Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 30 end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode

Young children’s use of syntactic cues to learn proper names and count nouns

In 6 experiments, 144 toddlers were tested in groups ranging in mean age from 20 to 37 months. In all experiments, children learned a novel label for a doll or a stuffed animal. The label was modeled syntactically as either a count noun (e.g., "This is a ZAV") or a proper name (e.g., "This is ZAV"). The object was then moved to a new location in front of the child, and a second identical-looking object was placed nearby. The children's task was to choose 1 of the 2 objects as a referent for the novel word. By 24 months, both girls (Experiment 2) and boys (Experiment 5) were significantly more likely to select the labeled object if they heard a proper name than if they heard a count noun. At 20 months, neither girls (Experiments 1 and 6) nor boys (Experiment 1) demonstrated this effect. By their 2nd birthdays, children can use syntactic information to distinguish appropriately between labels for individual objects and those for object categories. Any object in the world (e.g., a cat) can be conceptualized as a member of a category (e.g., as a cat) or as an individual in its own right (e.g., as Felix), and a sensitivity to this distinction is fundamental to human cognition (e.g., In a seminal study, Macnamara and his colleagues This research was supported by an operating grant from the Natural Sciences and Engineering Research Council of Canada. A portion of this work was reported in Sharon C. Lee's honors thesis submitted to the Department of Psychology, University of British Columbia, and was presented at the Boston University Conference on Language Development, Boston, MA, November 1999. We thank Elizabeth Job, Hana Motozono, Jodi Pawluski, Kelley Persoage, and Jennifer Wide for their assistance with all aspects of the work and Susan Graham for helpful comments on a previous version of this article. Correspondence concerning this article should be addressed to D. Geoffrey Hall, Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, British Columbia V6T 1Z4, Canada. Electronic mail may be sent to [email protected]. noun (CN) condition or the proper name (PN) condition. In the CN condition, children heard the novel word modeled in the sentence "This is a ZAV" and applied to one of two dolls that differed in hair color (and that differed in both hair and dress color in a follow-up experiment). These children were expected to interpret the word as a count noun, designating an entire category (e.g., DOLL). As a result, they were expected to select each doll about half the time when subsequently asked to extend the word ZAV. In the PN condition, children heard the same word applied to the same doll, but it was modeled in the sentence "This is ZAV." These children were expected to interpret the word as a proper name designating the labeled doll. As a result, they were expected to choose only the labeled doll when subsequently asked to extend the word ZAV. A key result from the studies by Macnamara and his colleagues is that girls as young as 17 months of age chose the labeled doll significantly more often in the PN condition than in the CN conditio

Neural responses to a modified Stroop paradigm in patients with complex chronic musculoskeletal pain compared to matched controls: an experimental functional magnetic resonance imaging study

Background: Chronic musculoskeletal pain (CMSKP) is attentionally demanding, complex and multi-factorial; neuroimaging research in the population seen in pain clinics is sparse. A better understanding of the neural activity underlying attentional processes to pain related information compared to healthy controls may help inform diagnosis and management in the future. Methods: Blood oxygenation level dependent functional magnetic resonance imaging (BOLD fMRI) compared brain responses in patients with CMSKP (n=15) and healthy controls (n=14) while completing a modified Stroop task using pain-related, positive-emotional, and neutral control words. Results: Response times in the Stroop task were no different for CMSKP patients compared with controls, but patients were less accurate in their responses to all word types. BOLD fMRI responses during presentation of pain-related words suggested increases in neural activation in patients compared to controls in regions previously reported as being involved in pain perception and emotion: the anterior cingulate cortex, insula and primary and secondary somatosensory cortex. No fMRI differences were seen between groups in response to positive or control words. Conclusions: Using this modified Stroop tasks, specific differences were identified in brain activity between CMSKP patients and controls in response to pain-related information using fMRI. This provided evidence of differences in the way that pain-related information is processed in those with chronic complex musculoskeletal pain that were not detectable using the behavioural measures of speed and accuracy. The study may be helpful in gaining new insights into the impact of attention in those living with chronic pai

Estimating Foodborne Gastroenteritis, Australia

An estimated 4.0–6.9 million episodes of foodborne gastroenteritis occur in Australia each year

Combination of linear classifiers using score function -- analysis of possible combination strategies

In this work, we addressed the issue of combining linear classifiers using their score functions. The value of the scoring function depends on the distance from the decision boundary. Two score functions have been tested and four different combination strategies were investigated. During the experimental study, the proposed approach was applied to the heterogeneous ensemble and it was compared to two reference methods -- majority voting and model averaging respectively. The comparison was made in terms of seven different quality criteria. The result shows that combination strategies based on simple average, and trimmed average are the best combination strategies of the geometrical combination

Cerebral blood flow response to acute hypoxic hypoxia

Hypoxic hypoxia (inspiratory hypoxia) stimulates an increase in cerebral blood flow (CBF) maintaining oxygen delivery to the brain. However, this response, particularly at the tissue level, is not well characterised. This study quantifies the CBF response to acute hypoxic hypoxia in healthy subjects. A 20-min hypoxic (mean PETo2 = 52 mmHg) challenge was induced and controlled by dynamic end-tidal forcing whilst CBF was measured using pulsed arterial spin labelling perfusion MRI. The rate constant, temporal delay and magnitude of the CBF response were characterised using an exponential model for whole-brain and regional grey matter. Grey matter CBF increased from 76.1 mL/100 g/min (95% confidence interval (CI) of fitting: 75.5 mL/100 g/min, 76.7 mL/100 g/min) to 87.8 mL/100 g/min (95% CI: 86.7 mL/100 g/min, 89.6 mL/100 g/min) during hypoxia, and the temporal delay and rate constant for the response to hypoxia were 185 s (95% CI: 132 s, 230 s) and 0.0035 s–1 (95% CI: 0.0019 s–1, 0.0046 s–1), respectively. Recovery from hypoxia was faster with a delay of 20 s (95% CI: –38 s, 38 s) and a rate constant of 0.0069 s–1 (95% CI: 0.0020 s–1, 0.0103 s–1). R2*, an index of blood oxygenation obtained simultaneously with the CBF measurement, increased from 30.33 s–1 (CI: 30.31 s–1, 30.34 s–1) to 31.48 s–1 (CI: 31.47 s–1, 31.49 s–1) with hypoxia. The delay and rate constant for changes in R2* were 24 s (95% CI: 21 s, 26 s) and 0.0392 s–1 (95% CI: 0.0333 s–1, 0.045 s–1 ), respectively, for the hypoxic response, and 12 s (95% CI: 10 s, 13 s) and 0.0921 s–1 (95% CI: 0.0744 s–1, 0.1098 s–1/) during the return to normoxia, confirming rapid changes in blood oxygenation with the end-tidal forcing system. CBF and R2* reactivity to hypoxia differed between subjects, but only R2* reactivity to hypoxia differed significantly between brain regions

The Impact of COVID-19 on Perceived Barriers and Facilitators to the Healthfulness of Communities With Low-Income

Background: The COVID-19 pandemic brought new challenges affecting the wellbeing of individuals in communities with low income. Understanding where people live and how those environments can facilitate or hinder living a healthy lifestyle is essential for developing interventions that target behavior change and health promotion. Objective: This study compares Extension Nutrition Educators’ (NEs) perceptions of the barriers and facilitators impacting the healthfulness of the environment of communities with low income in eleven states before and during the COVID-19 pandemic

In vivo assessment of human brainstem cerebrovascular function: a multi-inversion time pulsed arterial spin labelling study

The brainstem (BS) is involved in critical physiologic processes, including control of cardiovascular and respiratory functions. This study implements a multi-inversion time pulsed arterial spin labelling (MTI PASL) imaging sequence that addresses the challenges of BS imaging and aims to measure normal and elevated BS perfusion in healthy volunteers. An initial experiment was performed to obtain the kinetic curve of the label in the BS and consequently to estimate the label arrival times and tissue perfusion in seven participants. A second experiment estimated the BS cerebral vascular reactivity (CVR) to hypercapnia in 10 participants. Images were acquired with a gradient-echo sequence with two spiral interleaves and short echo time (TE=2.7 ms). Data were analyzed with a two-compartment model, including a tissue and arterial component. In both experiments, perfusion in the BS was significantly lower than in cortical gray matter (repeated measures analysis of variance (RM-ANOVA), P<0.05), which is as expected since the BS consists of gray and white matter, the latter typically showing lower perfusion. The BS CVR found here is comparable to previous reports obtained with positron emission tomography (PET) imaging. Multi-inversion time pulsed ASL in combination with a two-compartment signal model can be used to assess BS perfusion and CVR

Discovery and Rossiter-McLaughlin Effect of Exoplanet Kepler-8b

We report the discovery and the Rossiter-McLaughlin effect of Kepler-8b, a transiting planet identified by the NASA Kepler Mission. Kepler photometry and Keck-HIRES radial velocities yield the radius and mass of the planet around this F8IV subgiant host star. The planet has a radius RP = 1.419 RJ and a mass, MP = 0.60 MJ, yielding a density of 0.26 g cm^-3, among the lowest density planets known. The orbital period is P = 3.523 days and orbital semima jor axis is 0.0483+0.0006/-0.0012 AU. The star has a large rotational v sin i of 10.5 +/- 0.7 km s^-1 and is relatively faint (V = 13.89 mag), both properties deleterious to precise Doppler measurements. The velocities are indeed noisy, with scatter of 30 m s^-1, but exhibit a period and phase consistent with the planet implied by the photometry. We securely detect the Rossiter-McLaughlin effect, confirming the planet's existence and establishing its orbit as prograde. We measure an inclination between the projected planetary orbital axis and the projected stellar rotation axis of lambda = -26.9 +/- 4.6 deg, indicating a moderate inclination of the planetary orbit. Rossiter-McLaughlin measurements of a large sample of transiting planets from Kepler will provide a statistically robust measure of the true distribution of spin-orbit orientations for hot jupiters in general.Comment: 26 pages, 8 figures, 2 tables; In preparation for submission to the Astrophysical Journa

Communication style and exercise compliance in physiotherapy (CONNECT). A cluster randomized controlled trial to test a theory-based intervention to increase chronic low back pain patients’ adherence to physiotherapists’ recommendations: study rationale, design, and methods

Physical activity and exercise therapy are among the accepted clinical rehabilitation guidelines and are recommended self-management strategies for chronic low back pain. However, many back pain sufferers do not adhere to their physiotherapist’s recommendations. Poor patient adherence may decrease the effectiveness of advice and home-based rehabilitation exercises. According to self-determination theory, support from health care practitioners can promote patients’ autonomous motivation and greater long-term behavioral persistence (e.g., adherence to physiotherapists’ recommendations). The aim of this trial is to assess the effect of an intervention designed to increase physiotherapists’ autonomy-supportive communication on low back pain patients’ adherence to physical activity and exercise therapy recommendations. \ud \ud This study will be a single-blinded cluster randomized controlled trial. Outpatient physiotherapy centers (N =12) in Dublin, Ireland (population = 1.25 million) will be randomly assigned using a computer-generated algorithm to either the experimental or control arm. Physiotherapists in the experimental arm (two hospitals and four primary care clinics) will attend eight hours of communication skills training. Training will include handouts, workbooks, video examples, role-play, and discussion designed to teach physiotherapists how to communicate in a manner that promotes autonomous patient motivation. Physiotherapists in the waitlist control arm (two hospitals and four primary care clinics) will not receive this training. Participants (N = 292) with chronic low back pain will complete assessments at baseline, as well as 1 week, 4 weeks, 12 weeks, and 24 weeks after their first physiotherapy appointment. Primary outcomes will include adherence to physiotherapy recommendations, as well as low back pain, function, and well-being. Participants will be blinded to treatment allocation, as they will not be told if their physiotherapist has received the communication skills training. Outcome assessors will also be blinded. \ud \ud We will use linear mixed modeling to test between arm differences both in the mean levels and the rates of change of the outcome variables. We will employ structural equation modeling to examine the process of change, including hypothesized mediation effects. \ud \ud This trial will be the first to test the effect of a self-determination theory-based communication skills training program for physiotherapists on their low back pain patients’ adherence to rehabilitation recommendations. Current Controlled Trials ISRCTN63723433\u