Simulation techniques for cosmological simulations

Modern cosmological observations allow us to study in great detail the evolution and history of the large scale structure hierarchy. The fundamental problem of accurate constraints on the cosmological parameters, within a given cosmological model, requires precise modelling of the observed structure. In this paper we briefly review the current most effective techniques of large scale structure simulations, emphasising both their advantages and shortcomings. Starting with basics of the direct N-body simulations appropriate to modelling cold dark matter evolution, we then discuss the direct-sum technique GRAPE, particle-mesh (PM) and hybrid methods, combining the PM and the tree algorithms. Simulations of baryonic matter in the Universe often use hydrodynamic codes based on both particle methods that discretise mass, and grid-based methods. We briefly describe Eulerian grid methods, and also some variants of Lagrangian smoothed particle hydrodynamics (SPH) methods.Comment: 42 pages, 16 figures, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 12; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeke

The Public Repository of Xenografts enables discovery and randomized phase II-like trials in mice

More than 90% of drugs with preclinical activity fail in human trials, largely due to insufficient efficacy. We hypothesized that adequately powered trials of patient-derived xenografts (PDX) in mice could efficiently define therapeutic activity across heterogeneous tumors. To address this hypothesis, we established a large, publicly available repository of well-characterized leukemia and lymphoma PDXs that undergo orthotopic engraftment, called the Public Repository of Xenografts (PRoXe). PRoXe includes all de-identified information relevant to the primary specimens and the PDXs derived from them. Using this repository, we demonstrate that large studies of acute leukemia PDXs that mimic human randomized clinical trials can characterize drug efficacy and generate transcriptional, functional, and proteomic biomarkers in both treatment-naive and relapsed/refractory disease

Detectable clonal mosaicism and its relationship to aging and cancer

In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases

Effectiveness of Transdiagnostic Cognitive-Behavioral Psychotherapy Compared With Management as Usual for Youth With Common Mental Health Problems: A Randomized Clinical Trial.

Behavioral therapy and cognitive-behavioral therapy (CBT) programs targeting a single class of problems have not been widely implemented. The population of youths with common mental health problems is markedly undertreated. To determine the effectiveness of a new transdiagnostic CBT program (Mind My Mind [MMM]) compared with management as usual (MAU) in youths with emotional and behavioral problems below the threshold for referral to mental health care. This pragmatic, multisite, randomized clinical trial of MMM vs MAU was conducted from September 7, 2017, to August 28, 2019, including 8 weeks of postintervention follow-up, in 4 municipalities in Denmark. Consecutive help-seeking youths were randomized (1:1) to the MMM or the MAU group. Main inclusion criteria were age 6 to 16 years and anxiety, depressive symptoms, and/or behavioral disturbances as a primary problem. Data were analyzed from August 12 to October 25, 2019. The MMM intervention consisted of 9 to 13 weekly, individually adapted sessions of manualized CBT delivered by local psychologists. The MAU group received 2 care coordination visits to enhance usual care. The primary outcome was change in mental health problems reported by parents at week 18, using the Strengths and Difficulties Questionnaire (SDQ) Impact scale (range, 0-10 points, with higher scores indicating greater severity of distress and impairment). Primary and secondary outcomes were assessed in the intention-to-treat population at week 18. Maintenance effects were assessed at week 26. A total of 396 youths (mean [SD] age, 10.3 [2.4] years; 206 [52.0%] boys) were randomized to MMM (n = 197) or MAU (n = 199), with primary outcome data available in 177 (89.8%) and 167 (83.9%), respectively, at 18 weeks. The SDQ Impact score decreased by 2.34 points with MMM and 1.23 with MAU, from initial scores of 4.12 and 4.21, respectively (between-group difference, 1.10 [95% CI, 0.75-1.45]; P < .001; Cohen d = 0.60). Number of responders (≥1-point reduction in SDQ Impact score) was greater with MMM than with MAU (144 of 197 [73.1%] vs 93 of 199 [46.7%]; number needed to treat, 4 [95% CI, 3-6]). Secondary outcomes indicated statistically significant benefits in parent-reported changes of anxiety, depressive symptoms, daily functioning, school attendance, and the principal problem. All benefits were maintained at week 26 except for school attendance. In this randomized clinical trial, the scalable transdiagnostic cognitive-behavioral intervention MMM outperformed MAU in a community setting on multiple, clinically relevant domains in youth with emotional and behavioral problems. ClinicalTrials.gov Identifier: NCT03535805

Systematic identification and stratification of help-seeking school-aged youth with mental health problems: a novel approach to stage-based stepped-care.

We investigated whether a novel visitation model for school-aged youth with mental health problems based on a stage-based stepped-care approach facilitated a systematic identification and stratification process without problems with equity in access. The visitation model was developed within the context of evaluating a new transdiagnostic early treatment for youth with anxiety, depressive symptoms, and/or behavioural problems. The model aimed to identify youth with mental health problems requiring an intervention, and to stratify the youth into three groups with increasing severity of problems. This was accomplished using a two-phase stratification process involving a web-based assessment and a semi-structured psychopathological interview of the youth and parents. To assess problems with inequity in access, individual-level socioeconomic data were obtained from national registers with data on both the youth participating in the visitation and the background population. Altogether, 573 youth and their parents took part in the visitation process. Seventy-five (13%) youth had mental health problems below the intervention threshold, 396 (69%) were deemed eligible for the early treatment, and 52 (9%) had symptoms of severe mental health problems. Fifty (9%) youth were excluded for other reasons. Eighty percent of the 396 youth eligible for early treatment fulfilled criteria of a mental disorder. The severity of mental health problems highlights the urgent need for a systematic approach. Potential problems in reaching youth of less resourceful parents, and older youth were identified. These findings can help ensure that actions are taken to avoid equity problems in future mental health care implementations