Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data.

MicroRNAs (miRNAs) are key regulators of cell-fate decisions in development and disease with a vast array of target interactions that can be investigated using computational approaches. For this study, we developed metaMIR, a combinatorial approach to identify miRNAs that co-regulate identified subsets of genes from a user-supplied list. We based metaMIR predictions on an improved dataset of human miRNA-target interactions, compiled using a machine-learning-based meta-analysis of established algorithms. Simultaneously, the inverse dataset of negative interactions not likely to occur was extracted to increase classifier performance, as measured using an expansive set of experimentally validated interactions from a variety of sources. In a second differential mode, candidate miRNAs are predicted by indicating genes to be targeted and others to be avoided to potentially increase specificity of results. As an example, we investigate the neural crest, a transient structure in vertebrate development where miRNAs play a pivotal role. Patterns of metaMIR-predicted miRNA regulation alone partially recapitulated functional relationships among genes, and separate differential analysis revealed miRNA candidates that would downregulate components implicated in cancer progression while not targeting tumour suppressors. Such an approach could aid in therapeutic application of miRNAs to reduce unintended effects. The utility is available at http://rna.informatik.uni-freiburg.de/metaMIR/.

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs.

A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Based on genetic and transcriptomic evidence, two associated endoribonucleases, Cas6-1 and Cas6-2a, were postulated to be involved in crRNA maturation from CRISPR1 or CRISPR2, respectively. Here, we report a promiscuity of both enzymes to process in vitro not only their cognate transcripts, but also the respective non-cognate precursors, whereas they are specific in vivo Moreover, while most of the repeats serving as substrates were cleaved in vitro, some were not. RNA structure predictions suggested that the context sequence surrounding a repeat can interfere with its stable folding. Indeed, structure accuracy calculations of the hairpin motifs within the repeat sequences explained the majority of analyzed cleavage reactions, making this a good measure for predicting successful cleavage events. We conclude that the cleavage of CRISPR1 and CRISPR2 repeat instances requires a stable formation of the characteristic hairpin motif, which is similar between the two types of repeats. The influence of surrounding sequences might partially explain variations in crRNA abundances and should be considered when designing artificial CRISPR arrays.

RNA-binding protein HuR and the members of the miR-200 family play an unconventional role in the regulation of c-Jun mRNA.

Post-transcriptional gene regulation is a fundamental step for coordinating cellular response in a variety of processes. RNA-binding proteins (RBPs) and microRNAs (miRNAs) are the most important factors responsible for this regulation. Here we report that different components of the miR-200 family are involved in c-Jun mRNA regulation with the opposite effect. While miR-200b inhibits c-Jun protein production, miR-200a tends to increase the JUN amount through a stabilization of its mRNA. This action is dependent on the presence of the RBP HuR that binds the 3'UTR of c-Jun mRNA in a region including the mir-200a binding site. The position of the binding site is fundamental; by mutating this site, we demonstrate that the effect is not micro-RNA specific. These results indicate that miR-200a triggers a microRNA-mediated stabilization of c-Jun mRNA, promoting the binding of HuR with c-Jun mRNA. This is the first example of a positive regulation exerted by a microRNA on an important oncogene in proliferating cells.

Characterizing leader sequences of CRISPR loci.

MOTIVATION: The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs or their possible functions. Leader properties have mainly been characterized through transcriptional initiation data from single organisms but large-scale characterization of leaders has remained challenging due to their low level of sequence conservation. RESULTS: We developed a method to successfully detect leader sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from distinctive sizes to preferential indel localization. CRISPRleader provides a full annotation of the CRISPR array, its strand orientation as well as conserved core leader boundaries that can be uploaded to any genome browser. In addition, it outputs reader-friendly HTML pages for conserved leader clusters from our database. AVAILABILITY AND IMPLEMENTATION: CRISPRleader and multiple sequence alignments for all 195 leader clusters are available at http://www.bioinf.uni-freiburg.de/Software/CRISPRleader/ CONTACT: costa@informatik.uni-freiburg.de or backofen@informatik.uni-freiburg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein.

The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3' handle are still active in triggering an interference reaction. The complete 3' handle could be removed without loss of activity. However, manipulations of the 5' handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference.

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci.

MOTIVATION: The discovery of CRISPR-Cas systems almost 20 years ago rapidly changed our perception of the bacterial and archaeal immune systems. CRISPR loci consist of several repetitive DNA sequences called repeats, inter-spaced by stretches of variable length sequences called spacers. This CRISPR array is transcribed and processed into multiple mature RNA species (crRNAs). A single crRNA is integrated into an interference complex, together with CRISPR-associated (Cas) proteins, to bind and degrade invading nucleic acids. Although existing bioinformatics tools can recognize CRISPR loci by their characteristic repeat-spacer architecture, they generally output CRISPR arrays of ambiguous orientation and thus do not determine the strand from which crRNAs are processed. Knowledge of the correct orientation is crucial for many tasks, including the classification of CRISPR conservation, the detection of leader regions, the identification of target sites (protospacers) on invading genetic elements and the characterization of protospacer-adjacent motifs. RESULTS: We present a fast and accurate tool to determine the crRNA-encoding strand at CRISPR loci by predicting the correct orientation of repeats based on an advanced machine learning approach. Both the repeat sequence and mutation information were encoded and processed by an efficient graph kernel to learn higher-order correlations. The model was trained and tested on curated data comprising >4500 CRISPRs and yielded a remarkable performance of 0.95 AUC ROC (area under the curve of the receiver operator characteristic). In addition, we show that accurate orientation information greatly improved detection of conserved repeat sequence families and structure motifs. We integrated CRISPRstrand predictions into our CRISPRmap web server of CRISPR conservation and updated the latter to version 2.0. AVAILABILITY: CRISPRmap and CRISPRstrand are available at http://rna.informatik.uni-freiburg.de/CRISPRmap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Macintosh-style videolaryngoscope use for tracheal intubation in elective surgical patients revisited: a sub-analysis of the 2022 Cochrane review data.

The Cochrane systematic review and meta-analysis published in 2022 that compared videolaryngoscopy (VL) with direct laryngoscopy (DL) for facilitating tracheal intubation in adults found that all three types of VL device (Macintosh-style, hyper-angulated and channeled) reduced the risk of failed intubation and increased the likelihood of first-pass success. We report the findings of a subgroup re-analysis of the 2022 Cochrane meta-analysis data focusing on the Macintosh-style VL group. This was undertaken to establish whether sufficient evidence exists to guide airway managers in making purchasing decisions for their local institutions based upon individual device-specific performance. This re-analysis confirmed the superiority of Macintosh-style VL over Macintosh DL in elective surgical patients, with similar efficacy demonstrated between the Macintosh-style VL devices examined. Thus, when selecting which VL device(s) to purchase for their hospital, airway managers decisions are likely to remain focused upon issues such as financial costs, portability, cleaning schedules and previous device experience.

A first assessment of the safe brain initiative care bundle for addressing postoperative delirium in the postanesthesia care unit.

BACKGROUND: Postoperative delirium (POD) following surgery is a prevalent and distressing condition associated with adverse patient outcomes and an increased healthcare burden. OBJECTIVES: To assess the effectiveness of the Safe Brain Initiative care bundle (SBI-CB) in reducing POD in the postanesthesia care unit (PACU). DESIGN: A multicenter, quality-improvement initiative with retrospective analysis of collected data. SETTING: The study was conducted in the operating rooms and postanesthesia care units (PACUs) of four hospitals across Denmark and Turkey. PATIENTS: The convenience sample of patients were aged ≥18 years, scheduled for surgery, and could communicate verbally. Age, sex, preoperative delirium, and the American Society for Anesthesiology physical status classification were used in statistical methods to control for potential confounding influences. INTERVENTION: The SBI-CB, 18 delirium-reducing recommendations aligned with international guidelines. The intervention included patient education, staff training, coordination meetings across centers, and a dashboard for the monitoring of outcomes in the PACU. MAIN OUTCOME MEASURES: The primary outcome was the POD trend in the PACU during implementation months, assessed through Nu-DESC screening at up to three time points in the PACU. We also examined the length of hospital stay. RESULTS: Data were collected from 18,697 adult patients across four hospitals. Initial POD incidence in the PACU after the first three months was 16.36% across all sites (n = 1021). POD in the PACU was observed across all age groups, with peak incidence in younger (18-35 years) and older (>75 years) patients. General anesthesia and longer surgical duration (>1 h) were identified as significant risk factors for POD in the PACU. Matched patients who experienced POD in the PACU had longer stays in hospital, with a mean increase from 35 to 69 h (p < 0.001). Implementation of the SBI-CB was associated with a decreased risk of POD in the PACU for each month of SBI-CB implementation (adjusted odds ratio 0.96, 95% confidence interval: [0.94, 0.97], p < 0.001). CONCLUSIONS: The presented pragmatic implementation of a multidisciplinary care bundle, encompassing pre-, intra-, and postoperative measures alongside outcome monitoring, has the potential to significantly reduce the incidence of POD in the PACU. Improved patient outcomes may be achieved for general surgical departments with patient cohorts not typically considered at risk for developing POD. TRIAL REGISTRATION: Clinicaltrials.gov, identifier NCT05765162.

Moving preinduction cervical ripening to a lower acuity inpatient setting using the synthetic hygroscopic cervical dilator: a cost-consequence analysis for the United States.

BACKGROUND: Leveraging the safety profile of the synthetic hygroscopic cervical dilator (SHCD), one potential way to reduce the burden-of-care provision in the labor-and-delivery unit without compromising safety is to introduce a low-acuity care room (ripening room) for patients undergoing cervical ripening as a part of labor induction at term. METHODS: Implementing a ripening room using SHCDs was compared to scenarios using prostaglandins including a dinoprostone insert (PGE2 insert) or gel (PGE2 gel) and misoprostol given orally (oral PGE1) or vaginally (vaginal PGE1). A theoretical, cost-consequence model was developed to assess costs, staff time, and selected clinical outcomes related to cervical ripening. The model assessed a hypothetical cohort where patients remained in hospital from admission for induction of labor (IOL) to delivery, taking the US labor-and-delivery unit perspective. Model inputs were taken from structured searches of PubMed and ClinicalTrials.gov, published US guidance, and clinical practice. Results are presented as mean (95% credible interval [CrI]). RESULTS: The ripening room using SHCDs cost US$3,210 and required 10.22 hours (h) of nurse time on average per patient. The cost difference to prostaglandins ranged from -$894 (-$2,269 to $398) for PGE2 gel to +$460 (-$1,467 to $1,539) for vaginal PGE1. Mean nurse time was shorter than all prostaglandins, with time savings ranging from -7.05 (-24.55 to 5.73) h for PGE2 insert to -0.97 (-14.69 to 9.59) h for vaginal PGE1. When outcomes of the probabilistic sensitivity analysis were ranked from 1 (best) to 5 (worst), the ripening room using SHCDs ranked 1.94 for costs and 1.97 for nurse time. In a nulliparous population, results improved for the ripening room using SHCDs relative to all prostaglandins. CONCLUSION: In this theoretical study, implementing a ripening room using SHCDs resulted in the lowest time burden and the second lowest costs. The cheapest option for preinduction cervical ripening was vaginal misoprostol.

It is estimated that approximately 20% of deliveries in the USA are submitted to cervical ripening prior to induction of labor to facilitate a vaginal delivery. Cervical ripening can be achieved either by administering a synthetic hormone, called a prostaglandin (e.g. misoprostol or dinoprostone), or by using mechanical means of stretching the cervix (e.g. using the synthetic hygroscopic cervical dilator ­ SHCD). Prostaglandins have been associated with an increased risk of overstimulating uterus contractions such that the person undergoing cervical ripening with prostaglandins requires close monitoring. Each method for cervical ripening has advantages and disadvantages and there is no high-quality evidence to recommend one from the others based on clinical outcomes. In this theoretical study, we estimated the hospital costs and staff time for induction of labor care when using the SHCD in a lower acuity setting within the hospital, without monitoring facilities, in comparison to the patient remaining in the labor-and-delivery room using misoprotol or dinoprostone preparations. Our results suggest that misoprostol resulted in the least expensive option closely followed by the SHCD in a lower acuity setting, both with the potential for notable cost savings when compared to using dinoprostone preparations for cervical ripening. In addition, we associated up to several hours less staff time with the use of the SHCD in a lower acuity setting in comparison to misoprostol and dinoprostone. Patients that were delivering for the first time benefitted more from using the SHCD in a lower acuity setting in comparison to those who had delivered previously.

Synthetic osmotic dilators (Dilapan-S) or dinoprostone vaginal inserts (Propess) for inpatient induction of labour: A UK cost-consequence model.

OBJECTIVE: To estimate the costs of synthetic osmotic dilators (Dilapan-S) compared to dinoprostone vaginal inserts (Propess) for inpatient induction of labour (IOL). STUDY DESIGN: A population-level, Markov model-based cost-consequence analysis was developed to compare the impact of using Dilapan-S versus Propess. The time horizon was modelled from admission to birth. The target population was women requiring inpatient IOL from 37 weeks with an unfavourable cervix in the UK. Mean population characteristics reflected those of the SOLVE (NCT03001661) trial. No patient data were included in this analysis. The care pathways and staff workload were modelled using data from the SOLVE trial and clinical experience. Cost and clinical inputs were sourced from the SOLVE trial and peer-reviewed literature. Costs were inflated to 2020 British pounds (GBP, £). Outcomes were reported as an average per woman for total costs and required staff time (minutes) from admission for IOL until birth. The model robustness was assessed using a probabilistic, multivariate sensitivity analysis of 2,000 simulations with results presented as the median (interquartile range, IQR). RESULTS: Dilapan-S was cost neutral compared to Propess. Midwife and obstetrician times were decreased by 146 min (-11%) and 11 min (-54%), respectively. Sensitivity analysis showed that in 78% of simulations, use of Dilapan-S reduced midwife time with a median of -160 min (IQR -277 to -24 min). Costs were reduced in 54% of simulations (median -£33, IQR -£319 to £282). CONCLUSIONS: The model indicates that adoption of Dilapan-S is likely to be cost-neutral and reduce staff workload in comparison to Propess. Results require support from real-world data and further exploration of Dilapan-S is to be encouraged.

Out-of-Hospital Cervical Ripening With a Synthetic Hygroscopic Cervical Dilator May Reduce Hospital Costs and Cesarean Sections in the United States-A Cost-Consequence Analysis.

Objective: Out-of-hospital (outpatient) cervical ripening prior to induction of labor (IOL) is discussed for its potential to decrease the burden on hospital resources. We assessed the cost and clinical outcomes of adopting an outpatient strategy with a synthetic hygroscopic cervical dilator, which is indicated for use in preinduction cervical ripening. Methods: We developed a cost-consequence model from the hospital perspective with a time period from IOL to post-delivery discharge. A hypothetical cohort of women to undergo IOL at term with an unfavorable cervix (all risk levels) were assessed. As the standard of care (referred to as IP-only) all women were ripened as inpatients using the vaginal PGE2 insert or the single-balloon catheter. In the comparison (OP-select), 50.9% of low-risk women (41.4% of the study population) received outpatient cervical ripening using a synthetic hygroscopic cervical dilator and the remaining women were ripened as inpatients as in the standard of care. Model inputs were sourced from a structured literature review of peer-reviewed articles in PubMed. Testing of 2,000 feasible scenarios (probabilistic multivariate sensitivity analysis) ascertained the robustness of results. Outcomes are reported as the average over all women assessed, comparing OP-select to IP-only. Results: Implementing OP-select resulted in hospital savings of US$689 per delivery, with women spending 1.48 h less time in the labor and delivery unit and 0.91 h less in the postpartum recovery unit. The cesarean-section rate was decreased by 3.78 percentage points (23.28% decreased to 19.50%). In sensitivity testing, hospital costs and cesarean-section rate were reduced in 91% of all instances. Conclusion: Our model analysis projects that outpatient cervical ripening has the potential to reduce hospital costs, hospital stay, and the cesarean section rate. It may potentially allow for better infection-prevention control during the ongoing COVID-19 pandemic and to free up resources such that more women might be offered elective IOL at 39 weeks.

Critical Review of European Health-Economic Guidelines for the Health Technology Assessment of Medical Devices.

Background: Health-technology assessment (HTA) is a recognized mechanism to determine the relative benefits of innovative medical technologies. One aspect is their health-economic impact. While the process and methodology for pharmaceuticals is well-established, guidance for medical devices is sparse. Aim: To provide an overview of the health-economic aspect in current European HTA guidelines concerning medical devices and identifying issues raised and potential improvements proposed in recent literature. Methodology: Available guidelines by European agencies were each reviewed and summarized. To complement this, a full systematic review of current literature concerning potential improvements to existing HTA practices for medical devices, from PubMed and EMBASE, was conducted; the focus was on health economics. Authors could only review documents in English, French, or German. The systematic review yielded 518 unique articles concerning HTA for medical devices, 32 of which were considered for full-text review after screening of all abstracts. Results: There is very limited consensus in-and mostly a complete lack of-guidance specific to medical devices in official HTA guidelines, for both clinical and economic analyses. Twenty two of 41 European countries had published official HTA guidance in English, French, or German. Among these only 4 (England, France, the Netherlands, and Sweden) dedicated a chapter or separate document to medical devices. In the literature, there is sufficient evidence to suggest medical devices need to be addressed separately from pharmaceuticals. However, mostly challenges are discussed rather than implementable solutions offered. We present the following set of frequently discussed issues and summarize any solutions that pertain to them: a weak evidence base, learning-curve effects, organizational impact, incremental innovation, diversity of devices, dynamic pricing, and transferability. We further combine reviewed information to suggest a set of possible best practices for health-economic assessment of medical devices. Conclusion: For greater efficiency in medical-device innovation, European agencies should look to (re-)address the specific requirements of medical devices in their HTA guidelines. When both the health-economic and data requirements for the HTA of medical devices are defined, the development of practical solutions will likely follow.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.

An updated evolutionary classification of CRISPR-Cas systems.

The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.