While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited ...scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.
Many thinkers lament the decline of liberal democracy. Some argue that, to rejuvenate it, we must think big. Thinking big involves generating new ideas about how to achieve an unprecedented level of ...social transformation aimed at cultivating solidarity, empowering citizen efficacy, and promoting the common good. We propose that fundamental to such a transformation must be a radical change in how people speak to one another. To this end, the primary objective of this paper is to offer a framework for understanding how speech currently erodes democratic engagement. The central idea is that much of speech today both reflects and perpetuates a culture of wilful incommensurability . The core features of this culture are totalizing safetyism , expressive safetyism , dismissive intransigence , and polarized alienation , all of which have been worsened by the current trajectory of social media. The result is that people are increasingly prone to engage in degraded free speech , which is characterized by a pervasive aversion to reach out, identify points of unity, benefit from diverse perspectives, and discover truth in all its potential complexity. In view of this diagnosis and the response of those who advocate for freedom of speech, a second objective of this paper is to introduce the concept of attentive free speech . Attentive free speech has similarities with civil discourse but is specifically characterized by discernment and thoughtfulness and is imbued with key dispositions such as courage, reverence, and love. We end by inviting future research into how such speech can promote the social and spiritual health of the public sphere and freedom itself at a practical level.
True malignant mixed tumors, also known as salivary gland carcinosarcoma (SCS), are uncommon yet highly aggressive lesions associated with a poor prognosis. These tumors exhibit a distinctive ...biphasic structure characterized by both epithelial and mesenchymal components. Recent research has shown that the majority of SCS cases stem from pre-existing pleomorphic adenomas (PAs), suggesting a stepwise developmental pattern. In this report, we present a case of a 73-year-old female with SCS and describe the clinical, radiographic, and pathologic observations. Notably, the SCS was associated with a residual PA. The SCS displayed a CTNNB1::PLAG1 gene rearrangement, providing a molecular basis for its origin from the PA. Further DNA genomic analysis exposed mutations in BAP1, PER1, and LRPB1. Our findings provide support to the theory that SCS emerges from a pre-existing PA while highlighting the multiple genetic changes that could contribute to malignant transformation.
Recent characterizations of pioneer transcription factors provide insights into their structures and patterns of chromatin recognition associated with their roles in cell fate commitment and ...transformation. Intersecting with these basic science concepts, identification of pioneer factors (PFs) fused together as driver translocations in childhood cancers raises questions of whether these fusions retain the fundamental ability to invade repressed chromatin, consistent with their monomeric PF constituents. This study defines the cellular and chromatin localization of PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a ChIP-seq workflow with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal insights into inactive chromatin localization of PAX3-FOXO1. Taken together, our studies are consistent with pioneer function for a driver oncoprotein in RMS, with repressed chromatin binding and nucleosome-motif targeting.
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•The fusion oncoprotein PAX3-FOXO1 binds to both active and repressed chromatin•PAX3-FOXO1-binding sites are adjacent to H3K9me3 domains•PAX3-FOXO1 engages partial DNA motifs at early timepoints•PAX3-FOXO1 can bind stably to inaccessible chromatin without inducing accessibility
Molecular Genetics; Systems biology; Transcriptomics
Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing ...has utility in providing a cost-effective approach for evaluating isoform expression, although short-read assembly displays limitations in the accurate inference of full-length transcripts. Long-read RNA sequencing (Iso-Seq), using the Pacific Biosciences (PacBio) platform, can overcome such limitations by providing full-length isoform sequence resolution which requires no read assembly and represents native expressed transcripts. A constraint of the Iso-Seq protocol is due to fewer reads output per instrument run, which, as an example, can consequently affect the detection of lowly expressed transcripts. To address these deficiencies, we developed a concatenation workflow, PacBio Full-Length Isoform Concatemer Sequencing (PB_FLIC-Seq), designed to increase the number of unique, sequenced PacBio long-reads thereby improving overall detection of unique isoforms. In addition, we anticipate that the increase in read depth will help improve the detection of moderate to low-level expressed isoforms.
In sequencing a commercial reference (Spike-In RNA Variants; SIRV) with known isoform complexity we demonstrated a 3.4-fold increase in read output per run and improved SIRV recall when using the PB_FLIC-Seq method compared to the same samples processed with the Iso-Seq protocol. We applied this protocol to a translational cancer case, also demonstrating the utility of the PB_FLIC-Seq method for identifying differential full-length isoform expression in a pediatric diffuse midline glioma compared to its adjacent non-malignant tissue. Our data analysis revealed increased expression of extracellular matrix (ECM) genes within the tumor sample, including an isoform of the Secreted Protein Acidic and Cysteine Rich (SPARC) gene that was expressed 11,676-fold higher than in the adjacent non-malignant tissue. Finally, by using the PB_FLIC-Seq method, we detected several cancer-specific novel isoforms.
This work describes a concatenation-based methodology for increasing the number of sequenced full-length isoform reads on the PacBio platform, yielding improved discovery of expressed isoforms. We applied this workflow to profile the transcriptome of a pediatric diffuse midline glioma and adjacent non-malignant tissue. Our findings of cancer-specific novel isoform expression further highlight the importance of long-read sequencing for characterization of complex tumor transcriptomes.
This study tested a novel explanation for the positive relation between social class and mental health among university students. Students with a higher social class were expected to have experienced ...more authoritative and less authoritarian parenting styles; these parenting styles were expected to lead to greater friendship and social integration at university; and greater friendship and integration were expected to lead to better mental health.
To test this model, the researchers asked 397 Australian undergraduate students to complete an online survey. The research used a cross-sectional correlational design, and the data was analysed using bootstrapped multiple serial mediation tests.
Consistent with predictions, parenting style, general friendship and support, and social integration at university mediated the relation between social class and mental health.
The present results suggest that working-class parenting styles may inhibit the development of socially-supportive friendships that protect against mental health problems. The potential effectiveness of interventions based on (a) social integration and (b) parenting style is discussed. Future research in this area should employ a longitudinal research design in order to arrive at clearer causal conclusions about the relations between social class, parenting styles, friendship, social integration, and mental health.
Regular physical activity (PA) can reduce the risk of developing type 2 diabetes, but adherence to time-orientated (150 min week
or more) PA guidelines is very poor. A practical and time-efficient PA ...regime that was equally efficacious at controlling risk factors for cardio-metabolic disease is one solution to this problem. Herein, we evaluate a new time-efficient and genuinely practical high-intensity interval training (HIT) protocol in men and women with pre-existing risk factors for type 2 diabetes.
One hundred eighty-nine sedentary women (
= 101) and men (
= 88) with impaired glucose tolerance and/or a body mass index >27 kg m
mean (range) age: 36 (18-53) years participated in this multi-center study. Each completed a fully supervised 6-week HIT protocol at work-loads equivalent to ~100 or ~125% Formula: see text. Change in Formula: see text was used to monitor protocol efficacy, while Actiheart™ monitors were used to determine PA during four, weeklong, periods. Mean arterial (blood) pressure (MAP) and fasting insulin resistance homeostatic model assessment (HOMA)-IR represent key health biomarker outcomes.
The higher intensity bouts (~125% Formula: see text) used during a 5-by-1 min HIT protocol resulted in a robust increase in Formula: see text (136 participants, +10.0%,
< 0.001; large size effect). 5-by-1 HIT reduced MAP (~3%;
< 0.001) and HOMA-IR (~16%;
< 0.01). Physiological responses were similar in men and women while a sizeable proportion of the training-induced changes in Formula: see text, MAP, and HOMA-IR was retained 3 weeks after cessation of training. The supervised HIT sessions accounted for the entire quantifiable increase in PA, and this equated to 400 metabolic equivalent (MET) min week
. Meta-analysis indicated that 5-by-1 HIT matched the efficacy and variability of a time-consuming 30-week PA program on Formula: see text, MAP, and HOMA-IR.
With a total time-commitment of <15 min per session and reliance on a practical ergometer protocol, 5-by-1 HIT offers a new solution to modulate cardio-metabolic risk factors in adults with pre-existing risk factors for type 2 diabetes while approximately meeting the MET min week
PA guidelines. Long-term randomized controlled studies will be required to quantify the ability for 5-by-1 HIT to reduce the incidence of type 2 diabetes, while strategies are required to harmonize the adaptations to exercise across individuals.
Abstract Background and aims Smokers typically have a lower body mass index (BMI) than non‐smokers, while smoking cessation is associated with weight gain. In pre‐clinical research, nicotine in ...tobacco smoking suppresses appetite and influences subsequent eating behaviour; however, this relationship is unclear in humans. This study measured the associations of smoking with different eating and dietary behaviours. Design A cross‐sectional analysis of data from health assessments conducted between 2004 and 2022. Setting An independent healthcare‐based charity within the United Kingdom. Participants A total of 80 296 men and women (mean ± standard deviation SD: age, 43.0 ± 10.4 years; BMI, 25.7 ± 4.2 kg/m 2 ; 62.5% male) stratified into two groups based on their status as a smoker ( n = 6042; 7.5%) or non‐smoker ( n = 74 254; 92.5%). Measurements Smoking status (self‐report) was the main exposure, while the primary outcomes were selected eating and dietary behaviours. Age, sex and socioeconomic status (index of multiple deprivation IMD) were included as covariates and interaction terms, while moderate‐to‐vigorous exercise and sleep quality were included as covariates only. Findings Smokers had lower odds of snacking between meals and eating food as a reward or out of boredom versus non‐smokers (all odds ratio OR ≤ 0.82; P < 0.001). Furthermore, smokers had higher odds of skipping meals, going more than 3 h without food, adding salt and sugar to their food, overeating and finding it hard to leave something on their plate versus non‐smokers (all OR ≥ 1.06; P ≤ 0.030). Additionally, compared with non‐smokers, smoking was associated with eating fried food more times per week (rate ratio RR = 1.08; P < 0.001), eating fewer meals per day, eating sweet foods between meals and eating dessert on fewer days per week (all RR ≤ 0.93; P < 0.001). Several of these relationships were modified by age, sex and IMD. Conclusions Smoking appears to be associated with eating and dietary behaviours consistent with inhibited food intake, low diet quality and altered food preference. Several of these relationships are moderated by age, sex and socioeconomic status.
Finding effective intervention strategies to combat rising obesity levels could significantly reduce the burden that obesity and associated non-communicable diseases places on both individuals and ...the National Health Service.
In this parallel randomised-controlled trial, 76 participants who are overweight or obese (50 female) were given free access to a fitness centre for the duration of the 12-week intervention and randomised to one of three interventions. The commercial intervention, the Healthy Weight Programme, (HWP, n = 25, 10/15 men/women) consisted of twelve 1-h nutrition coaching sessions with a nutritionist delivered as a mixture of group and 1 to 1 sessions. In addition, twice-weekly exercise sessions (24 in total) were delivered by personal trainers for 12 weeks. The NHS intervention (n = 25, 8/17 men/women) consisted of following an entirely self-managed 12-week online NHS resource. The GYM intervention (n = 26, 8/18 men/women) received no guidance or formal intervention. All participants were provided with a gym induction for safety and both the NHS and GYM participants were familiarised with ACSM physical activity guidelines by way of a hand-out.
The overall follow-up rate was 83%. Body mass was significantly reduced at post-intervention in all groups (HWP: N = 18, - 5.17 ± 4.22 kg, NHS: N = 21-4.19 ± 5.49 kg; GYM: N = 24-1.17 ± 3.00 kg; p < 0.001) with greater reductions observed in HWP and NHS groups compared to GYM (p < 0.05). Out with body mass and BMI, there were no additional statistically significant time x intervention interaction effects.
This is the first study to evaluate the efficacy of both a free online NHS self-help weight-loss tool and a commercial weight loss programme that provides face-to-face nutritional support and supervised exercise. The findings suggest that both interventions are superior to an active control condition with regard to eliciting short-term weight-loss.
ISRCTN Registry - ISRCTN31489026. Prospectively registered: 27/07/16.
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