A software package for efficient patient trajectory analysis applied to analyzing bladder cancer development

We present the Patient Trajectory Analysis Library (PTRA), a software package for explorative analysis of patient development. PTRA provides the tools for extracting statistically relevant trajectories from the medical event histories of a patient population. These trajectories can additionally be clustered for visual inspection and identifying key events in patient progression. The algorithms of PTRA are based on a statistical method developed previously by Jensen et al, but we contribute several modifications and extensions to enable the implementation of a practical tool. This includes a new clustering strategy, filter mechanisms for controlling analysis to specific cohorts and for controlling trajectory output, a parallel implementation that executes on a single server rather than a high-performance computing (HPC) cluster, etc. PTRA is furthermore open source and the code is organized as a framework so researchers can reuse it to analyze new data sets. We illustrate our tool by discussing trajectories extracted from the TriNetX Dataworks database for analyzing bladder cancer development. We show this experiment uncovers medically sound trajectories for bladder cancer.

The effect of myofascial and physical therapy on trunk, shoulder, and elbow movement patterns in women with pain and myofascial dysfunctions after breast cancer surgery: Secondary analyses of a randomized controlled trial

INTRODUCTION

Secondary upper limb dysfunctions are common after breast cancer treatment. Myofascial treatment may be a valuable physical therapy modality for this problem.

OBJECTIVE

To investigate the effect of myofascial therapy in addition to physical therapy on shoulder, trunk, and elbow movement patterns in women with pain and myofascial dysfunctions at the upper limb after breast cancer surgery.

DESIGN

A double-blinded randomized controlled trial.

SETTING

Rehabilitation unit of a university hospital.

PARTICIPANTS

Forty-eight women with persistent pain after finishing breast cancer treatment.

INTERVENTIONS

Over 3 months, all participants received a standard physical therapy program. The experimental (n = 24) and control group (n = 24) received 12 additional sessions of myofascial therapy or placebo therapy, respectively.

MAIN OUTCOME MEASURES

Outcomes of interest were movement patterns of the humerothoracic joint, scapulothoracic joint, trunk, and elbow, measured with an optoelectronic measurement system during the performance of a forward flexion and scaption task. Statistical parametric mapping (SPM) analyses were used for assessing the effect of treatment on movement patterns between both groups (group × time interaction effect).

RESULTS

A significantly decreased protraction and anterior tilting was found after experimental treatment. No beneficial effects on movement patterns of the humerothoracic joint, trunk, or elbow were found.

CONCLUSION

Myofascial therapy in addition to a 12-week standard physical therapy program can decrease scapular protraction and anterior tilting (scapulothoracic joint) during arm movements. Given the exploratory nature of these secondary analyses, the clinical relevance of these results needs to be investigated further.

Lung proliferation is dependent on the duration not the timepoint of tracheal occlusion in nitrofen rats with diaphragmatic hernia

OBJECTIVE

Prenatal tracheal occlusion (TO) promotes lung growth and is applied clinically in fetuses with congenital diaphragmatic hernia (CDH). Limited data are available regarding the effect of duration versus timepoint of TO. Our objective was to document the impact of TO on lung development in the near-term period in rats with nitrofen-induced CDH.

METHOD

Nitrofen was administered on embryonic day (ED)9 and fetal TO was performed on ED18.5, 19, or 20 (term = ED22). Sham-operated and untouched littermates served as controls. Lungs were harvested in 0.5-day steps and only fetuses with a left-sided CDH were included in further analyses. Healthy fetuses provided a reference for normal near-term lung development.

RESULTS

Duration of TO in the nitrofen rat model for CDH predicts lung growth in terms of lung-body-weight ratio as well as an increased mRNA level of the proliferation marker Ki67. Longer TO also induced a more complex airway architecture. The timepoint of TO was not predictive of lung growth.

CONCLUSION

In the nitrofen rat model of CDH, a longer period of TO leads to enhanced lung growth and more refined airway architecture.

The association of hypoglycemia with outcome of critically ill children in relation to nutritional and blood glucose control strategies

BACKGROUND

Withholding parenteral nutrition (PN) until one week after PICU admission facilitated recovery from critical illness and protected against emotional and behavioral problems 4 years later. However, the intervention increased the risk of hypoglycemia, which may have counteracted part of the benefit. Previously, hypoglycemia occurring under tight glucose control in critically ill children receiving early PN did not associate with long-term harm. We investigated whether hypoglycemia in PICU differentially associates with outcome in the context of withholding early PN, and whether any potential association with outcome may depend on the applied glucose control protocol.

METHODS

In this secondary analysis of the multicenter PEPaNIC RCT, we studied whether hypoglycemia in PICU associated with mortality (N = 1440) and 4-years neurodevelopmental outcome (N = 674) through univariable comparison and multivariable regression analyses adjusting for potential confounders. In patients with available blood samples (N = 556), multivariable models were additionally adjusted for baseline serum NSE and S100B concentrations as biomarkers of neuronal, respectively, astrocytic damage. To study whether an association of hypoglycemia with outcome may be affected by the nutritional strategy or center-specific glucose control protocol, we further adjusted the models for the interaction between hypoglycemia and the randomized nutritional strategy, respectively, treatment center. In sensitivity analyses, we studied whether any association with outcome was different in patients with iatrogenic or spontaneous/recurrent hypoglycemia.

RESULTS

Hypoglycemia univariably associated with higher mortality in PICU, at 90 days and 4 years after randomization, but not when adjusted for risk factors. After 4 years, critically ill children with hypoglycemia scored significantly worse for certain parent/caregiver-reported executive functions (working memory, planning and organization, metacognition) than patients without hypoglycemia, also when adjusted for risk factors including baseline NSE and S100B. Further adjustment for the interaction of hypoglycemia with the randomized intervention or treatment center revealed a potential interaction, whereby tight glucose control and withholding early PN may be protective. Impaired executive functions were most pronounced in patients with spontaneous or recurrent hypoglycemia.

CONCLUSION

Critically ill children exposed to hypoglycemia in PICU were at higher risk of impaired executive functions after 4 years, especially in cases of spontaneous/recurrent hypoglycemia.

Therapeutic administration of mouse mast cell protease 6 improves functional recovery after traumatic spinal cord injury in mice by promoting remyelination and reducing glial scar formation

Traumatic spinal cord injury (SCI) most often leads to permanent paralysis due to the inability of axons to regenerate in the adult mammalian central nervous system (CNS). In the past, we have shown that mast cells (MCs) improve the functional outcome after SCI by suppressing scar tissue formation at the lesion site via mouse mast cell protease 6 (mMCP6). In this study, we investigated whether recombinant mMCP6 can be used therapeutically to improve the functional outcome after SCI. Therefore, we applied mMCP6 locally via an intrathecal catheter in the subacute phase after a spinal cord hemisection injury in mice. Our findings showed that hind limb motor function was significantly improved in mice that received recombinant mMCP6 compared with the vehicle-treated group. In contrast to our previous findings in mMCP6 knockout mice, the lesion size and expression levels of the scar components fibronectin, laminin, and axon-growth-inhibitory chondroitin sulfate proteoglycans were not affected by the treatment with recombinant mMCP6. Surprisingly, no difference in infiltration of CD4+ T cells and reactivity of Iba-1+ microglia/macrophages at the lesion site was observed between the mMCP6-treated mice and control mice. Additionally, local protein levels of the pro- and anti-inflammatory mediators IL-1β, IL-2, IL-4, IL-6, IL-10, TNF-α, IFNγ, and MCP-1 were comparable between the two treatment groups, indicating that locally applied mMCP6 did not affect inflammatory processes after injury. However, the increase in locomotor performance in mMCP6-treated mice was accompanied by reduced demyelination and astrogliosis in the perilesional area after SCI. Consistently, we found that TNF-α/IL-1β-astrocyte activation was decreased and that oligodendrocyte precursor cell (OPC) differentiation was increased after recombinant mMCP6 treatment in vitro. Mechanistically, this suggests effects of mMCP6 on reducing astrogliosis and improving (re)myelination in the spinal cord after injury. In conclusion, these data show for the first time that recombinant mMCP6 is therapeutically active in enhancing recovery after SCI.

The dynamic transcriptome during maturation of biofilms formed by methicillin-resistant Staphylococcus aureus

Background

Methicillin-resistant Staphylococcus aureus (MRSA), a leading cause of chronic infections, forms prolific biofilms which afford an escape route from antibiotic treatment and host immunity. However, MRSA clones are genetically diverse, and mechanisms underlying biofilm formation remain under-studied. Such studies form the basis for developing targeted therapeutics. Here, we studied the temporal changes in the biofilm transcriptome of three pandemic MRSA clones: USA300, HEMRSA-15, and ST239.

Methods

Biofilm formation was assessed using a static model with one representative strain per clone. Total RNA was extracted from biofilm and planktonic cultures after 24, 48, and 72 h of growth, followed by rRNA depletion and sequencing (Illumina Inc., San Diego, CA, United States, NextSeq500, v2, 1 × 75 bp). Differentially expressed gene (DEG) analysis between phenotypes and among early (24 h), intermediate (48 h), and late (72 h) stages of biofilms was performed together with in silico co-expression network construction and compared between clones. To understand the influence of SCCmec and ACME on biofilm formation, isogenic mutants containing deletions of the entire elements or of single genes therein were constructed in USA300.

Results

Genes involved in primarily core genome-encoded KEGG pathways (transporters and others) were upregulated in 24-h biofilm culture compared to 24-h planktonic culture. However, the number of affected pathways in the ST239 24 h biofilm (n = 11) was remarkably lower than that in USA300/EMRSA-15 biofilms (USA300: n = 27, HEMRSA-15: n = 58). The clfA gene, which encodes clumping factor A, was the single common DEG identified across the three clones in 24-h biofilm culture (2.2- to 2.66-fold). In intermediate (48 h) and late (72 h) stages of biofilms, decreased expression of central metabolic and fermentative pathways (glycolysis/gluconeogenesis, fatty acid biosynthesis), indicating a shift to anaerobic conditions, was already evident in USA300 and HEMRSA-15 in 48-h biofilm cultures; ST239 showed a similar profile at 72 h. Last, SCCmec+ACME deletion and opp3D disruption negatively affected USA300 biofilm formation.

Conclusion

Our data show striking differences in gene expression during biofilm formation by three of the most important pandemic MRSA clones, USA300, HEMRSA-15, and ST239. The clfA gene was the only significantly upregulated gene across all three strains in 24-h biofilm cultures and exemplifies an important target to disrupt early biofilms. Furthermore, our data indicate a critical role for arginine catabolism pathways in early biofilm formation.

Overexpression of the scopoletin biosynthetic pathway enhances lignocellulosic biomass processing

Lignin is the main factor limiting the enzymatic conversion of lignocellulosic biomass into fermentable sugars. To reduce the recalcitrance engendered by the lignin polymer, the coumarin scopoletin was incorporated into the lignin polymer through the simultaneous expression of FERULOYL-CoA 6'-HYDROXYLASE 1 (F6'H1) and COUMARIN SYNTHASE (COSY) in lignifying cells in Arabidopsis. The transgenic lines overproduced scopoletin and incorporated it into the lignin polymer, without adversely affecting plant growth. About 3.3% of the lignin units in the transgenic lines were derived from scopoletin, thereby exceeding the levels of the traditional p-hydroxyphenyl units. Saccharification efficiency of alkali-pretreated scopoletin-overproducing lines was 40% higher than for wild type.

Identification of the major fermentation inhibitors of recombinant 2G yeasts in diverse lignocellulose hydrolysates

BACKGROUND

Presence of inhibitory chemicals in lignocellulose hydrolysates is a major hurdle for production of second-generation bioethanol. Especially cheaper pre-treatment methods that ensure an economical viable production process generate high levels of these inhibitory chemicals. The effect of several of these inhibitors has been extensively studied with non-xylose-fermenting laboratory strains, in synthetic media, and usually as single inhibitors, or with inhibitor concentrations much higher than those found in lignocellulose hydrolysates. However, the relevance of individual inhibitors in inhibitor-rich lignocellulose hydrolysates has remained unclear.

RESULTS

The relative importance for inhibition of ethanol fermentation by two industrial second-generation yeast strains in five lignocellulose hydrolysates, from bagasse, corn cobs and spruce, has now been investigated by spiking higher concentrations of each compound in a concentration range relevant for industrial hydrolysates. The strongest inhibition was observed with industrially relevant concentrations of furfural causing partial inhibition of both D-glucose and D-xylose consumption. Addition of 3 or 6 g/L furfural strongly reduced the ethanol titer obtained with strain MD4 in all hydrolysates evaluated, in a range of 34 to 51% and of 77 to 86%, respectively. This was followed by 5-hydroxymethylfurfural, acetic acid and formic acid, for which in general, industrially relevant concentrations caused partial inhibition of D-xylose fermentation. On the other hand, spiking with levulinic acid, 4-hydroxybenzaldehyde, 4-hydroxybenzoic acid or vanillin caused little inhibition compared to unspiked hydrolysate. The further evolved MD4 strain generally showed superior performance compared to the previously developed strain GSE16-T18.

CONCLUSION

The results highlight the importance of individual inhibitor evaluation in a medium containing a genuine mix of inhibitors as well as the ethanol that is produced by the fermentation. They also highlight the potential of increasing yeast inhibitor tolerance for improving industrial process economics.

C9orf72-derived arginine-containing dipeptide repeats associate with axonal transport machinery and impede microtubule-based motility

A hexanucleotide repeat expansion in the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). How this mutation leads to these neurodegenerative diseases remains unclear. Here, we show using patient stem cell-derived motor neurons that the repeat expansion impairs microtubule-based transport, a process critical for neuronal survival. Cargo transport defects are recapitulated by treating neurons from healthy individuals with proline-arginine and glycine-arginine dipeptide repeats (DPRs) produced from the repeat expansion. Both arginine-rich DPRs similarly inhibit axonal trafficking in adult Drosophila neurons in vivo. Physical interaction studies demonstrate that arginine-rich DPRs associate with motor complexes and the unstructured tubulin tails of microtubules. Single-molecule imaging reveals that microtubule-bound arginine-rich DPRs directly impede translocation of purified dynein and kinesin-1 motor complexes. Collectively, our study implicates inhibitory interactions of arginine-rich DPRs with axonal transport machinery in C9orf72-associated ALS/FTD and thereby points to potential therapeutic strategies.

Dissolution behavior of precious metals and selective palladium leaching from spent automotive catalysts by trihalide ionic liquids

The dissolution behavior of the precious metals gold, platinum, rhodium and palladium in the trihexyl(tetradecyl)phosphonium trihalide ionic liquids [P66614][Cl3], [P66614][Br3], [P66614][IBr2] and [P66614][I3] was investigated. The highest dissolution rates were observed for the trichloride ionic liquid [P66614][Cl3] and this system was investigated in more detail. The effects of the trichloride concentration in the ionic liquid and temperature were studied, reaching higher leaching rates at higher trichloride conversions and increased temperatures. The stability of the trichloride anion at these elevated temperatures was studied by Raman spectroscopy. It was found that the trichloride anion decomposed during leaching at higher temperatures, showing the requirement to store these reactive compounds in sealed and cool environments, shielded from light. The optimal leaching conditions were applied for the recovery of palladium from ceramic monolith powder, obtained from end-of-life automotive catalysts. The catalyst powder was contacted with the ionic liquid [P66614][Cl3] and the metal concentrations in the ionic liquid were monitored. The trihalide ionic liquid allowed a more selective leaching of palladium compared to other metals present at very high concentrations in the monolith structure, like magnesium. The relative ratio of palladium over magnesium increased by two orders of magnitude compared to the original catalyst composition. The effect of the contact time between the catalyst powder and the ionic liquid on the metal concentrations in the leachate was investigated, but no significant improvement in the selectivity was observed.

Mechanisms and therapeutic potential of interactions between human amyloids and viruses

The aggregation of specific proteins and their amyloid deposition in affected tissue in disease has been studied for decades assuming a sole pathogenic role of amyloids. It is now clear that amyloids can also encode important cellular functions, one of which involves the interaction potential of amyloids with microbial pathogens, including viruses. Human expressed amyloids have been shown to act both as innate restriction molecules against viruses as well as promoting agents for viral infectivity. The underlying molecular driving forces of such amyloid-virus interactions are not completely understood. Starting from the well-described molecular mechanisms underlying amyloid formation, we here summarize three non-mutually exclusive hypotheses that have been proposed to drive amyloid-virus interactions. Viruses can indirectly drive amyloid depositions by affecting upstream molecular pathways or induce amyloid formation by a direct interaction with the viral surface or specific viral proteins. Finally, we highlight the potential of therapeutic interventions using the sequence specificity of amyloid interactions to drive viral interference.

Is early integration of palliative home care in oncology treatment feasible and acceptable for advanced cancer patients and their health care providers? A phase 2 mixed-methods study

BACKGROUND

To support the early integration of palliative home care (PHC) in cancer treatment, we developed the EPHECT intervention and pilot tested it with 30 advanced cancer patients in Belgium using a pre post design with no control group. We aim to determine the feasibility, acceptability and perceived effectiveness of the EPHECT intervention.

METHODS

Interviews with patients (n = 16 of which 11 dyadic with family caregivers), oncologists and GPs (n = 11) and a focus group with the PHC team. We further analyzed the study materials and logbooks of the PHC team (n = 8). Preliminary effectiveness was assessed with questionnaires EORTC QLQ C-30, HADS and FAMCARE and were filled in at baseline and 12, 18 and 24 weeks.

RESULTS

In the interviews after the intervention period, patients reported feelings of safety and control and an optimized quality of life. The PHC team could focus on more than symptom management because they were introduced earlier in the trajectory of the patient. Telephone-based contact appeared to be insufficient to support interprofessional collaboration. Furthermore, some family caregivers reported that the nurse of the PHC team was focused little on them.

CONCLUSION

Nurses of PHC teams are able to deliver early palliative care to advanced cancer patients. However, more attention needs to be given to family caregivers as caregiver and client. Furthermore, the home visits by the PHC team have to be further evaluated and adapted. Lastly, professionals have to find a more efficient way to discuss future care.

Exploring Virulence Factors and Alternative Therapies against Staphylococcus aureus Pneumonia

Pneumonia is an acute pulmonary infection associated with high mortality and an immense financial burden on healthcare systems. Staphylococcus aureus is an opportunistic pathogen capable of inducing S. aureus pneumonia (SAP), with some lineages also showing multidrug resistance. Given the high level of antibiotic resistance, much research has been focused on targeting S. aureus virulence factors, including toxins and biofilm-associated proteins, in an attempt to develop effective SAP therapeutics. Despite several promising leads, many hurdles still remain for S. aureus vaccine research. Here, we review the state-of-the-art SAP therapeutics, highlight their pitfalls, and discuss alternative approaches of potential significance and future perspectives.

Wearable monitoring of sleep-disordered breathing: estimation of the apnea-hypopnea index using wrist-worn reflective photoplethysmography

A large part of the worldwide population suffers from obstructive sleep apnea (OSA), a disorder impairing the restorative function of sleep and constituting a risk factor for several cardiovascular pathologies. The standard diagnostic metric to define OSA is the apnea-hypopnea index (AHI), typically obtained by manually annotating polysomnographic recordings. However, this clinical procedure cannot be employed for screening and for long-term monitoring of OSA due to its obtrusiveness and cost. Here, we propose an automatic unobtrusive AHI estimation method fully based on wrist-worn reflective photoplethysmography (rPPG), employing a deep learning model exploiting cardiorespiratory and sleep information extracted from the rPPG signal trained with 250 recordings. We tested our method with an independent set of 188 heterogeneously disordered clinical recordings and we found it estimates the AHI with a good agreement to the gold standard polysomnography reference (correlation = 0.61, estimation error = 3±10 events/h). The estimated AHI was shown to reliably assess OSA severity (weighted Cohen's kappa = 0.51) and screen for OSA (ROC-AUC = 0.84/0.86/0.85 for mild/moderate/severe OSA). These findings suggest that wrist-worn rPPG measurements that can be implemented in wearables such as smartwatches, have the potential to complement standard OSA diagnostic techniques by allowing unobtrusive sleep and respiratory monitoring.

Recycling of Flexible Polyurethane Foam by Split-Phase Alcoholysis: Identification of Additives and Alcoholyzing Agents to Reach Higher Efficiencies

Split-phase alcoholysis of flexible polyurethane (PU) foam yields an apolar phase containing the recycled polyether polyol, and a lower, polar phase of the alcoholyzing agent and aromatic compounds. However, multiple purification steps are required to render the polyether polyol suitable for synthesis of new flexible PU foams; the unfavorable mass balance limits industrial applications. In this work, 2-pyrrolidone was identified as a performant additive for accelerating the dissolution and depolymerization process. By applying a lactam to PU foam in a weight ratio of 0.1:1, the glycol to PU foam weight ratio can be decreased from 1.5:1 to only 0.5:1, without loss of purity or yield of the recycled polyether polyol. Diglycerol was discovered as a novel, promising alcoholyzing agent; it allows the recycling of the polyether polyol in high purity (97 %) and excellent yields (98 %), and after a single washing with diglycerol, a sufficiently low hydroxyl value (61 mgKOH  g-1 ) is reached. The recycled polyether polyol can replace the virgin polyether polyol (48 mgKOH  g-1 ) for up to 50 % in the synthesis of new flexible PU foams with effects on the foam quality that stay within the limits of generally accepted specifications. A first step towards the valorization of the lower phase was also taken by applying hydrolysis of the newly formed carbamates to toluenediamines, which are readily reintegrated in new PU foams.

Polygenic analysis of very high acetic acid tolerance in the yeast Saccharomyces cerevisiae reveals a complex genetic background and several new causative alleles

BACKGROUND

High acetic acid tolerance is of major importance in industrial yeast strains used for second-generation bioethanol production, because of the high acetic acid content of lignocellulose hydrolysates. It is also important in first-generation starch hydrolysates and in sourdoughs containing significant acetic acid levels. We have previously identified snf4 ^E269* as a causative allele in strain MS164 obtained after whole-genome (WG) transformation and selection for improved acetic acid tolerance.

RESULTS

We have now performed polygenic analysis with the same WG transformant MS164 to identify novel causative alleles interacting with snf4 ^E269* to further enhance acetic acid tolerance, from a range of 0.8-1.2% acetic acid at pH 4.7, to previously unmatched levels for Saccharomyces cerevisiae. For that purpose, we crossed the WG transformant with strain 16D, a previously identified strain displaying very high acetic acid tolerance. Quantitative trait locus (QTL) mapping with pooled-segregant whole-genome sequence analysis identified four major and two minor QTLs. In addition to confirmation of snf4 ^E269* in QTL1, we identified six other genes linked to very high acetic acid tolerance, TRT2, MET4, IRA2 and RTG1 and a combination of MSH2 and HAL9, some of which have never been connected previously to acetic acid tolerance. Several of these genes appear to be wild-type alleles that complement defective alleles present in the other parent strain.

CONCLUSIONS

The presence of several novel causative genes highlights the distinct genetic basis and the strong genetic background dependency of very high acetic acid tolerance. Our results suggest that elimination of inferior mutant alleles might be equally important for reaching very high acetic acid tolerance as introduction of rare superior alleles. The superior alleles of MET4 and RTG1 might be useful for further improvement of acetic acid tolerance in specific industrial yeast strains.

Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers

Butyrate has been used extensively as a feed additive to improve gut health and to decrease Salmonella colonization in poultry. Salmonella mainly colonizes the ceca so butyrate concentrations should be increased in this gut segment. Discrepancies on the effects of butyrate on Salmonella colonization, described in the scientific literature, could thus be due to butyrate release location effects. In this study, newly developed butyrate formulations were evaluated for their effect on cecal butyrate concentrations and on colonization by Salmonella Enteritidis. In a first trial, broilers were randomly allocated to 7 dietary treatment groups with formulations based on different approaches to modify the butyrate release profile: release from wax matrices based on diffusion/erosion; micropellets supposedly release butyrate around pH 7 in the colon; tributyrin is based on the hydrolysis of esters in the small intestine. Fat-protected butyrate was included as a reference, because of its known effect on reduction of Salmonella colonization. Four days after infection, the number of cfu Salmonella per g cecal content and spleen were determined. Butyrate formulations in a wax matrix significantly reduced the Salmonella colonization in cecal content. In a second trial, wax and fat-protected butyrate treatments were replicated and results from the first trial were confirmed. Compared to the control group a higher proportion of butyrate concentration was observed in ceca for those groups with reduced Salmonella colonization. This was associated with a beneficial shift in the cecal microbiota. In conclusion, formulations that increase cecal butyrate concentrations are superior in protecting against Salmonella Enteritidis colonization.

Development of a neonatal adverse event severity scale through a Delphi consensus approach

BACKGROUND

Assessment of the seriousness, expectedness and causality are necessary for any adverse event (AE) in a clinical trial. In addition, assessing AE severity helps determine the importance of the AE in the clinical setting. Standardisation of AE severity criteria could make safety information more reliable and comparable across trials. Although standardised AE severity scales have been developed in other research fields, they are not suitable for use in neonates. The development of an AE severity scale to facilitate the conduct and interpretation of neonatal clinical trials is therefore urgently needed.

METHODS

A stepwise consensus process was undertaken within the International Neonatal Consortium (INC) with input from all relevant stakeholders. The consensus process included several rounds of surveys (based on a Delphi approach), face-to-face meetings and a pilot validation.

RESULTS

Neonatal AE severity was classified by five grades (mild, moderate, severe, life threatening or death). AE severity in neonates was defined by the effect of the AE on age appropriate behaviour, basal physiological functions and care changes in response to the AE. Pilot validation of the generic criteria revealed κ=0.23 and guided further refinement. This generic scale was applied to 35 typical and common neonatal AEs resulting in the INC neonatal AE severity scale (NAESS) V.1.0, which is now publicly available.

DISCUSSION

The INC NAESS is an ongoing effort that will be continuously updated. Future perspectives include further validation and the development of a training module for users.

Mechanical Ventilation Impairs IL-17 Cytokine Family Expression in Ventilator-Associated Pneumonia

Mechanical ventilation (MV) is the primary risk factor for the development of ventilator-associated pneumonia (VAP). Besides inducing a pro-inflammatory T-helper (Th)-1 cytokine response, MV also induces an anti-inflammatory Th2 cytokine response, marked by increased IL-4 secretion and reduced bacterial phagocytic capacity of rodent lung macrophages. Since IL-4 is known to downregulate both Th1 and Th17 cytokines, the latter is important in mediating mucosal immunity and combating bacterial and fungal growth, we studied and showed here in a rat model of MV that Th17 cytokines (IL-17A, IL-17F, and IL-22) were significantly upregulated in the lung as a response to different MV strategies currently utilized in clinic. To study whether the increased IL-4 levels are associated with downregulation of the anti-bacterial Th17 cytokines, we subsequently challenged mechanically ventilated rats with an intratracheal inoculation of Pseudomonas aeruginosa (VAP model) and showed a dramatic downregulation of IL-17A, IL-17F, and IL-22, compared to animals receiving the same bacterial burden without MV. For the studied Th1 cytokines (IFNγ, TNFα, IL-6, and IL-1β), only IFNγ showed a significant decrease as a consequence of bacterial infection in mechanically ventilated rats. We further studied IL-17A, the most studied IL-17 family member, in intensive care unit (ICU) pneumonia patients and showed that VAP patients had significantly lower levels of IL-17A in the endotracheal aspirate compared to patients entering ICU with pre-existing pneumonia. These translational data, obtained both in animal models and in humans, suggest that a deficient anti-bacterial Th17 response in the lung during MV is associated with VAP development.

Are spasticity, weakness, selectivity, and passive range of motion related to gait deviations in children with spastic cerebral palsy? A statistical parametric mapping study

This study aimed to identify the relationships between clinical impairments and gait deviations in children with cerebral palsy (CP). A retrospective convenience sample of 367 children with CP was selected (3–18 years old) and divided in two groups based on clinical symptomatology [unilateral (uCP) / bilateral CP (bCP), (n = 167/200)]. All children underwent a three-dimensional gait analysis and a standardized clinical examination. Gait was inspected on a vector level (all sagittal motions combined), and an individual joint level (pelvis, hip, knee and ankle joint motions). Statistical non-parametric mapping was applied to identify specific parts of the gait cycle displaying relationships between the gait deviations of both groups and the impairment scores of spasticity, weakness, selectivity, and passive range of motion. Impairment scores were summarized in two ways: a) composite impairment scores (e.g. combined spasticity of all assessed muscles acting around the hip, knee and ankle joints) and b) joint specific impairment scores (e.g. spasticity of the muscles acting around the knee joint). Results showed that the vector and most of the individual motions were related to the composite scores. Direct and carry-over relationships were found between certain individual motions and joint impairment scores (around the same or neighboring joints, respectively). All correlations were more prominent for children with bCP compared to uCP, especially regarding the relationships of gait deviations with weakness and reduced selectivity. In conclusion, this study enabled the mapping of relationships between clinical impairments and gait deviations in children with CP, by identifying specific parts of the gait cycle that are related to each of these impairments. These results provide a comprehensive description of these relationships, while simultaneously highlighting the differences between the two CP groups. Integration of these findings could lead to a better understanding of the pathophysiology of gait deviations and, eventually, support individualized treatment planning.

Building a Bridge between Chemotherapy and Immunotherapy in Malignant Pleural Mesothelioma: Investigating the Effect of Chemotherapy on Immune Checkpoint Expression

In light of the promising results of immune checkpoint blockade (ICPB) in malignant pleural mesothelioma (MPM), we investigated the effect of different chemotherapeutic agents on the expression of immune checkpoints (ICPs) in order to rationally design a good treatment schedule for their combination with ICP blocking antibodies. Cisplatin, oxaliplatin and pemetrexed are interesting chemotherapeutic agents to combine with immunotherapy given their immunomodulatory capacities. We looked into cisplatin and pemetrexed because their combination is used as first-line treatment of MPM. Additionally, the effect of the immunogenic chemotherapeutic agent, oxaliplatin, was also studied. Three different MPM cell lines were used for representation of both epithelioid and sarcomatoid subtypes. The desired inhibitory concentrations of the chemotherapeutic agents were determined with the SRB-assay. Allogeneic co-cultures of MPM cells with healthy donor peripheral blood mononuclear cells (PBMC) were set up to assess the effect of these chemotherapeutic agents on the expression of ICPs (PD-1, LAG-3, TIM-3) and their ligands (PD-L1, PD-L2, galectin-9). Cisplatin might be a promising treatment to combine with ICP blocking antibodies since our MPM cell lines were most susceptible to this stand-alone treatment. We found that the expression of ICPs and their ligands on both MPM cells and PBMC was mostly downregulated or unaltered when treated with chemotherapeutic agents, though no clear trend could be determined.

Local DRLs and automated risk estimation in paediatric interventional cardiology

Introduction

Cardiac catheterization procedures result in high radiation doses and often multiple procedures are necessary for congenital heart disease patients. However, diagnostic reference levels (DRL) remain scarce. Our first goal was finding the optimal DRL parameter and determining appropriate DRLs. The second goal was to calculate organ doses (OD), effective doses (ED) and lifetime attributable risks (LAR) per procedure and to provide conversion factors based on dose area product (DAP).

Materials and methods

DRLs are calculated for each procedure type, as the 75^th percentile of the cumulative value per procedure from the corresponding parameter. All irradiation events in the DICOM Structured Reports were automatically processed and simulated using PCXMC, resulting in OD, ED and LAR. Using a Kruskal Wallis H test and subsequent pairwise comparisons, differences in median values of the DRL parameter between procedure types were assessed.

Results

Linear regression showed a strong correlation and narrow confidence interval between DAP and product of body weight and fluoroscopy time (BWxFT), even when all procedures (diagnostic and interventional) are combined. Only 15% of the pairwise comparisons were statistically significant for DAP normalized to BWxFT (DAP_BWxFT). The latter pairs contained less frequent procedure types with significant outliers. For DAP normalized to BW (DAP_BW), 38% of the pairwise comparisons showed statistically significant differences. Conversion factors from DAP_BW to OD and ED were reported for various weight groups, due to the higher correlation between DAP_BW and both OD and ED than between DAP and both OD and ED.

Conclusions

The P75 of DAP_BWxFT for all procedures combined serves as an appropriate DRL value. This facilitates local DRL determination in smaller paediatric centres, which often have insufficient data to produce appropriate DRLs for different procedure types. Conversion factors are more reliable starting from DAP_BW instead of DAP and should be used according to the appropriate BW group.

International survey of De-implementation of initiating parenteral nutrition early in Paediatric intensive care units

BACKGROUND

Initiating parenteral nutrition (PN) within 24 h in critically ill children is inferior to withholding PN during the first week, as was found in the PEPaNIC study. The aims of this study were to investigate de-implementation of early initiation of PN at PICUs worldwide, and to identify factors influencing de-implementation.

METHODS

A cross-sectional online survey was conducted (May - October 2017), consisting of 41 questions addressing current PN practices, the degree of de-implementation, and factors affecting de-implementation.

RESULTS

We analysed 81 responses from 39 countries. Of these 81 respondents, 53 (65%) were aware of the findings of the PEPaNIC study, and 43 (53%) have read the article. In these 43 PICUs, PN was completely withheld during the first week in 10 PICUs, of which 5 already withheld PN (12%), and 5 de-implemented early initiation of PN (12%). Partial de-implementation was reported by 17 (40%) and no de-implementation by 16 (37%). Higher de-implementation rates were observed when the interpreted level of evidence and grade of recommendation of PEPaNIC was high. Predominant reasons for retaining early initiation of PN were concerns on withholding amino acids, the safety in undernourished children and neonates, and the long-term consequences. Furthermore, the respondents were waiting for updated guidelines.

CONCLUSIONS

One year after the publication of the PEPaNIC trial, only two-thirds of the respondents was aware of the study results. Within this group, early initiation of PN was de-implemented completely in 12% of the PICUs, while 40% asserted partial de-implementation. Increasing the awareness, addressing the intervention-specific questions and more frequently revising international guidelines might help to accelerate de-implementation of ineffective, unproven or harmful healthcare.

Measuring brand association strength with EEG: A single-trial N400 ERP study

Companies need to ensure that customers perceive their brands as intended, with strong and unique associations, when facing a competitive market. Traditionally, brand associations are measured using conventional techniques such as surveys and questionnaires albeit both conscious and unconscious factors can influence the collected data and the outcome of a campaign. Neuromarketing can shed light on how the customer’s brain processes marketing stimuli. We report here on an EEG study aimed at gauging mental associations with brands. We focus on the N400 event-related potential, an EEG component most strongly elicited in response to a concept unrelated to a preceding concept. We considered two video on demand brands, Netflix and Rex&Rio, and selected a set of words grouped in 4 categories that were either related (Television, Relaxation, and Price), in varying degrees, or unrelated (Unrelated) to the said brands. The experiment started with both brands’ TV commercials, as a common reference for our participants. We then applied a semantic priming paradigm in which a brand logo (“prime”) was followed by a word (“target”), and the strength of the N400 response to the word used as an inverted measure of the association strength with the brand logo. We clustered N400 responses to identify, for each brand, natural groups of associated words. As a result, for Netflix the cluster with the smallest N400 responses (i.e., strongest associations) consisted of words related to Television but for Rex&Rio it consisted of words related to Relaxation. We also evaluated the relationship between the two brands and determined which associations they share or which ones not. It turned out that associations related to Relaxation and Television distinguish the two brands. Interestingly, survey data did not show any difference between the two brands as they were equally associated with Television and Relaxation. These findings show that our N400 technique can reveal brand associations, and natural categories thereof, that would otherwise go unnoticed when using conventional surveys.

Model-based control for exoskeletons with series elastic actuators evaluated on sit-to-stand movements

BACKGROUND

Currently, control of exoskeletons in rehabilitation focuses on imposing desired trajectories to promote relearning of motions. Furthermore, assistance is often provided by imposing these desired trajectories using impedance controllers. However, lower-limb exoskeletons are also a promising solution for mobility problems of individuals in daily life. To develop an assistive exoskeleton which allows the user to be autonomous, i.e. in control of his motions, remains a challenge. This paper presents a model-based control method to tackle this challenge.

METHODS

The model-based control method utilizes a dynamic model of the exoskeleton to compensate for its own dynamics. After this compensation of the exoskeleton dynamics, the exoskeleton can provide a desired assistance to the user. While dynamic models of exoskeletons used in the literature focus on gravity compensation only, the need for modelling and monitoring of the ground contact impedes their widespread use. The control strategy proposed here relies on modelling of the full exoskeleton dynamics and of the contacts with the environment. A modelling strategy and general control scheme are introduced.

RESULTS

Validation of the control method on 15 non-disabled adults performing sit-to-stand motions shows that muscle effort and joint torques are similar in the conditions with dynamically compensated exoskeleton and without exoskeleton. The condition with exoskeleton in which the compensating controller was not active showed a significant increase in human joint torques and muscle effort at the knee and hip. Motor saturation occurred during the assisted condition, which limited the assistance the exoskeleton could deliver.

CONCLUSIONS

This work presents the modelling steps and controller design to compensate the exoskeleton dynamics. The validation seems to indicate that the presented model-based controller is able to compensate the exoskeleton.

Evaluation of the 'Colli-Pee', a first-void urine collection device for self-sampling at home for the detection of sexually transmitted infections, versus a routine clinic-based urine collection in a one-to-one comparison study design: efficacy and acceptability among MSM in Belgium

OBJECTIVES

Pre-exposure prophylaxis (PrEP) users are screened bi-annual for sexually transmitted infections (STIs). A novel device, called the Colli-Pee, collects first-void urine in a standardised way and the collector tube can be easily delivered by regular post to a certified laboratory. The aim of the study was a one-to-one comparison between the STI test results obtained with the urine collected in the clinic, versus urine collected at home in a real-life setting by Men who have Sex with Men (MSM) in Belgium. The user-friendliness and acceptability of the Colli-Pee device by the users was also evaluated.

DESIGN

A single-site nested substudy in a prospective PrEP demonstration project (Be-PrEP-ared) among MSM in Belgium.

PARTICIPANTS

A total of 473 home-based samples from 213 MSM were received with a mean age of 38.5 years.

INTERVENTIONS

Participants were requested to collect a urine sample at home using the Colli-Pee device and to send it to the laboratory via regular mail.

PRIMARY AND SECONDARY OUTCOME MEASURES

The presence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) was determined using molecular amplification assays. Agreement between test results of samples collected at the clinic and collected at home were evaluated using Cohen's kappa statistic.

RESULTS

TV was not detected. A very good to almost perfect agreement was found for CT, NG and MG of κ=0.75, 0.87 and 0.85, respectively. Using the Colli-Pee device only one low positive CT and two MG infections were missed, however, three additional CT, two NG and six MG infections were detected.

CONCLUSIONS

The Colli-Pee device is a feasible and convenient way to collect urine at home for STI testing. This may be particularly relevant for populations that need frequent STI testing, such as PrEP users and patients who prefer home-sampling.

TRIAL REGISTRATION NUMBER

NCT02552914; Pre-results.

Who finds the road to palliative home care support? A nationwide analysis on the use of supportive measures for palliative home care using linked administrative databases

Background

Many countries developed supportive measures for palliative home care, such as financial incentives or multidisciplinary palliative home care teams. For policy makers, it is important to evaluate the use of these national palliative home care supportive measures on a population level.

Methods and findings

Using routinely-collected data on all deaths in Belgium in 2012 (n = 107,847) we measured the use of four statutory supportive measures, specifically intended for patients who have obtained the legal palliative status, and three non-statutory supportive measures. Factors associated with uptake were analysed using multivariable logistic regression. Of all deaths of adult home-dwelling persons in Belgium (n = 87,007), 17.9 percent used at least one statutory supportive measure and 51.5 percent used at least one non-statutory supportive measure. In those who died of an illness indicative of palliative care needs 33.1 percent used at least one statutory supportive measure and 62.2 percent used at least one non-statutory supportive measure. Younger people and persons dying from cancer were more likely to use a statutory policy measure. Older people and persons dying from COPD were most likely to use a non-statutory policy measure. Women, non-single people, and those living in less urbanised areas were most likely to use any supportive measure.

Conclusions

Statutory supportive measures for palliative home care are underused, even in a subpopulation of persons with potential palliative care needs. Policy makers should stimulate an equitable uptake, and reducing the observed inequalities is an important focus for health care policy.

Longitudinal assessment of cerebral perfusion and vascular response to hypoventilation in a bigenic mouse model of Alzheimer's disease with amyloid and tau pathology

Alzheimer's disease is the most common neurodegenerative disease, and many patients also present with vascular dysfunction. In this study, we aimed to assess cerebral blood flow (CBF) and cerebrovascular response (CVR) as early, pre-symptomatic (3 months of age), imaging markers in a bigenic model of Alzheimer's disease (APP.V717IxTau.P301L, biAT) and in the monogenic parental strains. We further developed our previously published combination of pulsed arterial spin labeling perfusion MRI and hypo-ventilation paradigm, which allows weaning of the mice from the ventilator. Furthermore, the commonly used isoflurane anesthesia induces vasodilation and is thereby inherently a vascular challenge. We therefore assessed perfusion differences in the mouse models under free-breathing isoflurane conditions. We report (i) that we can determine CBF and hypoventilation-based CVR under ketamine/midazolam anesthesia and wean mice from the ventilator, making it a valuable tool for assessment of CBF and CVR in mice, (ii) that biAT mice exhibit lower cortical CBF than wild-type mice at age 3 months, (iii) that CVR was increased in both biAT and APP.V717I mice but not in Tau.P301L mice, identifying the APP genotype as a strong influencer of brain CVR and (iv) that perfusion differences at baseline are masked by the widely used isoflurane anesthesia.

Use and timing of referral to specialized palliative care services for people with cancer: A mortality follow-back study among treating physicians in Belgium

Background

Referral to specialized palliative care services (SPCS) occurs often late in the illness trajectory but may differ across cancer types. We examined differences between cancer types in the use and timing of referral to specialized palliative care services (SPCS) and in the reasons for non-referral.

Methods

We conducted a population-based mortality follow-back survey among physicians who certified a representative sample of deaths in Flanders, Belgium. We focused only on sampled death cases of cancer (n = 2392). The questionnaire asked about the use of the existing types of SPCS and the timing of referral to these services.

Results

Response rate was 58% (1394/2392). Patients who died from breast, respiratory, head and neck, genitourinary or gastrointestinal cancer had higher chances of using SPCS compared to hematologic cancer patients. The most prevalent reason for non-referral was that regular care sufficiently addressed palliative and supportive care needs (51%). This differed significantly between cancer types ranging from 77,8% for breast cancer and 42.1% for hematologic cancer. A second prevalent reason for not using SPCS was that it was not meaningful (enough) (23.9%), particularly for hematologic malignancies (35,1%) and only in 5.3% for breast cancer.

Conclusion

Differences in referral across different types of cancer were found. Referral is more often delayed or not initiated for patients with hematologic cancer, possibly due to differences in illness trajectory. An influencing reason is that physicians perceive palliative care as not meaningful or not meaningful enough for these patients which may be linked to the uncertainty in the disease trajectory of hematologic malignancies.

The validation of Short Interspersed Nuclear Elements (SINEs) as a RT-qPCR normalization strategy in a rodent model for temporal lobe epilepsy

Background

In gene expression studies via RT-qPCR many conclusions are inferred by using reference genes. However, it is generally known that also reference genes could be differentially expressed between various tissue types, experimental conditions and animal models. An increasing amount of studies have been performed to validate the stability of reference genes. In this study, two rodent-specific Short Interspersed Nuclear Elements (SINEs), which are located throughout the transcriptome, were validated and assessed against nine reference genes in a model of Temporal Lobe Epilepsy (TLE). Two different brain regions (i.e. hippocampus and cortex) and two different disease stages (i.e. acute phase and chronic phase) of the systemic kainic acid rat model for TLE were analyzed by performing expression analyses with the geNorm and NormFinder algorithms. Finally, we performed a rank aggregation analysis and validated the reference genes and the rodent-specific SINEs (i.e. B elements) individually via Gfap gene expression.

Results

GeNorm ranked Hprt1, Pgk1 and Ywhaz as the most stable genes in the acute phase, while Gusb and B2m were ranked as the most unstable, being significantly upregulated. The two B elements were ranked as most stable for both brain regions in the chronic phase by geNorm. In contrast, NormFinder ranked the B1 element only once as second best in cortical tissue for the chronic phase. Interestingly, using only one of the two algorithms would have led to skewed conclusions. Finally, the rank aggregation method indicated the use of the B1 element as the best option to normalize target genes, independent of the disease progression and brain region. This result was supported by the expression profile of Gfap.

Conclusion

In this study, we demonstrate the potential of implementing SINEs -notably the B1 element- as a stable normalization factor in a rodent model of TLE, independent of brain region or disease progression.

Body fluid volume homeostasis is abnormal in pregnancies complicated with hypertension and/or poor fetal growth

OBJECTIVES

To evaluate body water volumes and cardiac output in each trimester of pregnancies complicated with hypertension and/or poor fetal growth, relative to uncomplicated pregnancy.

METHODS

In this semi-longitudinal cohort study, a standardised non-invasive maternal hemodynamics assessment in first, second or third trimester was performed in 1068 women with uncomplicated pregnancy (UP), 75 with early onset (EPE) and 117 with late onset preeclampsia (LPE), 139 with gestational hypertension (GH), 129 with small for gestational age (SGA) neonates and 43 with essential hypertension (EH). Women with hypertension or SGA were included prior to onset of symptoms or at diagnosis of disease; 46% of women (758/1631) were assessed in ≥ 2 trimesters. Impedance cardiography and spectrum analysis were used to measure cardiac output, total body water (TBW), extracellular (ECW) and intracellular water (ICW). A linear mixed model was used for inter-trimestrial comparison of parity-, age- and BMI-corrected values within and between groups.

RESULTS

For all pregnancies, TBW is higher in each consecutive trimester, mainly due to increasing fraction of ECW (ECW%). Compared to first trimester UP, ECW and ECW% are higher in EPE whereas TBW, ECW and ICW are lower in SGA. Compared to inter-trimestrial differences in UP, abnormal changes for body water volumes are observed in GH, EPE and LPE and for CO in EPE and LPE. Changes in EH are not different from UP.

CONCLUSIONS

This study is the first to show that concomitant gestational changes of ECW and CO are different from UP already in preclinical stages of pregnancies complicated with hypertension and/or poor fetal growth, except EH. This finding highlights the relevance of early gestational assessment of maternal body fluid status in pregnancies at risk for hypertension or poor fetal growth.

Unplanned Readmission prevention by Geriatric Emergency Network for Transitional care (URGENT): protocol of a prospective single centre quasi-experimental study

BACKGROUND

International guidelines recommend adapting the classic emergency department (ED) management model to the needs of older adults in order to ameliorate post-ED outcomes among this vulnerable group. To improve the care for older ED patients and especially prevent unplanned ED readmissions, the URGENT care model was developed.

METHODS

The URGENT care model is a nurse-led, comprehensive geriatric assessment based care model in the ED with geriatric follow-up after ED discharge. A prospective single centre quasi-experimental study (sequential design with two cohorts) is used to evaluate its effectiveness on unplanned ED readmission compared to usual ED care. Secondary outcome measures are hospitalization rate, ED length of stay, in-hospital length of stay, higher level of care, functional decline and mortality.

DISCUSSION

URGENT builds on previous research with adaptations tailored to the local context and addresses the needs of older patients in the ED with a special focus on transition of care. Although the selected approaches have been tested in other settings, evidence on this type of innovative care models in the ED setting is inconclusive.

TRIAL REGISTRATION

The study protocol is registered retrospectively with ISRCTN ( ISRCTN91449949 ).

Randomized controlled trial to evaluate a prevention program for frail community-dwelling older adults: a D-SCOPE protocol

BACKGROUND

Frail community-dwelling older adults, whom might experience problems regarding physical, cognitive, psychological, social and environmental factors, are at risk for adverse outcomes such as disability, institutionalization and mortality. People in need of help do not always find their way to care and support services and are left undetected. The aim of the D-SCOPE project is to detect frail community-dwelling older adults who previously went unnoticed and to improve their access to care and support. Goal is to increase their frailty-balance, quality of life, meaning in life, life satisfaction, mastery, community inclusion and ageing well in place.

METHODS/DESIGN

The study is a prospective, longitudinal randomized four-armed controlled trial with follow-up at 6 months. The study group aims to include 900 community-dwelling older adults aged 60 years and over from 3 municipalities in Flanders (Belgium). While selecting the study group, risk profiles for frailty will be taken into account. Participants will be randomly selected from the census records in each municipality. Data will be collected prospectively at baseline (T0) and at follow-up, 6 months after baseline (T1). At baseline, participants who are at least mild frail on one of the 5 domains of frailty (CFAI-plus) or feel frail based on the subjective assessment of frailty will be randomly assigned to (1) the study group or (2) the control group. A mixed method design with the inclusion of quantitative and qualitative data analyses will be used to evaluate the efficacy and experiences of the detection and prevention program on frailty.

DISCUSSION

The study will contribute to an innovative vision concerning the organization of care and support, and a timely and accurate detection and support of community-dwelling older adults at risk for frailty.

TRIAL REGISTRATION

This trial was registered at ClinicalTrials.gov, on May 26, 2017, identifier: NCT03168204 .

Exploring of the feature space of de novo developed post-transcriptional riboregulators

Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation.

To allow reliable forward engineering of microbial cell factories, various metabolic engineering efforts rely on RNA-based technology. As such, programmable riboregulators allow dynamic control over gene expression. However, no clear design principles exist for de novo developed repressing riboregulators, which limits their applicability. Here, various engineering principles are identified and computationally explored. Subsequently, various design criteria are used in an experimental design, which were explored in an in vivo study. This resulted in a regression model that enables a more reliable computational design of repression small RNAs.

Y-box-binding protein 1 supports the early and late steps of HIV replication

The human immunodeficiency virus (HIV) depends on cellular proteins, so-called cofactors, to complete its replication cycle. In search for new therapeutic targets we identified the DNA and RNA binding protein Y-box-binding Protein 1 (YB-1) as a cofactor supporting early and late steps of HIV replication. YB-1 depletion resulted in a 10-fold decrease in HIV-1 replication in different cell lines. Dissection of the replication defects revealed that knockdown of YB-1 is associated with a 2- to 5-fold decrease in virion production due to interference with the viral RNA metabolism. Using single-round virus infection experiments we demonstrated that early HIV-1 replication also depends on the cellular YB-1 levels. More precisely, using quantitative PCR and an in vivo nuclear import assay with fluorescently labeled viral particles, we showed that YB-1 knockdown leads to a block between reverse transcription and nuclear import of HIV-1. Interaction studies revealed that YB-1 associates with integrase, although a direct interaction with HIV integrase could not be unambiguously proven. In conclusion, our results indicate that YB-1 affects multiple stages of HIV replication. Future research on the interaction between YB-1 and the virus will reveal whether this protein qualifies as a new antiviral target.

Disbiome database: linking the microbiome to disease

BACKGROUND

Recent research has provided fascinating indications and evidence that the host health is linked to its microbial inhabitants. Due to the development of high-throughput sequencing technologies, more and more data covering microbial composition changes in different disease types are emerging. However, this information is dispersed over a wide variety of medical and biomedical disciplines.

DESCRIPTION

Disbiome is a database which collects and presents published microbiota-disease information in a standardized way. The diseases are classified using the MedDRA classification system and the micro-organisms are linked to their NCBI and SILVA taxonomy. Finally, each study included in the Disbiome database is assessed for its reporting quality using a standardized questionnaire.

CONCLUSIONS

Disbiome is the first database giving a clear, concise and up-to-date overview of microbial composition differences in diseases, together with the relevant information of the studies published. The strength of this database lies within the combination of the presence of references to other databases, which enables both specific and diverse search strategies within the Disbiome database, and the human annotation which ensures a simple and structured presentation of the available data.

Functional characterization of oxazolone-induced colitis and survival improvement by vagus nerve stimulation

Background

Oxazolone-induced colitis has been frequently used in literature as a model of IBD, but insights into the underlying immune response and pathological features are surprisingly still very limited. Vagus nerve stimulation (VNS) has proven to be effective in innate and Th1/Th17 predominant inflammatory models, including pre-clinical models of colitis, however to what extent VNS is also effective in ameliorating Th2-driven colitis remains to be studied. In the present study, we therefore further characterized the immune response in oxazolone-induced colitis and investigated the potential therapeutic effect of VNS.

Methods

Colitis was induced in Balb/c mice by cutaneous sensitization with 3% oxazolone followed by intracolonic administration of 1% oxazolone 7 days later. To evaluate the effect of VNS on the development of Th2-driven colitis, VNS and sham-treated mice were challenged with 1% oxazolone.

Results

Intracolonic oxazolone administration resulted in a severe destruction of the colonic mucosa and a rapid drop in body temperature leading to a 65% mortality rate at day 5. Severe infiltration of neutrophils and monocytes was detected 6h after oxazolone administration which was associated with a Th2-type inflammatory response. VNS significantly improved survival rate which correlated with decreased levels of HMGB1 and reduced colonic (il6 and cxcl1 mRNA) and serum cytokine levels (IL-6, TNFα and CXCL1) compared to sham treated mice.

Conclusions

Oxazolone-induced colitis rather represents a model of sepsis and, at best, may resemble a severe type of ulcerative colitis, associated with early and severe mucosal damage and a high mortality rate. VNS reduces colonic inflammation and improves survival in this model, supporting the anti-inflammatory properties of VNS, even in an aggressive model as oxazolone-induced colitis.

Effect of combining glucocorticoids with Compound A on glucocorticoid receptor responsiveness in lymphoid malignancies

Glucocorticoids (GCs) are a cornerstone in the treatment of lymphoid malignancies such as multiple myeloma (MM) and acute lymphoblastic leukemia (ALL). Yet, prolonged GC use is hampered by deleterious GC-related side effects and the emergence of GC resistance. To tackle and overcome these GC-related problems, the applicability of selective glucocorticoid receptor agonists and modulators was studied, in search of fewer side-effects and at least equal therapeutic efficacy as classic GCs. Compound A (CpdA) is a prototypical example of such a selective glucocorticoid receptor modulator and does not support GR-mediated transactivation. Here, we examined whether the combination of CpdA with the classic GC dexamethasone (Dex) may improve GC responsiveness of MM and ALL cell lines. We find that the combination of Dex and CpdA does not substantially enhance GC-mediated cell killing. In line, several apoptosis hallmarks, such as caspase 3/7 activity, PARP cleavage and the levels of cleaved-caspase 3 remain unchanged upon combining Dex with CpdA. Moreover, we monitor no additional inhibition of cell proliferation and the homologous downregulation of GR is not counteracted by the combination of Dex and CpdA. In addition, CpdA is unable to modulate Dex-liganded GR transactivation and transrepression, yet, Dex-mediated transrepression is also aberrant in these lymphoid cell lines. Together, transrepression-favoring compounds, alone or combined with GCs, do not seem a valid strategy in the treatment of lymphoid malignancies.

Modelling upper respiratory tract diseases: getting grips on host-microbe interactions in chronic rhinosinusitis using in vitro technologies

Chronic rhinosinusitis (CRS) is a chronic inflammation of the mucosa of the nose and paranasal sinuses affecting approximately 11% of the adult population in Europe. Inadequate immune responses, as well as a dysbiosis of the sinonasal microbiota, have been put forward as aetiological factors of the disease. However, despite the prevalence of this disease, there is no consensus on the aetiology and mechanisms of pathogenesis of CRS. Further research requires in vitro models mimicking the healthy and diseased host environment along with the sinonasal microbiota. This review aims to provide an overview of CRS model systems and proposes in vitro modelling strategies to conduct mechanistic research in an ecological framework on the sinonasal microbiota and its interactions with the host in health and CRS.

Real-time loudness normalisation with combined cochlear implant and hearing aid stimulation

BACKGROUND

People who use a cochlear implant together with a contralateral hearing aid-so-called bimodal listeners-have poor localisation abilities and sounds are often not balanced in loudness across ears. In order to address the latter, a loudness balancing algorithm was created, which equalises the loudness growth functions for the two ears. The algorithm uses loudness models in order to continuously adjust the two signals to loudness targets. Previous tests demonstrated improved binaural balance, improved localisation, and better speech intelligibility in quiet for soft phonemes. In those studies, however, all stimuli were preprocessed so spontaneous head movements and individual head-related transfer functions were not taken into account. Furthermore, the hearing aid processing was linear.

STUDY DESIGN

In the present study, we simplified the acoustical loudness model and implemented the algorithm in a real-time system. We tested bimodal listeners on speech perception and on sound localisation, both in normal loudness growth configuration and in a configuration with a modified loudness growth function. We also used linear and compressive hearing aids.

RESULTS

The comparison between the original acoustical loudness model and the new simplified model showed loudness differences below 3% for almost all tested speech-like stimuli and levels. We found no effect of balancing the loudness growth across ears for speech perception ability in quiet and in noise. We found some small improvements in localisation performance. Further investigation with a larger sample size is required.

An evaluation tool for Myofascial Adhesions in Patients after Breast Cancer (MAP-BC evaluation tool): Concurrent, face and content validity

Purpose

To investigate the concurrent, face and content validity of an evaluation tool for Myofascial Adhesions in Patients after Breast Cancer (MAP-BC evaluation tool).

Methods

1) Concurrent validity of the MAP-BC evaluation tool was investigated by exploring correlations (Spearman’s rank Correlation Coefficient) between the subjective scores (0 –no adhesions to 3 –very strong adhesions) of the skin level using the MAP-BC evaluation tool and objective elasticity parameters (maximal skin extension and gross elasticity) generated by the Cutometer Dual MPA 580. Nine different examination points on and around the mastectomy scar were evaluated. 2) Face and content validity were explored by questioning therapists experienced with myofascial therapy in breast cancer patients about the comprehensibility and comprehensiveness of the MAP-BC evaluation tool.

Results

1) Only three meaningful correlations were found on the mastectomy scar. For the most lateral examination point on the mastectomy scar a moderate negative correlation (-0.44, p = 0.01) with the maximal skin extension and a moderate positive correlation with the resistance versus ability of returning or ‘gross elasticity’ (0.42, p = 0.02) were found. For the middle point on the mastectomy scar an almost moderate positive correlation with gross elasticity was found as well (0.38, p = 0.04) 2) Content and face validity have been found to be good. Eighty-nine percent of the respondent found the instructions understandable and 98% found the scoring system obvious. Thirty-seven percent of the therapists suggested to add the possibility to evaluate additional anatomical locations in case of reconstructive and/or bilateral surgery.

Conclusions

The MAP-BC evaluation tool for myofascial adhesions in breast cancer patients has good face and content validity. Evidence for good concurrent validity of the skin level was found only on the mastectomy scar itself.

High-performance membranes with full pH-stability

Following current strong demands from, among others, paper, food and mining industries, a novel type of nanofiltration membrane was developed, which displays excellent performance in terms of selectivity/flux with a unique combination of chemical stability over the full (0-14) pH-range and thermal stability up to 120 °C. The membrane consists of polyvinylidene fluoride grafted with polystyrene sulfonic acid. The optimum membrane showed water permeances of 2.4 L h-1 m-2 bar-1 while retaining NaCl, MgSO4 and Rhodamine B (479 Da) for respectively ≈60%, ≈80% and >96%.

Systemic fluoroquinolone prescriptions for hospitalized children in Belgium, results of a multicenter retrospective drug utilization study

BACKGROUND

Fluoroquinolones (FQ) are increasingly prescribed for children, despite being labeled for only a limited number of labeled pediatric indications. In this multicenter retrospective drug utilization study, we analyzed indications for systemic FQ prescriptions in hospitalized children and the appropriateness of the prescribed dose.

METHODS

Using data obtained from electronic medical files, the study included all children who received a systemic FQ prescription in two Belgian university children's hospitals between 2010 and 2013. Two authors reviewed prescribed daily doses. Univariate and multivariate logistic regression models were used to analyze risk factors for inadequately dosing. Results262 FQ prescriptions for individual patients were included for analysis. 16.8% of these prescriptions were for labeled indications, and 35.1% were guided by bacteriological findings. Prescribed daily dose was considered to be inappropriate in 79 prescriptions (30.2%). Other FQ than ciprofloxacin accounted for 9 prescriptions (3.4%), of which 8 were correctly dosed. Underdosing represented 45 (56.9%) dosing errors. Infants and preschool children were at particular risk for dosing errors, with associated adjusted OR of 0.263 (0.097-0.701) and 0.254 (0.106-0.588) respectively.

CONCLUSIONS

FQ were often prescribed off-label and not guided by bacteriological findings in our study population. Dosing errors were common, particularly in infants and preschool children. FQ prescriptions for children should be improved by specific pediatric antimicrobial stewardship teams. Furthermore, pharmacokinetic studies should optimise dosing recommendations for children.

Circulating microRNA-375 as biomarker of pancreatic beta cell death and protection of beta cell mass by cytoprotective compounds

Objective

Previous studies demonstrated that circulating microRNA-375 (miR-375) is a suitable plasma biomarker for real-time detection of beta cell death. The present study evaluated the use of this biomarker to assess the beta cytoprotective effect of phenylpropenoic acid glucoside (PPAG), which was previously demonstrated to protect beta cells against various types of injury, and of exendin-4, which is an established antidiabetic drug.

Methods

PPAG or exendin-4 were administered in mice treated with streptozotocin (STZ) to acutely induce beta cell death. Beta cell mass and apoptotic death were measured in pancreatic tissue sections. Circulating miR-375 was measured in blood plasma by RT-qPCR. The release of miR-375 was also measured in vitro by MIN-6 beta cells.

Results

Administration of STZ resulted in measurable circulating levels of miR-375, a decrease in beta cell mass and increase in frequency of apoptotic beta cells. In vitro, there was a good correlation between miR-375 release and the extent of beta cell death. Treatment of mice with PPAG or exendin-4 significantly attenuated STZ-induced loss of beta cell mass and beta cell apoptosis, and normalized the blood level of miR-375.

Conclusions

These findings show the potential use of serological miR-375 measurements to evaluate the beta cytoprotective effect of (potential) antidiabetic drugs in vivo.

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying "personal" gene regulatory network. We validated μ-cisTarget by re-analyzing the TAL1 and LMO1 enhancer mutations in T-ALL, and the TERT promoter mutation in melanoma. Next, we re-sequenced the full genomes of ten cancer cell lines and used matched transcriptome data and motif discovery to identify master regulators with de novo binding sites that result in the up-regulation of nearby oncogenic drivers. μ-cisTarget is available from http://mucistarget.aertslab.org .

Vitamin D supplementation in cutaneous malignant melanoma outcome (ViDMe): a randomized controlled trial

BACKGROUND

Previous studies have investigated the protective effect of vitamin D serum levels, at diagnosis and during the follow-up period after treatment, on melanoma outcome. In the present study we assess whether vitamin D supplementation, in the follow-up period after diagnosis and surgical resection of the primary tumor, has a protective effect on relapse of cutaneous malignant melanoma and whether this protective effect correlates with vitamin D levels in serum and Vitamin D Receptor immunoreactivity in the primary tumor.

METHODS/DESIGN

This study is a multicenter randomized double blind placebo- controlled phase III trial. Patients between the age of 18 and 80 years diagnosed and treated surgically for a melanoma stage IB-III are eligible for randomization in a 1:1 ratio to active treatment or placebo. The study drug is taken each month and consists of either 100,000 International Unit cholecalciferol or arachidis oleum raffinatum used as a placebo. The primary endpoint is relapse free survival. The secondary endpoints are 25 hydroxyvitamin D3 serum levels at diagnosis and at 6 month intervals, melanoma subtype, melanoma site and stage of melanoma at diagnosis according to the 2009 American Joint Committee on Cancer melanoma staging and classification. At randomization a bloodsample is taken for DNA analysis. The study is approved by the local Ethics Committees.

DISCUSSION

If we can confirm our hypothesis that vitamin D supplementation after removal of the tumor has a protective effect on relapse of cutaneous malignant melanoma we may reduce the burden of CMM at several levels. Patients, diagnosed with melanoma may have a better clinical outcome and improved quality of life. There will be a decrease in health care costs related to treatment of metastatic disease and there will be a decrease in loss of professional years, which will markedly reduce the economic burden of the disease.

TRIAL REGISTRATION

Clinical Trial.gov, NCT01748448 , 05/12/2012.

State of play and clinical prospects of antibody gene transfer

Recombinant monoclonal antibodies (mAbs) are one of today's most successful therapeutic classes in inflammatory diseases and oncology. A wider accessibility and implementation, however, is hampered by the high product cost and prolonged need for frequent administration. The surge in more effective mAb combination therapies further adds to the costs and risk of toxicity. To address these issues, antibody gene transfer seeks to administer to patients the mAb-encoding nucleotide sequence, rather than the mAb protein. This allows the body to produce its own medicine in a cost- and labor-effective manner, for a prolonged period of time. Expressed mAbs can be secreted systemically or locally, depending on the production site. The current review outlines the state of play and clinical prospects of antibody gene transfer, thereby highlighting recent innovations, opportunities and remaining hurdles. Different expression platforms and a multitude of administration sites have been pursued. Viral vector-mediated mAb expression thereby made the most significant strides. Therapeutic proof of concept has been demonstrated in mice and non-human primates, and intramuscular vectored mAb therapy is under clinical evaluation. However, viral vectors face limitations, particularly in terms of immunogenicity. In recent years, naked DNA has gained ground as an alternative. Attained serum mAb titers in mice, however, remain far below those obtained with viral vectors, and robust pharmacokinetic data in larger animals is limited. The broad translatability of DNA-based antibody therapy remains uncertain, despite ongoing evaluation in patients. RNA presents another emerging platform for antibody gene transfer. Early reports in mice show that mRNA may be able to rival with viral vectors in terms of generated serum mAb titers, although expression appears more short-lived. Overall, substantial progress has been made in the clinical translation of antibody gene transfer. While challenges persist, clinical prospects are amplified by ongoing innovations and the versatility of antibody gene transfer. Clinical introduction can be expedited by selecting the platform approach currently best suited for the mAb or disease of interest. Innovations in expression platform, administration and antibody technology are expected to further improve overall safety and efficacy, and unlock the vast clinical potential of antibody gene transfer.

Optical control of pain in vivo with a photoactive mGlu5 receptor negative allosteric modulator

Light-operated drugs constitute a major target in drug discovery, since they may provide spatiotemporal resolution for the treatment of complex diseases (i.e. chronic pain). JF-NP-26 is an inactive photocaged derivative of the metabotropic glutamate type 5 (mGlu5) receptor negative allosteric modulator raseglurant. Violet light illumination of JF-NP-26 induces a photochemical reaction prompting the active-drug's release, which effectively controls mGlu5 receptor activity both in ectopic expressing systems and in striatal primary neurons. Systemic administration in mice followed by local light-emitting diode (LED)-based illumination, either of the thalamus or the peripheral tissues, induced JF-NP-26-mediated light-dependent analgesia both in neuropathic and in acute/tonic inflammatory pain models. These data offer the first example of optical control of analgesia in vivo using a photocaged mGlu5 receptor negative allosteric modulator. This approach shows potential for precisely targeting, in time and space, endogenous receptors, which may allow a better management of difficult-to-treat disorders.

Biological Recovery of Platinum Complexes from Diluted Aqueous Streams by Axenic Cultures

The widespread use of platinum in high-tech and catalytic applications has led to the production of diverse Pt loaded wastewaters. Effective recovery strategies are needed for the treatment of low concentrated waste streams to prevent pollution and to stimulate recovery of this precious resource. The biological recovery of five common environmental Pt-complexes was studied under acidic conditions; the chloro-complexes PtCl₄^2- and PtCl₆^2-, the amine-complex Pt(NH₃)₄Cl₂ and the pharmaceutical complexes cisplatin and carboplatin. Five bacterial species were screened on their platinum recovery potential; the Gram-negative species Shewanella oneidensis MR-1, Cupriavidus metallidurans CH34, Geobacter metallireducens, and Pseudomonas stutzeri, and the Gram-positive species Bacillus toyonensis. Overall, PtCl₄^2- and PtCl₆^2- were completely recovered by all bacterial species while only S. oneidensis and C. metallidurans were able to recover cisplatin quantitatively (99%), all in the presence of H₂ as electron donor at pH 2. Carboplatin was only partly recovered (max. 25% at pH 7), whereas no recovery was observed in the case of the Pt-tetraamine complex. Transmission electron microscopy (TEM) revealed the presence of both intra- and extracellular platinum particles. Flow cytometry based microbial viability assessment demonstrated the decrease in number of intact bacterial cells during platinum reduction and indicated C. metallidurans to be the most resistant species. This study showed the effective and complete biological recovery of three common Pt-complexes, and estimated the fate and transport of the Pt-complexes in wastewater treatment plants and the natural environment.