Abstract
Gene transcription by RNA polymerase II (Pol II) is under control of promoters and distal regulatory elements known as enhancers. Enhancers are themselves transcribed by Pol II correlating ...with their activity. How enhancer transcription is regulated and coordinated with transcription at target genes has remained unclear. Here, we developed a high-sensitive native elongating transcript sequencing approach, called HiS-NET-seq, to provide an extended high-resolution view on transcription, especially at lowly transcribed regions such as enhancers. HiS-NET-seq uncovers new transcribed enhancers in human cells. A multi-omics analysis shows that genome-wide enhancer transcription depends on the BET family protein BRD4. Specifically, BRD4 co-localizes to enhancer and promoter-proximal gene regions, and is required for elongation activation at enhancers and their genes. BRD4 keeps a set of enhancers and genes in proximity through long-range contacts. From these studies BRD4 emerges as a general regulator of enhancer transcription that may link transcription at enhancers and genes.
Tensors provide a powerful language to describe physical phenomena. Consequently, they have a long tradition in physics and appear in various application areas, either as the final result of ...simulations or as intermediate product. Due to their complexity, tensors are hard to interpret. This motivates the development of well‐conceived visualization methods. As a sub‐branch of scientific visualization, tensor field visualization has been especially pushed forward by diffusion tensor imaging. In this review, we focus on second‐order tensors that are not diffusion tensors. Until now, these tensors, which might be neither positive‐definite nor symmetric, are under‐represented in visualization and existing visualization tools are often not appropriate for these tensors. Hence, we discuss the strengths and limitations of existing methods when dealing with such tensors as well as challenges introduced by them. The goal of this paper is to reveal the importance of the field and to encourage the development of new visualization methods for tensors from various application fields.
Tensors provide a powerful language to describe physical phenomena. In this review, we focus on second‐order tensors that are not diffusionensors. Until now, these tensors, which might be neither positive‐definite nor symmetric, are underrepresented in visualization and existing visualization tools are often not appropriate for these tensors. Hence, we discuss the strengths and limitations of existing methods when dealing with such tensors as well as challenges introduced by them. The goal of this paper is to reveal the importance of the field and to encourage the development of new visualization methods for tensors from various application fields.
Biological soil crusts (biocrusts) release the reactive nitrogen gases (N
) nitrous acid (HONO) and nitric oxide (NO) into the atmosphere, but the underlying microbial process controls have not yet ...been resolved. In this study, we analyzed the activity of microbial consortia relevant in N
emissions during desiccation using transcriptome and proteome profiling and fluorescence in situ hybridization. We observed that < 30 min after wetting, genes encoding for all relevant nitrogen (N) cycling processes were expressed. The most abundant transcriptionally active N-transforming microorganisms in the investigated biocrusts were affiliated with Rhodobacteraceae, Enterobacteriaceae, and Pseudomonadaceae within the Alpha- and Gammaproteobacteria. Upon desiccation, the nitrite (NO
) content of the biocrusts increased significantly, which was not the case when microbial activity was inhibited. Our results confirm that NO
is the key precursor for biocrust emissions of HONO and NO. This NO
accumulation likely involves two processes related to the transition from oxygen-limited to oxic conditions in the course of desiccation: (i) a differential regulation of the expression of denitrification genes; and (ii) a physiological response of ammonia-oxidizing organisms to changing oxygen conditions. Thus, our findings suggest that the activity of N-cycling microorganisms determines the process rates and overall quantity of N
emissions.
Team leadership skills of physicians working in high-performing medical teams are directly related to outcome. It is currently unclear how these skills can best be developed. Therefore, in this ...multi-national cross-sectional prospective study, we explored the development of these skills in relation to physician-, organization- and training characteristics of Helicopter Emergency Medicine Service (HEMS) physicians from services in Europe, the United States of America and Australia.
Physicians were asked to complete a survey regarding their HEMS service, training, and background as well as a full Leader Behavior Description Questionnaire (LBDQ). Primary outcomes were the 12 leadership subdomain scores as described in the LBDQ. Secondary outcome measures were the association of LBDQ subdomain scores with specific physician-, organization- or training characteristics and self-reported ways to improve leadership skills in HEMS physicians.
In total, 120 HEMS physicians completed the questionnaire. Overall, leadership LBDQ subdomain scores were high (10 out of 12 subdomains exceeded 70% of the maximum score). Whereas physician characteristics such as experience or base-specialty were unrelated to leadership qualities, both organization- and training characteristics were important determinants of leadership skill development. Attention to leadership skills during service induction, ongoing leadership training, having standards in place to ensure (regular) scenario training and holding structured mission debriefs each correlated with multiple LBDQ subdomain scores.
Ongoing training of leadership skills should be stimulated and facilitated by organizations as it contributes to higher levels of proficiency, which may translate into a positive effect on patient outcomes.
Not applicable.
Purpose Intensive repeated measures data collection procedures, such as ecological momentary assessment (EMA) and end-of-day (EOD) diaries, are becoming more prominent in pain research. Existing data ...on the feasibility of such methods is encouraging; however, almost nothing is known about feasibility in clinical populations with significant physical disabilities. Research methodology feasibility is crucial to the inclusion of individuals with physical disability in pain research given the high prevalence and impact of pain in these populations. The aim of this study was to examine study compliance, protocol acceptability, and reactivity of intensive data collection methods in adults with chronic pain and spinal cord injury (SCI). Methods Secondary analysis of data from a 7-day EMA and EOD diary study in a sample of 131 community dwelling adults with SCI. Results Results showed rates of missing data ranged from 18.4 to 22.8% across measures. Participant compliance was related to time of day/presence of audible prompts, mobility aid use, race, and baseline levels of pain and pain interference, with more missing data at wake and bedtimes/no prompts, and for those who used hand-held mobility devices, identified as black/African American, and/or reported higher baseline pain and pain interference. Participants rated the study methodology as generally highly acceptable and expressed willingness to participate in similar studies of much longer duration. There was no evidence of reactivity, defined as temporal shifts in pain or pain interference ratings. Conclusions Overall, intensive pain data collection is feasible in persons with SCI with no evidence that the methodology impacts pain intensity or pain interference ratings.
Organ-on-a-chip technology has the potential to accelerate pharmaceutical drug development, improve the clinical translation of basic research, and provide personalized intervention strategies. In ...the last decade, big pharma has engaged in many academic research cooperations to develop organ-on-a-chip systems for future drug discoveries. Although most organ-on-a-chip systems present proof-of-concept studies, miniaturized organ systems still need to demonstrate translational relevance and predictive power in clinical and pharmaceutical settings. This review explores whether microfluidic technology succeeded in paving the way for developing physiologically relevant human in vitro models for pharmacology and toxicology in biomedical research within the last decade. Individual organ-on-a-chip systems are discussed, focusing on relevant applications and highlighting their ability to tackle current challenges in pharmacological research.
Purpose Symptom progression in Huntington disease (HD) is associated with cognitive decline which may interfere with the self-report of symptoms. Unfortunately, data to support or refute the ...psychometric reliability of patient-reported outcomes (PROs) as HD progresses are limited. This is problematic given that PROs are increasingly recognized as important measures of efficacy for new treatments. Methods We examined PRO data from the HDQLIFE Measurement System (Speech Difficulties; Swallowing Difficulties; Chorea) in 509 individuals with premanifest, early-stage, or late-stage HD. Clinician-administered assessments of motor functioning (items from the UHDRS) and standardized objective assessments of cognition (Stroop, Symbol Digit Modalities) were also collected. We examined item bias using differential item functioning (DIF) across HD stage (premanifest, early-, late-) and relative to cognitive performance. We also examined the correlations between self-report and clinician ratings. Regression models that considered total cognitive ability were utilized to determine psychometric reliability of the PROs. Results Most PRO items were free from DIF for both staging and cognition. There were modest correlations between PROs and clinician report (ranged from -0.40 to -0.60). Modeling analyses indicated that psychometric reliability breaks down with poorer cognition and more progressed disease stage; split-half reliability was compromised (i.e., split-half reliability < 0.80) when scores were < 136 for Chorea, < 109 for Speech Difficulties, and < 179 for Swallowing Difficulties. Conclusions Results indicate that the psychometric reliability of PROs can be compromised as HD symptoms progress and cognition declines. Clinicians should consider PROs in conjunction with other types of assessments when total cognition scores exceed critical thresholds.
Introduction
The gold standard for the determination of the erythrocyte sedimentation rate (ESR) is the Westergren method. Other methods to measure the ESR have become available. They range from ...modest modifications of the Westergren method to very different methodologies. The ICSH therefore established a Working Group to investigate these new approaches and compile recommendations for their validation and verification.
Methods
A panel of six experts in laboratory hematology examined the peer‐reviewed literature and EQA surveys from over 6000 laboratories on four continents performing ESR testing. This information was used to create lists of ESR instrument manufacturers and their methods.
Results
Only 28% of laboratories surveyed used the unmodified Westergren method, while 72% of sites used modified or alternate methods. Results obtained with the new instruments could differ from results obtained with the Westergren method by up to 142%. Different non‐Westergren methods showed differences from each other of up to 42%. The new methods were often significantly faster, safer, and less labor‐intensive. They reduced costs and often used standard EDTA tubes, eliminating the need for a dedicated ESR tube.
Conclusion
Based on the consensus of the Working Group, recommendations for manufacturers for the validation of new ESR methods were developed. In addition, a list of recommendations for laboratories that are moving to modified or alternate methods was compiled, addressing instrument performance verification and communications of results to clinical users.
Rheumatoid arthritis is a chronic, systemic joint disease in which an autoimmune response translates into an inflammatory attack resulting in joint damage, disability and decreased quality of life. ...Despite recent introduction of therapeutic agents such as anti-TNFα, even the best current therapies fail to achieve disease remission in most arthritis patients. Therefore, research into the mechanisms governing the destructive inflammatory process in rheumatoid arthritis is of great importance and may reveal novel strategies for the therapeutic interventions. To gain deeper insight into its pathogensis, we have developed for the first time a three-dimensional synovium-on-a-chip system in order to monitor the onset and progression of inflammatory synovial tissue responses. In our study, patient-derived primary synovial organoids are cultivated on a single chip platform containing embedded organic-photodetector arrays for over a week in the absence and presence of tumor-necrosis-factor. Using a label-free and non-invasive optical light-scatter biosensing strategy inflammation-induced 3D tissue-level architectural changes were already detected after two days. We demonstrate that the integration of complex human synovial organ cultures in a lab-on-a-chip provides reproducible and reliable information on how systemic stress factors affect synovial tissue architectures.
We demonstrate that the integration of complex human synovial organ cultures in a lab-on-a-chip provides reproducible and reliable information on how systemic stress factors affect synovial tissue architectures using light scatter biosensing.
The re-creation of physiological cellular microenvironments that truly resemble complex
architectures is the key aspect in the development of advanced
organotypic tissue constructs. Among others, ...organ-on-a-chip technology has been increasingly used in recent years to create improved models for organs and tissues in human health and disease, because of its ability to provide spatio-temporal control over soluble cues, biophysical signals and biomechanical forces necessary to maintain proper organotypic functions. While media supply and waste removal are controlled by microfluidic channel by a network the formation of tissue-like architectures in designated micro-structured hydrogel compartments is commonly achieved by cellular self-assembly and intrinsic biological reorganization mechanisms. The recent combination of organ-on-a-chip technology with three-dimensional (3D) bioprinting and additive manufacturing techniques allows for an unprecedented control over tissue structures with the ability to also generate anisotropic constructs as often seen in
tissue architectures. This review highlights progress made in bioprinting applications for organ-on-a-chip technology, and discusses synergies and limitations between organ-on-a-chip technology and 3D bioprinting in the creation of next generation biomimetic
tissue models.
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