Cognitive Remediation and Social Recovery in Early Psychosis (CReSt-R): protocol for a pilot randomised controlled study.

BACKGROUND: Psychosis, even in its early stages, is associated with significant disability, causing it to be ranked ahead of paraplegia and blindness in those aged 18-35 in terms of years lived with disability. Current pharmacological and psychological interventions intervention have focused primarily on the reduction of positive symptoms (hallucinations and delusions), with little benefit to domains of psychosis such as cognitive difficulties and social and occupational functioning. METHODS/DESIGN: The CReSt-R intervention trial is a single center, pilot randomised controlled study based at the National University of Ireland (NUI), Galway. The trial will recruit participants from four clinical sites with assessment and intervention completed by the primary NUI Galway team. The trial will explore the feasibility, acceptability, and effectiveness of a novel psychosocial intervention for early psychosis based on a combined cognitive remediation training and cognitive behavioural therapy approach focused on social recovery. Participants, aged 16-35 within the first 5 years of a diagnosed psychotic disorder, will be recruited from the Children and Adolescent Mental Health Service and the Adult Mental Health Services in the region. DISCUSSION: Cognitive remediation training (for improving cognition) and social recovery focused cognitive behavioural therapy, have both separately demonstrated effectiveness. This trial will evaluate the feasibility, acceptability, and explore the efficacy of a treatment approach that combines both approaches as part of an integrated, multicomponent intervention. TRIAL REGISTRATION: Cognitive Remediation & Social Recovery in Early Psychosis (CReSt-R): ClincialTrials.gov Identifier NCT04273685. Trial registered Feb 18th, 2020. Last updated April 14th, 2021.

Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape.

Fitness landscapes, mappings of genotype/phenotype to their effects on fitness, are invaluable concepts in evolutionary biochemistry. Although widely discussed, measurements of phenotype-fitness landscapes in proteins remain scarce. Here, we quantify all single mutational effects on fitness and phenotype (EC50) of VIM-2 ß-lactamase across a 64-fold range of ampicillin concentrations. We then construct a phenotype-fitness landscape that takes variations in environmental selection pressure into account. We found that a simple, empirical landscape accurately models the ~39,000 mutational data points, suggesting that the evolution of VIM-2 can be predicted on the basis of the selection environment. Our landscape provides new quantitative knowledge on the evolution of the ß-lactamases and proteins in general, particularly their evolutionary dynamics under subinhibitory antibiotic concentrations, as well as the mechanisms and environmental dependence of non-specific epistasis.

Learning how to work in an interprofessional environment: how students transition to allied health professionals working interprofessionally.

Allied health professionals (AHPs) often work with other health professions to provide specialized support so that patients receive optimal care. Therefore, new graduate AHPs need to be able to engage collaboratively with various health professionals in the provision of health care services. This study examines new AHP graduates' experiences and reflections on the transition to working in an interprofessional environment. Participants were new graduates (n = 18) from different universities, working in a hospital context, from occupational therapy, speech pathology, social work, pharmacy, and physiotherapy. Qualitative data were collected via two semi-structured interviews conducted over 12 months. The data were analyzed using thematic analysis, with three key themes emerging: (a) The role of the work context, 2) Learning to work interprofessionally, and 3) Developing an interprofessional identity. We discuss the implications for universities and workplaces in enhancing interprofessional practice and learning opportunities among new graduates.

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.

The impact of air pollution on terrestrial managed and natural vegetation.

Although awareness that air pollution can damage vegetation dates back at least to the 1600s, the processes and mechanisms of damage were not rigorously studied until the late twentieth century. In the UK following the Industrial Revolution, urban air quality became very poor, with highly phytotoxic SO2 and NO2 concentrations, and remained that way until the mid-twentieth century. Since then both air quality, and our understanding of pollutants and their impacts, have greatly improved. Air pollutants remain a threat to natural and managed ecosystems. Air pollution imparts impacts through four major threats to vegetation are discussed through in a series of case studies. Gas-phase effects by the primary emissions of SO2 and NO2 are discussed in the context of impacts on lichens in urban areas. The effects of wet and dry deposited acidity from sulfur and nitrogen compounds are considered with a particular focus on forest decline. Ecosystem eutrophication by nitrogen deposition focuses on heathland decline in the Netherlands, and ground-level ozone at phytotoxic concentrations is discussed by considering impacts on semi-natural vegetation. We find that, although air is getting cleaner, there is much room for additional improvement, especially for the effects of eutrophication on managed and natural ecosystems. This article is part of a discussion meeting issue 'Air quality, past present and future'.

Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers.

Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New Zealand near Lincoln in 2014. The populations were genotyped with the 90K Infinium iSelect assay and quantitative trait loci (QTL) analysis was performed. A high density consensus map generated based on 14 doubled haploid populations and integrating SNP and SSR markers was used to compare QTL identified in different populations. AC Cadillac contributed QTL on chromosomes 2A, 3B and 7B (2 loci), Carberry on 1A, 2B (2 loci), 2D, 4B (2 loci), 5A, 6A, 7A and 7D, Lillian on 4A and 7D, Stettler on 2D and 6B, Vesper on 1B, 1D, 2A, 6B and 7B (2 loci), and Red Fife on 7A and 7B. Lillian contributed to a novel locus QLr.spa-4A, and similarly Carberry at QLr.spa-5A. The discovery of novel leaf rust resistance QTL QLr.spa-4A and QLr.spa-5A, and several others in contemporary Canada Western Red Spring wheat varieties is a tremendous addition to our present knowledge of resistance gene deployment in breeding. Carberry demonstrated substantial stacking of genes which could be supplemented with the genes identified in other cultivars with the expectation of increasing efficacy of resistance to leaf rust and longevity with little risk of linkage drag.

Correction to: Development of a new reproductive tissue cryopreservation clinical service for children: the Oxford programme.

In the published version, the Acknowledgements section was missing a funding note of co-author Dr C Verrill. The corrected version should read as follows.

Genome-Wide Identification and Characterization of the Wheat Remorin (TaREM) Family during Cold Acclimation.

Remorins (REMs) are plant-specific proteins that play an essential role in plant-microbe interactions. However, their roles in vernalization and abiotic stress responses remain speculative. Most remorins have a variable proline-rich -half and a more conserved -half that is predicted to form coils. A search of the wheat ( L.) database revealed the existence of 20 different genes, which we classified into six groups on the basis of whether they shared a common phylogenetic and structural origin. Analysis of the physical genomic distributions demonstrated that genes are dispersed in the wheat genome and have one to seven introns. Promoter analysis of genes revealed the presence of putative -elements related to diverse functions like development, hormonal regulation, and biotic and abiotic stress responsiveness. Expression levels of genes were measured in plants grown under field and controlled conditions and in response to hormone treatment. Our analyses revealed that 12 members of the REM family are regulated during cold acclimation in wheat in four different tissues (roots, crowns, stems, and leaves), with the highest expression in roots. Differential gene expression was found between wheat cultivars with contrasting degrees of cold tolerance, suggesting the implication of genes in cold response and tolerance. Additionally, eight genes were induced in response to abscisic acid and methyl jasmonate treatment. This genome-wide analysis of genes provides valuable resources for functional analysis aimed at understanding their role in stress adaptation.

Development of a new reproductive tissue cryopreservation clinical service for children: the Oxford programme.

PURPOSE: This article describes the development of a new reproductive tissue cryopreservation clinical service for children at high risk of infertility in the NHS during times of severe financial constraints in the health service. METHOD: A development plan with two phases was drawn up. Phase 1 restricted the service to childhood cancer patients referred to the Oxford Paediatric Oncology and Haematology Principle Treatment Centre. It was estimated that there would be 10 patients/year and used existing staff and facilities from paediatric oncology, surgery, anaesthetics radiology, pathology, psychology, teenage-young adult gynaecology, and an existing Human Tissue Authority tissue bank with a licence for storage of tissue under a Human Sector Licence. Phase 2 extended the service to include children and young adults across England, Wales and Ireland-patients from Scotland having access to a research programme in Edinburgh. The main challenge in phase 2 being resources and the need for patients to be able to be treated as close to home as safely as possible. RESULTS: The Oxford team developed information resources and eligibility criteria based on published best practice, referral and treatment pathways, multidisciplinary team meetings, a network of third party sites, and a dedicated case management and database. As the programme expanded, the Oxford team was able to justify to management the need for a dedicated theatre list. Patient feedback through questionnaires, qualitative work conducted as part of a Ph.D. thesis as well as direct patient stories and interviews in TV, and radio features underpins the positive impact the programme has on patients and their families. CONCLUSION: The Oxford Reproductive Cryopreservation programme delivers fertility preservation treatment to children and young adults at high risk of infertility safely, effectively and as close to home as possible. The onward view is to apply for national funding for this programme for recognition and sustainability.

Sleep duration and psychotic experiences in patients at risk of psychosis: A secondary analysis of the EDIE-2 trial.

Sleep disturbance is common among individuals at risk of psychosis, yet few studies have investigated the relationship between sleep disturbance and clinical trajectory. The Early Detection and Intervention Evaluation (EDIE-2) trial provides longitudinal data on sleep duration and individual psychotic experiences from a cohort of individuals at risk of psychosis, which this study utilises in an opportunistic secondary analysis. Shorter and more variable sleep was hypothesised to be associated with more severe psychotic experiences and lower psychological wellbeing. Mixed effect models were used to test sleep duration and range as predictors of individual psychotic experiences and psychological wellbeing over the 12-24 months (with assessments every 3 months) in 160 participants. Shorter sleep duration was associated with more severe delusional ideas and hallucinations cross-sectionally and longitudinally. The longitudinal relationships did not remain significant after conservative controls were added for the previous severity of psychotic experiences. No significant relationships were found between the sleep variables and other psychotic experiences (e.g. cognitive disorganisation), or psychological wellbeing. The results support a relationship between shorter sleep duration and delusional ideas and hallucinations. Future studies should focus on improving sleep disturbance measurement, and test whether treating sleep improves clinical trajectory in the at-risk group.

Whole-genome sequencing in the investigation of recurrent invasive group A streptococcus outbreaks in a maternity unit.

BACKGROUND: The clinical manifestations of group A streptococcus (GAS) (Streptococcus pyogenes) are diverse, ranging from asymptomatic colonization to devastating invasive disease. Maternity-related clusters of invasive GAS (iGAS) infection are complex to investigate and control, especially if recurrent. AIM: To investigate three episodes of emm 75 GAS/iGAS infection in maternity patients at one hospital site over a four-year period (two with monophyletic ancestry). METHODS: The episodes are described, together with whole-genome sequence (WGS) isolate analyses. Single nucleotide polymorphism differences were compared with contemporaneous emm 75 genomes. FINDINGS: Over the four-year study period, seven mothers had emm 75 GAS/iGAS and one mother had emm 3 iGAS (in year 4) (subsequently discounted as linked). Three (clinical/screening samples) of the seven babies of emm-75-positive mothers and three screened healthcare workers were positive for emm 75 GAS. WGS similarity suggested a shared ancestral lineage and a common source transmission, but directionality of transmission cannot be inferred. However, the findings indicate that persistence of a particular clone in a given setting may be long term. CONCLUSIONS: Occupational health procedures were enhanced, staff were screened, and antibiotic therapy was provided to GAS-positive staff and patients. The definitive source of infection could not be identified, although staff-patient transmission was the most likely route. The pattern of clonal GAS transmission over the four-year study period suggests that long-term persistence of GAS may have occurred.

Ice segregation in the crown of winter cereals: Evidence for extraorgan and extratissue freezing.

Meaningful improvements in winter cereal cold hardiness requires a complete model of freezing behaviour in the critical crown organ. Magnetic resonance microimaging diffusion-weighted experiments provided evidence that cold acclimation decreased water content and mobility in the vascular transition zone (VTZ) and the intermediate zone in rye (Secale cereale L. Hazlet) compared with wheat (Triticum aestivum L. Norstar). Differential thermal analysis, ice nucleation, and localization studies identified three distinct exothermic events. A high-temperature exotherm (-3°C to -5°C) corresponded with ice formation and high ice-nucleating activity in the leaf sheath encapsulating the crown. A midtemperature exotherm (-6°C and -8°C) corresponded with cavity ice formation in the VTZ but an absence of ice in the shoot apical meristem (SAM). A low-temperature exotherm corresponded with SAM injury and the killing temperature in wheat (-21°C) and rye (-27°C). The SAM had lower ice-nucleating activity and freezing survival compared with the VTZ when frozen in vitro. The intermediate zone was hypothesized to act as a barrier to ice growth into the SAM. Higher cold hardiness of rye compared with wheat was associated with higher VTZ and intermediate zone desiccation resulting in the formation of ice barriers surrounding the SAM.

Tissue-specific changes in apoplastic proteins and cell wall structure during cold acclimation of winter wheat crowns.

The wheat (Triticum aestivum L.) crown is the critical organ of low temperature stress survival over winter. In cold-acclimated crowns, ice formation in the apoplast causes severe tissue disruption as it grows at the expense of intracellular water. While previous crown studies have shown the vascular transition zone (VTZ) to have a higher freezing sensitivity than the shoot apical meristem (SAM), the mechanism behind the differential freezing response is not fully understood. Cooling cold-acclimated crowns to -10 °C resulted in an absence of VTZ tetrazolium chloride staining, whereas the temperatures at which 50% of the SAM stained positive and 50% of plants recovered (LT50) were similar after cold acclimation for 21 (-16 °C) and 42 d (-20 °C) at 4 °C. Proteomic analysis of the apoplastic fluids identified dehydrins, vernalization-responsive proteins, and cold shock proteins preferentially accumulated in the SAM. In contrast, modifications to the VTZ centered on increases in pathogenesis-related proteins, anti-freeze proteins, and sugar hydrolyzing enzymes. Fourier transform infrared spectroscopy focal plane array analysis identified the biochemical modification of the cell wall to enhance methyl-esterified cross-linking of glucuronoarabinoxylans in the VTZ. These findings indicate that the SAM and VTZ express two distinct tissue-specific apoplastic responses during cold acclimation.

Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field.

Cold acclimation and winter survival in cereal species is determined by complicated environmentally regulated gene expression. However, studies investigating these complex cold responses are mostly conducted in controlled environments that only consider the responses to single environmental variables. In this study, we have comprehensively profiled global transcriptional responses in crowns of field-grown spring and winter wheat (Triticum aestivum) genotypes and their near-isogenic lines with the VRN-A1 alleles swapped. This in-depth analysis revealed multiple signaling, interactive pathways that influence cold tolerance and phenological development to optimize plant growth and development in preparation for a wide range of over-winter stresses. Investigation of genetic differences at the VRN-A1 locus revealed that a vernalization requirement maintained a higher level of cold response pathways while VRN-A1 genetically promoted floral development. Our results also demonstrated the influence of genetic background on the expression of cold and flowering pathways. The link between delayed shoot apex development and the induction of cold tolerance was reflected by the gradual up-regulation of abscisic acid-dependent and C-REPEAT-BINDING FACTOR pathways. This was accompanied by the down-regulation of key genes involved in meristem development as the autumn progressed. The chromosome location of differentially expressed genes between the winter and spring wheat genetic backgrounds showed a striking pattern of biased gene expression on chromosomes 6A and 6D, indicating a transcriptional regulation at the genome level. This finding adds to the complexity of the genetic cascades and gene interactions that determine the evolutionary patterns of both phenological development and cold tolerance traits in wheat.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.

New Pharmacogenomics Research Network: An Open Community Catalyzing Research and Translation in Precision Medicine.

The goal of pharmacogenomics research is to discover genetic polymorphisms that underlie variation in drug response. Increasingly, pharmacogenomics research involves large numbers of patients and the application of new technologies and methodologies to enable discovery. The Pharmacogenomics Research Network (PGRN) has become a community-driven network of investigators spanning scientific and clinical disciplines. Here, we highlight the activities and types of resources that enable PGRN members to enhance and drive basic and translational research in pharmacogenomics.

Exploring new alleles for frost tolerance in winter rye.

KEY MESSAGE: Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr-2) in Triticeae. The Puma allele at the Fr-R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr-R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

Short-term outcome of substance-induced psychotic disorder in a large UK first episode psychosis cohort.

OBJECTIVE: The incidence and outcome of first-episode substance-induced psychotic disorder (SIPD) are unclear. The study aimed to compare the 1-year outcomes of those given a SIPD diagnosis by clinicians compared to other psychosis diagnoses in a first-episode cohort. METHOD: Data were from a large (n = 1027) cohort of first-episode psychosis (FEP) patients admitted to early intervention services in the UK (National EDEN). Diagnosis, including that of SIPD, was made by treating psychiatrists at baseline using ICD10 criteria. Details on symptoms, functioning, quality of life, relapse and recovery were available at baseline and 12 months. RESULTS: There were 67 cases of SIPD (6.5% of the cohort). At baseline, SIPD patients were no different to other psychoses on symptoms, functioning and quality of life. At 12 months, there was no difference in SIPD and other psychoses on functioning, quality of life or relapse and recovery rates. Levels of psychotic and general symptomatology were similar but depressive symptoms were higher in the SIPD group. CONCLUSIONS: First-episode psychosis patients with a diagnosis of SIPD do not appear to have better outcomes than those with other primary psychotic diagnoses. The higher levels of depressive symptoms may be a specific marker in these patients.

Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn's disease: an observational study.

BACKGROUND/OBJECTIVES: Enteral feeding will induce remission in as many as 80-90% of compliant patients with active Crohn's disease (CD), but its method of action remains uncertain. This study was designed to examine its effects on the colonic microbiome. METHODS/SUBJECTS: Healthy volunteers and patients with CD followed a regimen confined to enteral feeds alone for 1 or 2 weeks, respectively. Chemicals excreted on breath or in faeces were characterised at the start and at the end of the feeding period by gas chromatography/mass spectrometry. RESULTS: One week of feeding in healthy volunteers caused significant changes in stool colour and deterioration in breath odour, together with increased excretion of phenol and indoles on the breath. Feeding for 2 weeks in patients with CD produced significant improvements in symptoms and a decrease in the concentration of C-reactive protein. The faecal concentrations of microbial products, including short-chain fatty acids (SCFAs), and potentially toxic substances, including 1-propanol, 1-butanol and the methyl and ethyl esters of SCFAs, showed significant falls. CONCLUSIONS: A significant change occurs in the production of microbial metabolites after enteral feeding in both healthy volunteers and patients with CD. Many of those detected in CD are toxic and may feasibly lead to the immunological attack on the gut microbiota, which is characteristic of inflammatory bowel disease. The reduction in the production of such metabolites after enteral feeding may be the reason for its effectiveness in CD.