Broccoli aptamer allows quantitative transcription regulation studies in vitro.

Quantitative transcription regulation studies in vivo and in vitro often make use of reporter proteins. Here we show that using Broccoli aptamers, quantitative study of transcription in various regulatory scenarios is possible without a translational step. To explore the method we studied several regulatory scenarios that we analyzed using thermodynamic occupancy-based models, and found excellent agreement with previous studies. In the next step we show that non-coding DNA can have a dramatic effect on the level of transcription, similar to the influence of the lac repressor with a strong affinity to operator sites. Finally, we point out the limitations of the method in terms of delay times coupled to the folding of the aptamer. We conclude that the Broccoli aptamer is suitable for quantitative transcription measurements.

Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in the Fungal Pathogen Candida albicans.

Candida albicans is the most prevalent human fungal pathogen. Its pathogenicity is linked to the ability of C. albicans to reversibly change morphology and to grow as yeast, pseudohyphae, or hyphal cells in response to environmental stimuli. Understanding the molecular regulation controlling those morphological switches remains a challenge that, if solved, could help eradicate C. albicans infections.While numerous studies investigated gene expression changes occurring during C. albicans morphological switches using bulk approaches (e.g., RNA sequencing), here we describe a single-cell and single-molecule RNA imaging and analysis protocol to measure absolute mRNA counts in morphologically intact cells. To detect endogenous mRNAs in single fixed cells, we optimized a single-molecule fluorescent in situ hybridization (smFISH) protocol for C. albicans, which allows one to quantify the differential expression of mRNAs in yeast, pseudohyphae, or hyphal cells. We quantified the expression of two mRNAs, a cell cycle-controlled mRNA (CLB2) and a transcription factor (EFG1), which show expression changes in the different morphological cell types and nutrient conditions. In this protocol, we described in detail the major steps of this approach: growth and fixation, hybridization, imaging, cell segmentation, and mRNA spot analysis. Raw data is provided with the protocol to favor reproducibility. This approach could benefit the molecular characterization of C. albicans and other filamentous fungi, pathogenic or nonpathogenic.

Humor appreciation can be predicted with machine learning techniques.

Humor research is supposed to predict whether something is funny. According to its theories and observations, amusement should be predictable based on a wide variety of variables. We test the practical value of humor appreciation research in terms of prediction accuracy. We find that machine learning methods (boosted decision trees) can indeed predict humor appreciation with an accuracy close to its theoretical ceiling. However, individual demographic and psychological variables, while replicating previous statistical findings, offer only negligible gains in accuracy. Successful predictions require previous ratings by the same rater, unless highly specific interactions between rater and joke content can be assessed. We discuss implications for humor research, and offer advice for practitioners designing content recommendations engines or entertainment platforms, as well as other research fields aiming to review their practical usefulness.

Effectiveness of an Intervention Providing Digitally Generated Personalized Feedback and Education on Adherence to Continuous Positive Airway Pressure: Randomized Controlled Trial.

BACKGROUND: Many people worldwide experience obstructive sleep apnea, which is associated with medical and psychological problems. Continuous positive airway pressure (CPAP) is an efficacious therapy for obstructive sleep apnea, but its effect is limited by nonadherence. Studies show that personalized education and feedback can increase CPAP adherence. Moreover, tailoring the style of information to the psychological profile of a patient has been shown to enhance the impact of interventions. OBJECTIVE: This study aimed to assess the effect of an intervention providing digitally generated personalized education and feedback on CPAP adherence and the additional effect of tailoring the style of the education and feedback to an individual's psychological profile. METHODS: This study was a 90-day, multicenter, parallel, single-blinded, and randomized controlled trial with 3 conditions: personalized content in a tailored style (PT) in addition to usual care (UC), personalized content in a nontailored style (PN) in addition to UC, and UC. To test the effect of personalized education and feedback, the PN + PT group was compared with the UC group. To test the additional effect of tailoring the style to psychological profiles, the PN and PT groups were compared. Overall, 169 participants were recruited from 6 US sleep clinics. The primary outcome measures were adherence based on minutes of use per night and on nights of use per week. RESULTS: We found a significant positive effect of personalized education and feedback on both primary adherence outcome measures. The difference in the estimated average adherence based on minutes of use per night between the PT + PN and UC groups on day 90 was 81.3 minutes in favor of the PT + PN group (95% CI -134.00 to -29.10; P=.002). The difference in the average adherence based on nights of use per week between the PT + PN and UC groups at week 12 was 0.9 nights per week in favor of the PT + PN group (difference in odds ratio 0.39, 95% CI 0.21-0.72; P=.003). We did not find an additional effect of tailoring the style of the intervention to psychological profiles on the primary outcomes. The difference in nightly use between the PT and PN groups on day 90 (95% CI -28.20 to 96.50; P=.28) and the difference in nights of use per week between the PT and PN groups at week 12 (difference in odds ratio 0.85, 95% CI 0.51-1.43; P=.054) were both nonsignificant. CONCLUSIONS: The results show that personalized education and feedback can increase CPAP adherence substantially. Tailoring the style of the intervention to the psychological profiles of patients did not further increase adherence. Future research should investigate how the impact of interventions can be enhanced by catering to differences in psychological profiles. TRIAL REGISTRATION: ClinicalTrials.gov NCT02195531; https://clinicaltrials.gov/ct2/show/NCT02195531.

Remineralization of lytic spinal metastases after radiotherapy.

BACKGROUND CONTEXT: Palliative radiotherapy (RT) can lead to remineralization of osteolytic lesions thereby potentially restoring some of the weight-bearing capacity and preventing vertebral collapse. It is not clear, however, under which circumstances remineralization of osteolytic lesions occurs. PURPOSE: The aim of this study was to investigate the change in bone mineral density in spinal metastases after RT compared to a reference region, and find associated factors. STUDY DESIGN: Retrospective analysis within prospective observational cohort OUTCOME MEASURES: change in bone mineral density measured in Hounsfield Units (HU). PATIENT SAMPLE: patients treated with RT for (painful) bone metastases. METHODS: Patients with spinal metastases were included if computed tomography scans both pre- and post-RT were available. Bone density was measured in HU. A region of interest (ROI) was drawn manually in the metastatic lesion. As a reference, a measurement of bone density in adjacent, unaffected, and non-irradiated vertebrae was used. Factors tested for association were origin of the primary tumor, RT dose and fractionation scheme, and concomitant use of bisphosphonates. RESULTS: A total of 31 patients with 49 spinal metastases, originating from various primary tumors, were included. The median age on baseline was 58 years (IQR: 53-63) and median time between baseline and follow-up scan was 8.2 months (IQR: 3.0-18.4). Difference in HU in the lesion before and after treatment was 146.9 HU (95% CI 68.4-225.4; p<.01). Difference in HU in the reference vertebra between baseline and first follow-up was 19.1 HU (95% CI -47.9 to 86.0; p=.58). Difference between reference vertebrae and metastatic lesions on baseline was -194.1 HU (95% CI -276.2 to -112.0; p<.01). After RT, this difference was reduced to -50.3 HU (95% CI -199.6 to 99.0; p=.52). Patients using bisphosphonates showed a greater increase in HU, 194.1 HU versus 60.6 HU, p=.01. CONCLUSIONS: Palliative radiation of osteolytic lytic spinal metastases is positively associated with an increased bone mineral density at follow-up. The use of bisphosphonates was linked to an increased bone mineral density when used during or after RT.

Delayed cerebral atrophy after cerebellar stroke: topographical relation and clinical impact.

Remote dysconnectivity following cerebellar ischaemic stroke may have a negative impact on supratentorial brain tissue. Since the cerebellum is connected to the individual cerebral lobes via contralateral tracts, cerebellar lesion topography might determine the distribution of contralateral supratentorial brain tissue changes. We investigated (i) the occurrence of delayed cerebral atrophy after cerebellar ischaemic stroke and its relationship to infarct volume; (ii) whether cerebellar stroke topography determines supratentorial atrophy location; and (iii) how cortical atrophy after cerebellar stroke impacts clinical outcome. We performed longitudinal volumetric MRI analysis of patients with isolated cerebellar stroke from the Swiss Stroke Registry database. Stroke location and volume were determined at baseline MRI. Delayed cerebral atrophy was measured as supratentorial cortical volumetric change at follow-up, in contralateral target as compared to ipsilateral reference-areas. In patients with bilateral stroke, both hemispheres were analysed separately. We obtained maps of how cerebellar lesion topography, determines the probability of delayed atrophy per distinct cerebral lobe. Clinical performance was measured with the National Institutes of Health Stroke Scale and modified Rankin Scale. In 29 patients (age 58 ± 18; 9 females; median follow-up: 6.2 months), with 36 datasets (7 patients with bilateral cerebellar stroke), delayed cerebral atrophy occurred in 28 (78%) datasets. A multivariable generalized linear model for a Poisson distribution showed that infarct volume (milliliter) in bilateral stroke patients was positively associated with the number of atrophic target areas (Rate ratio = 1.08; P = 0.01). Lobe-specific cerebral atrophy related to distinct topographical cerebellar stroke patterns. By ordinal logistic regression (shift analysis), more atrophic areas predicted higher 3-month mRS scores in patients with low baseline scores (baseline score 3-5: Odds ratio = 1.34; P = 0.02; baseline score 0-2: OR = 0.71; P = 0.19). Our results indicate that (i) isolated cerebellar ischaemic stroke commonly results in delayed cerebral atrophy and stroke volume determines the severity of cerebral atrophy in patients with bilateral stroke; (ii) cerebellar stroke topography affects the location of delayed cerebral atrophy; and (iii) delayed cerebral atrophy negatively impacts clinical outcome.

Topographic volume-standardization atlas of the human brain.

Specific anatomical patterns are seen in various diseases affecting the brain. Clinical studies on the topography of pathologies are often limited by the absence of a normalization of the prevalence of pathologies to the relative volume of the affected anatomical structures. A comprehensive reference on the relative volumes of clinically relevant anatomical structures serving for such a normalization, is currently lacking. The analyses are based on anatomical high-resolution three-dimensional T1-weighted magnetic resonance imaging data of 30 healthy Caucasian volunteers, including 14 females (mean age 37.79 years, SD 13.04) and 16 males (mean age 38.31 years, SD 16.91). Semi-automated anatomical segmentation was used, guided by a neuroanatomical parcellation algorithm differentiating 96 structures. Relative volumes were derived by normalizing parenchymal structures to the total individual encephalic volume and ventricular segments to the total individual ventricular volume. The present investigation provides the absolute and relative volumes of 96 anatomical parcellation units of the human encephalon. A larger absolute volume in males than in females is found for almost all parcellation units. While parenchymal structures display a trend towards decreasing volumes with increasing age, a significant inverse effect is seen with the ventricular system. The variances in volumes as well as the effects of gender and age are given for each structure before and after normalization. The provided atlas constitutes an anatomically detailed and comprehensive analysis of the absolute and relative volumes of the human encephalic structures using a clinically oriented parcellation algorithm. It is intended to serve as a reference for volume-standardization in clinical studies on the topographic prevalence of pathologies.