risk copy number variant.
We have processed the available phenotype information to derive core variables that can be reliably analysed across groups. In addition, all data-sets with genotype information have undergone rigorous quality control, imputation, copy number variant calling and polygenic score generation.
DRAGON-Data combines genetic and non-genetic information, and is available as a resource for research across traditional psychiatric diagnostic categories. Algorithms and pipelines used for data harmonisation are currently publicly available for the scientific community, and an appropriate data-sharing protocol will be developed as part of ongoing projects (DATAMIND) in partnership with Health Data Research UK.
Dr. Sharpe was a leading eye movement researcher who had also been the editor of this journal. We wish to mark the 10th anniversary of his death by providing a sense of what he had achieved through some examples of his research.
Competition between genotypes within a plant population can result in the displacement of the least competitive by more competitive genotypes. Although evolutionary processes in plants may occur over thousands and millions of years, it has been suggested that changes in key fitness traits could occur in as little as decades, with herbicide resistance being a common example. However, the rapid evolution of complex traits has not been proven in weeds. We hypothesized that changes in weed growth and competitive ability can occur in just a few years because of selection in agroecosystems. Seed of multiple generations of a single natural population of the grassy weed giant foxtail (Setaria faberi Herrm.) were collected during 34 yr (i.e., 1983 to 2017). Using a “resurrection” approach, we characterized life-history traits of the different year-lines under noncompetitive and competitive conditions. Replacement-series experiments comparing the growth of the oldest year-line (1983) versus newer year-lines (1991, 1996, 1998, 2009, and 2017) showed that plant competitive ability decreased and then increased progressively in accordance with oscillating selection. The adaptations in competitive ability were reflected in dynamic changes in leaf area and biomass when plants were in competition. The onset of increased competitive ability coincided with the introduction of herbicide-resistant crops in the landscape in 1996. We also conducted a genome-wide association study and identified four loci that were associated with increased competitive ability over time, confirming that this trait changed in response to directional selection. Putative transcription factors and cell wall–associated enzymes were linked to those loci. This is the first study providing direct in situ evidence of rapid directional evolution of competitive ability in a plant species. The results suggest that agricultural systems can exert enough pressure to cause evolutionary adaptations of complex life-history traits, potentially increasing weediness and invasiveness.
The legal brief is a primary vehicle by which lawyers seek to persuade appellate judges. Despite wide acceptance that briefs are important, empirical scholarship has yet to establish their influence on the Supreme Court or fully explore justices’ preferences regarding them. We argue that emotional language conveys a lack of credibility to justices and thereby diminishes the party’s likelihood of garnering justices’ votes. The data concur. Using an automated textual analysis program, we find that parties who employ less emotional language in their briefs are more likely to win a justice’s vote, a result that holds even after controlling for other features correlated with success, such as case quality. These findings suggest that advocates seeking to influence judges can enhance their credibility and attract justices’ votes by employing measured, objective language.
Schizophrenia is a heterogeneous disorder and it is unknown what causes individual variability in symptoms and cognitive ability.
To examine the association between nine clinical predictors measurable at the onset of schizophrenia and five phenotype dimensions: positive, negative (diminished expressivity), negative (motivation and pleasure), disorganised symptoms and cognitive ability.
852 participants (mean age 49 years old) with a diagnosis of schizophrenia or schizoaffective depression were included from the CardiffCOGS cross-sectional sample. Phenotype dimensions were created using confirmatory factor analysis and a 5-factor model. Associations were tested using linear regression, adjusting for age and sex. A Bonferroni correction was applied for (p<1.1x10-3) for multiple testing.
Age of onset of psychosis was significantly associated with positive symptoms (β=-0.18, p=4.0 x10-6). Lower premorbid IQ was associated with diminished expressivity (β=-0.25, p= 7.0x10-13), reduced motivation and pleasure (β=-0.23, p= 4.3x10-11), disorganised symptoms (β=-0.14, p= 7.6x10-5) and reduced cognition (β=0.54, p= 4.8x10-77). Poor premorbid social adjustment held associations with all except positive. Developmental delay was associated with reduced cognition (β=-0.35, p= 4.3x10-5). Cannabis use (year before onset), psychosocial stressors (within 6 months), childhood abuse and family history of schizophrenia held no associations.
Clinical indicators measurable at schizophrenia onset are associated with lifetime symptom variability. A younger psychosis onset is associated with more severe positive symptoms, suggesting possible age-targeted management. Pre-established links of lower premorbid IQ with poor premorbid social adjustment and negative symptom severity with cognition are strengthened. Further investigation could potentially improve diagnosis and guide treatment choice for aspects of schizophrenia with poor outcomes.
Copy number variants (CNVs) have been associated with the risk of schizophrenia, autism and intellectual disability. However, little is known about their spectrum of psychopathology in adulthood.
We investigated the psychiatric phenotypes of adult CNV carriers and compared probands, who were ascertained through clinical genetics services, with carriers who were not. One hundred twenty-four adult participants (age 18–76), each bearing one of 15 rare CNVs, were recruited through a variety of sources including clinical genetics services, charities for carriers of genetic variants, and online advertising. A battery of psychiatric assessments was used to determine psychopathology.
The frequencies of psychopathology were consistently higher for the CNV group compared to general population rates. We found particularly high rates of neurodevelopmental disorders (NDDs) (48%), mood disorders (42%), anxiety disorders (47%) and personality disorders (73%) as well as high rates of psychiatric multimorbidity (median number of diagnoses: 2 in non-probands, 3 in probands). NDDs [odds ratio (OR) = 4.67, 95% confidence interval (CI) 1.32–16.51; p = 0.017) and psychotic disorders (OR = 6.8, 95% CI 1.3–36.3; p = 0.025) occurred significantly more frequently in probands (N = 45; NDD: 39[87%]; psychosis: 8[18%]) than non-probands (N = 79; NDD: 20 [25%]; psychosis: 3[4%]). Participants also had somatic diagnoses pertaining to all organ systems, particularly conotruncal cardiac malformations (in individuals with 22q11.2 deletion syndrome specifically), musculoskeletal, immunological, and endocrine diseases.
Adult CNV carriers had a markedly increased rate of anxiety and personality disorders not previously reported and high rates of psychiatric multimorbidity. Our findings support in-depth psychiatric and medical assessments of carriers of CNVs and the establishment of multidisciplinary clinical services.
The COVID-19 pandemic exacerbated gender disparities in some academic disciplines. This study examined the association of the pandemic with gender authorship disparities in clinical neuropsychology (CN) journals.
Author bylines of 1,018 initial manuscript submissions to four major CN journals from March 15 through September 15 of both 2019 and 2020 were coded for binary gender. Additionally, authorship of 40 articles published on pandemic-related topics (COVID-19, teleneuropsychology) across nine CN journals were coded for binary gender.
Initial submissions to these four CN journals increased during the pandemic (+27.2%), with comparable increases in total number of authors coded as either women (+23.0%) or men (+25.4%). Neither the average percentage of women on manuscript bylines nor the proportion of women who were lead and/or corresponding authors differed significantly across time. Moreover, the representation of women as authors of pandemic-related articles did not differ from expected frequencies in the field.
Findings suggest that representation of women as authors of peer-reviewed manuscript submissions to some CN journals did not change during the initial months of the COVID-19 pandemic. Future studies might examine how risk and protective factors may have influenced individual differences in scientific productivity during the pandemic.
Meeting the complex demands of conservation requires a multi-skilled workforce operating in a sector that is respected and supported. Although professionalization of conservation is widely seen as desirable, there is no consistent understanding of what that entails. Here, we review whether and how eight elements of professionalization observed in other sectors are applicable to conservation: (1) a defined and respected occupation; (2) official recognition; (3) knowledge, learning, competences and standards; (4) paid employment; (5) codes of conduct and ethics; (6) individual commitment; (7) organizational capacity; and (8) professional associations. Despite significant achievements in many of these areas, overall progress is patchy, and conventional concepts of professionalization are not always a good fit for conservation. Reasons for this include the multidisciplinary nature of conservation work, the disproportionate influence of elite groups on the development and direction of the profession, and under-representation of field practitioners and of Indigenous peoples and local communities with professional-equivalent skills. We propose a more inclusive approach to professionalization that reflects the full range of practitioners in the sector and the need for increased recognition in countries and regions of high biodiversity. We offer a new definition that characterizes conservation professionals as practitioners who act as essential links between conservation action and conservation knowledge and policy, and provide seven recommendations for building a more effective, inclusive and representative profession.
Studying phenotypic and genetic characteristics of age at onset (AAO) and polarity at onset (PAO) in bipolar disorder can provide new insights into disease pathology and facilitate the development of screening tools.
To examine the genetic architecture of AAO and PAO and their association with bipolar disorder disease characteristics.
Genome-wide association studies (GWASs) and polygenic score (PGS) analyses of AAO (n = 12 977) and PAO (n = 6773) were conducted in patients with bipolar disorder from 34 cohorts and a replication sample (n = 2237). The association of onset with disease characteristics was investigated in two of these cohorts.
Earlier AAO was associated with a higher probability of psychotic symptoms, suicidality, lower educational attainment, not living together and fewer episodes. Depressive onset correlated with suicidality and manic onset correlated with delusions and manic episodes. Systematic differences in AAO between cohorts and continents of origin were observed. This was also reflected in single-nucleotide variant-based heritability estimates, with higher heritabilities for stricter onset definitions. Increased PGS for autism spectrum disorder (β = −0.34 years, s.e. = 0.08), major depression (β = −0.34 years, s.e. = 0.08), schizophrenia (β = −0.39 years, s.e. = 0.08), and educational attainment (β = −0.31 years, s.e. = 0.08) were associated with an earlier AAO. The AAO GWAS identified one significant locus, but this finding did not replicate. Neither GWAS nor PGS analyses yielded significant associations with PAO.
AAO and PAO are associated with indicators of bipolar disorder severity. Individuals with an earlier onset show an increased polygenic liability for a broad spectrum of psychiatric traits. Systematic differences in AAO across cohorts, continents and phenotype definitions introduce significant heterogeneity, affecting analyses.
Herbicide-resistant (HR) kochia is a growing problem in the Great Plains region of Canada and the United States. Resistance to up to four herbicide sites of action, including photosystem II inhibitors, acetolactate synthase inhibitors, synthetic auxins, and the 5-enolpyruvylshikimate-3-phosphate synthase inhibitor glyphosate have been reported in many areas of this region. Despite being present in the United States since 1993/1994, auxinic-HR kochia is a recent and growing phenomenon in Canada. This study was designed to characterize 1) the level of resistance and 2) patterns of cross-resistance to dicamba and fluroxypyr in 12 putative auxinic-HR kochia populations from western Canada. The incidence of dicamba-resistant individuals ranged among populations from 0% to 85%, while fluroxypyr-resistant individuals ranged from 0% to 45%. In whole-plant dose-response bioassays, the populations exhibited up to 6.5-fold resistance to dicamba and up to 51.5-fold resistance to fluroxypyr based on visible injury 28 d after application. Based on plant survival estimates, the populations exhibited up to 3.7-fold resistance to dicamba and up to 72.5-fold resistance to fluroxypyr. Multiple patterns of synthetic auxin resistance were observed, in which one population from Cypress County, Alberta, was resistant to dicamba but not fluroxypyr, whereas another from Rocky View County, Alberta, was resistant to fluroxypyr but not dicamba based on single-dose population screening and dose-response bioassays. These results suggest that multiple mechanisms may confer resistance to dicamba and/or fluroxypyr in Canadian kochia populations. Further research is warranted to determine these mechanisms. Farmers are urged to adopt proactive nonchemical weed management practices in an effort to preserve efficacy of the remaining herbicide options available for control of HR kochia.
Fungal endocarditis classically involves dense heterogenous vegetations. However, several patients with fungal infections were noted to have myocardial changes ranging from focal brightening to nodular thickening of chordae or papillary muscles. This study evaluates whether these findings are associated with fungal infections.
In a retrospective case–control study, paediatric inpatients with fungal infections (positive blood, urine, or catheter tip culture) in a 5-year period were matched 1:1 to inpatients without positive fungal cultures. Echocardiograms were scored on a 5-point scale by two independent readers for presence of myocardial brightenings, nodular thickenings, and vegetations. Clinical data were compared.
Of 67 fungal cases, positive culture sites included blood (n = 44), vascular catheter tip (n = 7), and urine (n = 29); several had multiple positive sites. “Positive” echo findings (score ≥ 2+) were more frequent in the Fungal Group (33 versus 18%, p = 0.04). Fungal Group patients with “positive” versus “negative” echo findings had similar proportion of bacterial infections. Among fungal cases, those with “positive” echo findings had longer hospital length of stay than cases with “negative” echos (median 58 versus 40 days, p = 0.03) but no difference in intensive care unit admission, extracorporeal membranous oxygenation support, or mortality.
Myocardial and papillary muscle brightening with nodular thickening on echocardiogram appear to be associated with fungal infections. There may be prognostic implications of these findings as patients with “positive” echo have longer length of stay. Further studies are needed to better understand the mechanism and temporal progression of these changes and determine the prognostic value of this scoring system.
Individuals with schizophrenia are at higher risk of physical illnesses, which are a major contributor to their 20-year reduced life expectancy. It is currently unknown what causes the increased risk of physical illness in schizophrenia.
To link genetic data from a clinically ascertained sample of individuals with schizophrenia to anonymised National Health Service (NHS) records. To assess (a) rates of physical illness in those with schizophrenia, and (b) whether physical illness in schizophrenia is associated with genetic liability.
We linked genetic data from a clinically ascertained sample of individuals with schizophrenia (Cardiff Cognition in Schizophrenia participants, n = 896) to anonymised NHS records held in the Secure Anonymised Information Linkage (SAIL) databank. Physical illnesses were defined from the General Practice Database and Patient Episode Database for Wales. Genetic liability for schizophrenia was indexed by (a) rare copy number variants (CNVs), and (b) polygenic risk scores.
Individuals with schizophrenia in SAIL had increased rates of epilepsy (standardised rate ratio (SRR) = 5.34), intellectual disability (SRR = 3.11), type 2 diabetes (SRR = 2.45), congenital disorders (SRR = 1.77), ischaemic heart disease (SRR = 1.57) and smoking (SRR = 1.44) in comparison with the general SAIL population. In those with schizophrenia, carrier status for schizophrenia-associated CNVs and neurodevelopmental disorder-associated CNVs was associated with height (P = 0.015–0.017), with carriers being 7.5–7.7 cm shorter than non-carriers. We did not find evidence that the increased rates of poor physical health outcomes in schizophrenia were associated with genetic liability for the disorder.
This study demonstrates the value of and potential for linking genetic data from clinically ascertained research studies to anonymised health records. The increased risk for physical illness in schizophrenia is not caused by genetic liability for the disorder.
We report the effect of prospective audit and feedback (PAF) on inpatient fluoroquinolone (FQN) prescriptions. During the PAF period, FQN use decreased from 39.19 to 29.58 days of therapy per 1,000 patient days (P < .001) and appropriateness improved from 68% to 88% (P < .001). High-yield indications to target included noninfectious urinary tract and respiratory presentations.
A number of genomic conditions caused by copy number variants (CNVs) are associated with a high risk of neurodevelopmental and psychiatric disorders (ND-CNVs). Although these patients also tend to have cognitive impairments, few studies have investigated the range of emotion and behaviour problems in young people with ND-CNVs using measures that are suitable for those with learning difficulties.
A total of 322 young people with 13 ND-CNVs across eight loci (mean age: 9.79 years, range: 6.02–17.91, 66.5% male) took part in the study. Primary carers completed the Developmental Behaviour Checklist (DBC).
Of the total, 69% of individuals with an ND-CNV screened positive for clinically significant difficulties. Young people from families with higher incomes (OR = 0.71, CI = 0.55–0.91, p = .008) were less likely to screen positive. The rate of difficulties differed depending on ND-CNV genotype (χ2 = 39.99, p < 0.001), with the lowest rate in young people with 22q11.2 deletion (45.7%) and the highest in those with 1q21.1 deletion (93.8%). Specific patterns of strengths and weaknesses were found for different ND-CNV genotypes. However, ND-CNV genotype explained no more than 9–16% of the variance, depending on DBC subdomain.
Emotion and behaviour problems are common in young people with ND-CNVs. The ND-CNV specific patterns we find can provide a basis for more tailored support. More research is needed to better understand the variation in emotion and behaviour problems not accounted for by genotype.
Registry-based trials have emerged as a potentially cost-saving study methodology. Early estimates of cost savings, however, conflated the benefits associated with registry utilisation and those associated with other aspects of pragmatic trial designs, which might not all be as broadly applicable. In this study, we sought to build a practical tool that investigators could use across disciplines to estimate the ranges of potential cost differences associated with implementing registry-based trials versus standard clinical trials.
We built simulation Markov models to compare unique costs associated with data acquisition, cleaning, and linkage under a registry-based trial design versus a standard clinical trial. We conducted one-way, two-way, and probabilistic sensitivity analyses, varying study characteristics over broad ranges, to determine thresholds at which investigators might optimally select each trial design.
Registry-based trials were more cost effective than standard clinical trials 98.6% of the time. Data-related cost savings ranged from $4300 to $600,000 with variation in study characteristics. Cost differences were most reactive to the number of patients in a study, the number of data elements per patient available in a registry, and the speed with which research coordinators could manually abstract data. Registry incorporation resulted in cost savings when as few as 3768 independent data elements were available and when manual data abstraction took as little as 3.4 seconds per data field.
Registries offer important resources for investigators. When available, their broad incorporation may help the scientific community reduce the costs of clinical investigation. We offer here a practical tool for investigators to assess potential costs savings.
Optimal management of schizophrenia in adolescents is limited by the lack of available therapies. The efficacy and tolerability of aripiprazole was investigated in this patient population.
This 6-week, randomized, double-blind, placebo controlled trial was conducted at 101 international centers, with a safety monitoring board. 13-17 year-olds with a DSM-IV diagnosis of schizophrenia were randomized to placebo, or a fixed dose of aripiprazole 10 mg or 30 mg reached after a 5 or 11 day titration, respectively. The primary endpoint was mean change from baseline on the PANSS Total score at week 6. Secondary endpoints included the PANSS Positive and Negative subscales, and CGI Improvement score. Tolerabilility assessements included frequency and severity of adverse events, as well as blood chemistries, metabolic parameters and weight gain.
Over 85% of 302 patients completed this study. Both 10 mg and 30 mg doses were superior to placebo on the primary endpoint (PANSS total), with significant differences observed as early as Week 1 (30mg). Both doses showed significant improvement on the PANSS Positive and CGI-I scales; and the 10 mg dose group was superior on PANSS Negative score. Approximately 5% of aripiprazole patients discontinued due to AEs. Weight gain and changes in prolactin were minimal.
10mg and 30mg doses of aripiprazole were superior to placebo in the treatment of adolescents with schizophrenia. Aripiprazole was well tolerated, in general, with few discontinuations due to AEs. EPS was the most common AE. Change in body weight was similar to placebo.
This pilot study tested the feasibility, acceptability, and effect-sizes of a multimodal, individual intervention designed to optimize antipsychotic medication use in patients ≥40 years of age with schizophrenia or schizoaffective disorder.
We randomized 40 patients into two groups: usual care (UC) or a nine-session, manualized, antipsychotic adherence intervention (AAI). the AAI attempted to improve adherence by combining three psychosocial techniques:
b. skills training, and
c. alliance building.
Sessions employed a semi-structured format to facilitate open communication. the primary outcome was antipsychotic adherence at study end. We obtained qualitative data regarding patient preferences for the duration and modality for receiving the adherence intervention.
Compared to the UC group, a greater proportion of the AAI group was adherent post-intervention based on medication possession ratio, a commonly used measure of medication adherence (85% vs. 66.6%; OR=2.64), a difference that was statistically not significant. the entire AAI group reported that they intended to take medications, and 75% were satisfied with the intervention.
The AAI was feasible and acceptable. Preliminary data on its effectiveness warrant a larger study. Qualitative data shows that patients prefer brief adherence interventions and accept telephone strategies.