Virtual counts on Quot schemes and the higher rank local DT/PT correspondence

We show that the Quot scheme $\text{Quot}_{\mathbf{A}^3}(\mathcal{O}^r,n)$ admits a symmetric obstruction theory, and we compute its virtual Euler characteristic. We extend the calculation to locally free sheaves on smooth $3$-folds, thus refining a special case of a recent Euler characteristic calculation of Gholampour-Kool. We then extend Toda's higher rank DT/PT correspondence on Calabi-Yau $3$-folds to a local version centered at a fixed slope stable sheaf. This generalises (and refines) the local DT/PT correspondence around the cycle of a Cohen-Macaulay curve. Our approach clarifies the relation between Gholampour-Kool's functional equation for Quot schemes, and Toda's higher rank DT/PT correspondence

Investigating the reliability and validity of the Dutch versions of the illness management and recovery scales among clients with mental disorders

Background: The Illness Management and Recovery scales (IMRS) can measure the progress of clients’ illness self-management and recovery. Previous studies have examined the psychometric properties of the IMRS. Aims: This study examined the reliability and validity of the Dutch version of the IMRS. Method: Clients (n = 111) and clinicians (n = 40) completed the client and clinician versions of the IMRS, respectively. The scales were administered again 2 weeks later to assess stability over time. Validity was assessed with the Utrecht Coping List (UCL), Dutch Empowerment Scale (DES), and Brief Symptom Inventory (BSI). Results: The client and clinician versions of the IMRS had moderate internal reliability, with α = 0.69 and 0.71, respectively. The scales showed strong test–retest reliability, r = 0.79, for the client version and r = 0.86 for the clinician version. Correlations between client and clinician versions ranged from r = 0.37 to 0.69 for the total and subscales. We also found relationships in expected directions between the client IMRS and UCL, DES and BSI, which supports validity of the Dutch version of the IMRS. Conclusions: The Dutch version of the IMRS demonstrated good reliability and validity. The IMRS could be useful for Dutch-speaking programs interested in evaluating client progress on illness self-management and recovery

A blended electronic illness management and recovery program for people with severe mental illness : qualitative process evaluation alongside a randomized controlled trial

Background: We conducted a trial to test the electronic Illness Management and Recovery (e-IMR) intervention to provide conclusions on the potential efficacy of eHealth for people with severe mental illness (SMI). In the e-IMR intervention, we used the standard IMR program content and methodology and combined face-to-face sessions with internet-based strategies on the constructed e-IMR internet platform. During the trial, the e-IMR platform was sparsely used. Objective: This study aimed to evaluate the added value of the e-IMR intervention and the barriers and facilitators that can explain the low use of the e-IMR platform. Methods: This process evaluation was designed alongside a multicenter, cluster randomized controlled trial. In this study, we included all available participants and trainers from the intervention arm of the trial. Baseline characteristics were used to compare users with nonusers. Qualitative data were gathered at the end of the semistructured interviews. Using theoretical thematic analyses, the data were analyzed deductively using a pre-existing coding frame. Results: Out of 41 eligible participants and 14 trainers, 27 participants and 11 trainers were interviewed. Of the 27 participants, 10 were identified as users. eHealth components that had added value were the persuasive nature of the goal-tracking sheets, monitoring, and the peer testimonials, which had the potential to enhance group discussions and disclosure by participants. The low use of the e-IMR platform was influenced by the inflexibility of the platform, the lack of information technology (IT) resources, the group context, participants' low computer skills and disabilities, and the hesitant eHealth attitude of the trainers. Conclusions: The extent of eHealth readiness and correlations with vulnerabilities in persons with SMI need further investigation. This study shows that flexible options were needed for the use of e-IMR components and that options should be provided only in response to a participant's need. Use of the e-IMR intervention in the future is preconditioned by checking the available IT resources (such as tablets for participants) providing computer or internet guidance to participants outside the group sessions, evaluating the eHealth attitude and skills of trainers, and tailoring eHealth training to increase the skills of future e-IMR trainers

Salivary Gland Mucosa-Associated Lymphoid Tissue-Type Lymphoma From Sjogren's Syndrome Patients in the Majority Express Rheumatoid Factors Affinity-Selected for IgG

Objective: Patients with Sjӧgren's syndrome (SS) have an increased risk of developing malignant B cell lymphomas, particularly mucosa-associated lymphoid tissue (MALT)–type lymphomas. We have previously shown that a predominant proportion of patients with SS-associated salivary gland MALT lymphoma express somatically hypermutated IgM with strong amino acid sequence homology with stereotypic rheumatoid factors (RFs). The present study was undertaken in a larger cohort of patients with SS-associated MALT lymphoma to more firmly assess the frequency of RF reactivity and the significance of somatic IGV-region mutations for RF reactivity. Methods: B cell antigen receptors (BCRs) of 16 patients with SS-associated salivary gland MALT lymphoma were analyzed. Soluble recombinant IgM was produced of 12 MALT lymphoma samples, including 1 MALT lymphoma sample that expressed an IgM antibody fitting in a novel IGHV3-30–encoded stereotypic IGHV subset. For 4 of the 12 IgM antibodies from MALT lymphoma samples, the somatically mutated IGHV and IGKV gene sequences were reverted to germline configurations. Their RF activity and binding affinity were determined by enzyme-linked immunosorbent assay and surface plasmon resonance, respectively. Results: Nine (75%) of the 12 IgM antibodies identified in patients with SS-associated salivary gland MALT lymphoma displayed strong monoreactive RF activity. Reversion of the IGHV and IGKV mutations to germline configuration resulted in RF affinities for IgG that were significantly lower for 3 of the 4 somatically mutated IgM antibodies. In stereotypic IGHV3-7/IGKV3-15–encoded RFs, a recurrent replacement mutation in the IGKV3-15–third complementarity-determining region was found to play a pivotal role in the affinity for IgG-Fc. Conclusion: A majority of patients with SS-associated salivary gland MALT lymphoma express somatically mutated BCRs that are selected for monoreactive, high-affinity binding of IgG-Fc. These data underscore the notion that soluble IgG, most likely in immune complexes in inflamed tissues, is the principal autoantigen in the pathogenesis of a variety of B cell lymphomas, particularly SS-associated MALT lymphomas

Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells

Extrachromosomal DNA (ecDNA) are frequently observed in human cancers and are responsible for high levels of oncogene expression. In glioblastoma (GBM), ecDNA copy number correlates with poor prognosis. It is hypothesized that their copy number, size, and chromatin accessibility facilitate clustering of ecDNA and colocalization with transcriptional hubs, and that this underpins their elevated transcriptional activity. Here, we use super-resolution imaging and quantitative image analysis to evaluate GBM stem cells harbouring distinct ecDNA species (EGFR, CDK4, PDGFRA). We find no evidence that ecDNA routinely cluster with one another or closely interact with transcriptional hubs. Cells with EGFR-containing ecDNA have increased EGFR transcriptional output, but transcription per gene copy is similar in ecDNA compared to the endogenous chromosomal locus. These data suggest that it is the increased copy number of oncogene-harbouring ecDNA that primarily drives high levels of oncogene transcription, rather than specific interactions of ecDNA with each other or with high concentrations of the transcriptional machinery

Pervasive lesion segregation shapes cancer genome evolution

Cancers arise through the acquisition of oncogenic mutations and grow through clonal expansion. Here we reveal that most mutagenic DNA lesions are not resolved as mutations within a single cell-cycle. Instead, DNA lesions segregate unrepaired into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. We characterise this process in mutagen-induced mouse liver tumours and show that DNA replication across persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multi-allelic and combinatorial genetic diversity. The phasing of lesions enables the accurate measurement of strand biased repair processes, quantification of oncogenic selection, and fine mapping of sister chromatid exchange events. Finally, we demonstrate that lesion segregation is a unifying property of exogenous mutagens, including UV light and chemotherapy agents in human cells and tumours, which has profound implications for the evolution and adaptation of cancer genomes.This work was supported by: Cancer Research UK (20412, 22398), the European Research Council (615584, 682398), the Wellcome Trust (WT108749/Z/15/Z, WT106563/Z/14/A, WT202878/B/16/Z), the European Molecular Biology Laboratory, the MRC Human Genetics Unit core funding programme grants (MC_UU_00007/11, MC_UU_00007/16), and the ERDF/Spanish Ministry of Science, Innovation and Universities-Spanish State Research Agency/DamReMap Project (RTI2018-094095-B-I00)

Home media and science performance:A cross-national study

This study examines the effects of media resources in the parental home on the science performance of 15-year-old students. It employs data from the 2006 Programme for International Student Assessment (PISA) containing information on 345,967 respondents from 53 countries. Results show that media assets in the family home are indeed meaningful for children’s science performance, as a beneficial resource but also as a disadvantage. A positive reading climate in the parental home and the availability of computers benefits science performance. However, a television-rich home seems to hinder children’s school success. Furthermore, results indicate that, compared to less developed countries, in more modernized societies parental reading investments are even more beneficial to their children’s science performance, whereas a television-rich parental home is even more disadvantageous

Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids.

Altered daily patterns of hormone action are suspected to contribute to metabolic disease. It is poorly understood how the adrenal glucocorticoid hormones contribute to the coordination of daily global patterns of transcription and metabolism. Here, we examined diurnal metabolite and transcriptome patterns in a zebrafish glucocorticoid deficiency model by RNA-Seq, NMR spectroscopy and liquid chromatography-based methods. We observed dysregulation of metabolic pathways including glutaminolysis, the citrate and urea cycles and glyoxylate detoxification. Constant, non-rhythmic glucocorticoid treatment rescued many of these changes, with some notable exceptions among the amino acid related pathways. Surprisingly, the non-rhythmic glucocorticoid treatment rescued almost half of the entire dysregulated diurnal transcriptome patterns. A combination of E-box and glucocorticoid response elements is enriched in the rescued genes. This simple enhancer element combination is sufficient to drive rhythmic circadian reporter gene expression under non-rhythmic glucocorticoid exposure, revealing a permissive function for the hormones in glucocorticoid-dependent circadian transcription. Our work highlights metabolic pathways potentially contributing to morbidity in patients with glucocorticoid deficiency, even under glucocorticoid replacement therapy. Moreover, we provide mechanistic insight into the interaction between the circadian clock and glucocorticoids in the transcriptional regulation of metabolism

Fuelling conditions at staging sites can mitigate Arctic warming effects in a migratory bird

© 2018, The Author(s). Under climate warming, migratory birds should align reproduction dates with advancing plant and arthropod phenology. To arrive on the breeding grounds earlier, migrants may speed up spring migration by curtailing the time spent en route, possibly at the cost of decreased survival rates. Based on a decades-long series of observations along an entire flyway, we show that when refuelling time is limited, variation in food abundance in the spring staging area affects fitness. Bar-tailed godwits migrating from West Africa to the Siberian Arctic reduce refuelling time at their European staging site and thus maintain a close match between breeding and tundra phenology. Annual survival probability decreases with shorter refuelling times, but correlates positively with refuelling rate, which in turn is correlated with food abundance in the staging area. This chain of effects implies that conditions in the temperate zone determine the ability of godwits to cope with climate-related changes in the Arctic