bluuebunny/crossref_metadata_2025 huggingface dataset:
Zebrafish models for human ALA-dehydratase-deficient porphyria (ADP) and hereditary coproporphyria (HCP) generated with TALEN and CRISPR-Cas9
Authors: Zhang Shuqing , Meng Jiao , Niu Zhijie , Huang Yikai , Wang Jingjing , Su Xiong , Zhou Yi , Wang Han
Published: February 2017

Defects in the enzymes involved in heme biosynthesis result in a group of human metabolic genetic disorders known as porphyrias. Using a zebrafish model for human hepatoerythropoietic porphyria (HEP), caused by defective uroporphyrinogen decarboxylase (Urod), the fifth enzyme in the heme biosynthesis pathway, we recently have found a novel aspect of porphyria pathogenesis. However, no hereditable zebrafish models with genetic mutations ofaladandcpox, encoding the second enzyme delta-aminolevulinate dehydratase (Alad) and the sixth enzyme coproporphyrinogen oxidase (Cpox), have been established to date. Here we employed site-specific genome-editing tools transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) to generate zebrafish mutants foraladandcpox. These zebrafish mutants display phenotypes of heme deficiency, hypochromia, abnormal erythrocytic maturation and accumulation of heme precursor intermediates, reminiscent of human ALA-dehydratase-deficient porphyria (ADP) and hereditary coproporphyrian (HCP), respectively. Further, we observed altered expression of genes involved in heme biosynthesis and degradation and particularly down-regulation of exocrine pancreatic zymogens in ADP (alad-/-) and HCP (cpox-/-) fishes. These two zebrafish porphyria models can survive at least 7 days and thus provide invaluable resources for elucidating novel pathological aspects of porphyrias, evaluating mutated forms of humanALADandCPOX, discovering new therapeutic targets and developing effective drugs for these complex genetic diseases. Our studies also highlight generation of zebrafish models for human diseases with two versatile genome-editing tools.
The third moments of the site frequency spectrum
Authors: Klassmann A. , Ferretti L.
Published: February 2017

The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-calledsite frequency spectrum. For neutrally evolving sequences, some classical results are available, including the expected value and variance of the spectrum in the Kingman coalescent model without recombination as calculated by Fu(1995).

In this work, we use similar techniques to compute the third moments of the site frequency spectrum without recombination. We also account for the linkage pattern of mutations, yielding the full haplotype spectrum of three polymorphic sites. Based on these results, we derive analytical results for the bias of Tajima’sDand other neutrality tests.

As an application, we obtain the second moments of the spectrum of linked sites, which is related to the neutral spectrum of chromosomal inversions and other structural variants. These moments can be used for the normalisation of new neutrality tests relying on these spectra.
Emergent community agglomeration from data set geometry
Authors: Zhao Chenchao , Song Jun S.
Published: February 2017

In the statistical learning language, samples are snapshots of random vectors drawn from some unknown distribution. Such vectors usually reside in a high-dimensional Euclidean space, and thus, the "curse of dimensionality" often undermines the power of learning methods, including community detection and clustering algorithms, that rely on Euclidean geometry. This paper presents the idea of effective dissimilarity transformation (EDT) on empirical dissimilarity hyperspheres and studies its effects using synthetic and gene expression data sets. Iterating the EDT turns a static data distribution into a dynamical process purely driven by the empirical data set geometry and adaptively ameliorates the curse of dimensionality, partly through changing the topology of a Euclidean feature space into a compact hypersphere. The EDT often improves the performance of hierarchical clustering via the automatic grouping information emerging from global interactions of data points. The EDT is not restricted to hierarchical clustering, and other learning methods based on pairwise dissimilarity should also benefit from the many desirable properties of EDT.
Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells
Authors: Gómez-Schiavon Mariana , Chen Liang-Fu , West Anne E. , Buchler Nicolas E.
Published: February 2017

Single-molecule RNA fluorescencein situhybridization (smFISH) provides unparalleled resolution on the abundance and localization of nascent and mature transcripts in single cells. Gene expression dynamics are typically inferred by measuring mRNA abundance in small numbers of fixed cells sampled from a population at multiple time-points after induction. The sparse data that arise from the small number of cells obtained using smFISH present a challenge for inferring transcription dynamics. Here, we developed a computational pipeline (BayFish) to infer kinetic parameters of gene expression from smFISH data at multiple time points after induction. Given an underlying model of gene expression, BayFish uses a Monte Carlo method to estimate the Bayesian posterior probability of the model parameters and quantify the parameter uncertainty given the observed smFISH data. We tested BayFish on smFISH measurements of the neuronal activity inducible geneNpas4in primary neurons. We showed that a 2-state promoter model can recapitulateNpas4dynamics after induction and we inferred that the transition rate from the promoter OFF state to the ON state is increased by the stimulus.

Author Summary

Gene expression can exhibit cell-to-cell variability due to the stochastic nature of biochemical reactions. Single cell assays (e.g. smFISH) directly quantify stochastic gene expression by measuring the number of active promoters and transcripts per cell in a population of cells. The data are distributions and their shape and time-evolution contain critical information on the underlying process of gene expression. Recent work has combined models of stochastic gene expression with maximum likelihood methods to infer kinetic parameters from smFISH distributions. However, these approaches do not provide a probability distribution or likelihood of model parameters inferred from the smFISH data. This information is useful because it indicates which parameters are loosely constrained by the data and suggests follow up experiments. We developed a suite of MATLAB programs (BayFish) that estimate the Bayesian posterior probability of model parameters from smFISH data. The user specifies an underlying model of stochastic gene expression with unknown parameters (θ) and provides smFISH data (Y). BayFish uses a Monte Carlo algorithm to estimate the Bayesian posterior probabilityP(θ|Y) of model parameters. BayFish is easily modified and can be applied to other models of stochastic gene expression and smFISH data sets.
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients
Authors: Moss Eli L. , Falconer Shannon B. , Tkachenko Ekaterina , Wang Mingjie , Systrom Hannah , Mahabamunuge Jasmin , Relman David A. , Hohmann Elizabeth L. , Bhatt Ami S.
Published: February 2017

Immunocompromised individuals are at high risk of developing Clostridium difficile-associated disease (CDAD). Fecal microbiota transplantation (FMT) is a highly effective therapy for refractory or recurrent CDAD and, despite safety concerns, has recently been offered to immunocompromised patients. We investigated the genomics of bacterial composition following FMT in immunocompromised patients over a 1-year period. Metagenomic, strain and gene-level bacterial dynamics were characterized in two CDAD-affected hematopoietic stem cell (HCT) recipients following FMT. We found alterations in gene content, including loss of virulence and antibiotic resistance genes. These alterations were accompanied by long-term bacterial divergence at the species and strain levels. Our findings suggest limited durability of the specific bacterial consortium introduced with FMT and indicate that alterations of the functional potential of the microbiome are more complex than can be inferred by taxonomic information alone. Our observation that FMT alone cannot induce long-term donor-like alterations of the microbiota of HCT recipients suggests that FMT cannot indefinitely supersede environmental and/or host factors in shaping bacterial composition.
Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures
Authors: Sivley R. Michael , Kropski Jonathan , Sheehan Jonathan , Cogan Joy , Dou Xiaoyi , Blackwell Timothy S. , Phillips John , Meiler Jens , Bush William S. , Capra John A.
Published: February 2017

The spatial distribution of genetic variation within proteins is shaped by evolutionary constraint and thus can provide insights into the functional importance of protein regions and the potential pathogenicity of protein alterations. Here, we comprehensively evaluate the 3D spatial patterns of constraint on human germline and somatic variation in 4,568 solved protein structures. Different classes of coding variants have significantly different spatial distributions. Neutral missense variants exhibit a range of 3D constraint patterns, with a general trend of spatial dispersion driven by constraint on core residues. In contrast, germline and somatic disease-causing variants are significantly more likely to be clustered in protein structure space. We demonstrate that this difference in the spatial distributions of disease-associated and benign germline variants provides a signature for accurately classifying variants of unknown significance (VUS) that is complementary to current approaches for VUS classification. We further illustrate the clinical utility of our approach by classifying new mutations identified from patients with familial idiopathic pneumonia (FIP) that segregate with disease.
Metagenomic DNA sequencing for the diagnosis of intraocular infections
Authors: Doan Thuy , Acharya Nisha R. , Pinsky Benjamin A. , Sahoo Malaya K. , Chow Eric D. , Banaei Niaz , Budvytiene Indre , Cevallos Vicky , Zhong Lina , Zhou Zhaoxia , Lietman Thomas M. , DeRisi Joseph L.
Published: February 2017

Purpose

To compare the performance of unbiased high-throughput sequencing with pathogen directed PCR using DNA isolated from archived ocular fluid, approaches that are compatible with the current sample handling practice of ophthalmologists.

Design

Retrospective molecular study of banked vitreous samples.

Methods

We evaluated a metagenomic DNA sequencing-based approach (DNA-seq) using archived positive (n= 31) and negative (n=36) vitreous specimens as determined by reference pathogen-specific PCR assays (herpes simplex virus 1 and 2, cytomegalovirus, varicella-zoster virus, andToxoplasma gondii). Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from DNA-seq. Clinical samples were de-identified and laboratory personnel handling the samples and interpreting the data were masked.

Results

Metagenomic DNA sequencing detected 87% of positive reference samples. In the presumed negative reference samples, DNA-seq detected an additional 6 different pathogens in 8 samples (22% of negative samples) that were either not detected or not targeted with pathogen-specific PCR assays. Infectious agents identified only with DNA-seq wereCandida dubliniensis,Klebsiella pneumoniae, human herpesvirus 6 (HHV-6), and human T-cell leukemia virus type 1 (HTLV-1). Discordant samples were independently verified in CLIA-certified laboratories. CMV sequences were compared against the antiviral mutation database and 3 of the samples were found to have mutations conferring ganciclovir resistance.

Conclusions

Metagenomic DNA sequencing was highly concordant with pathogen-directed PCRs. The unbiased nature of metagenomics DNA sequencing allowed an expanded scope of pathogen detection, including bacteria, fungal species, and viruses, resolving 22% of cases that had previously escaped detection by routine pathogen-specific PCRs. The detection of drug resistance mutations highlights the potential for unbiased sequencing to provide clinically actionable information beyond pathogen species detection.
The locus coeruleus is a complex and differentiated neuromodulatory system
Authors: Totah Nelson K. , Neves Ricardo M. , Panzeri Stefano , Logothetis Nikos K. , Eschenko Oxana
Published: February 2017

Understanding the forebrain neuromodulation by the noradrenergic locus coeruleus (LC) is fundamental for cognitive and systems neuroscience. The diffuse projections of individual LC neurons and presumably their synchronous spiking have long been perceived as features of the global nature of noradrenergic neuromodulation. Yet, the commonly referenced “synchrony” underlying global neuromodulation, has never been assessed in a large population, nor has it been related to projection target specificity. Here, we recorded up to 52 single units simultaneously (3164 unit pairs in total) in rat LC and characterized projections by stimulating 15 forebrain sites. Spike count correlations were low and, surprisingly, only 13% of pairwise spike trains had synchronized spontaneous discharge. Notably, even noxious sensory stimulation did not activate the entire population, only evoking synchronized responses in ~16% of units on each trial. We also identified novel infra-slow (0.01-1 Hz) fluctuations of LC unit spiking that were asynchronous across the population. A minority, synchronized possibly by gap junctions, was biased toward restricted (non-global) forebrain projection patterns. Finally, we characterized two types of LC single units differing by waveform shape, propensity for synchronization, and interactions with cortex. These cell types formed finely-structured ensembles. Our findings suggest that the LC conveys a highly complex, differentiated, and potentially target-specific neuromodulatory signal.
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Authors: Khan Aziz , Mathelier Anthony
Published: February 2017

Background

A common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments. While several tools exist to intersect and visualize sets of genes, similar tools dedicated to the visualization of genomic region sets are currently limited.

Results

To address this gap, we have developed the Intervene tool, which provides an easy and automated interface for the effective intersection and visualization of genomic region or list sets, thus facilitating their analysis and interpretation. Intervene contains three modules:vennto generate Venn diagrams of up to six sets,upsetto generate UpSet plots of multiple sets, andpairwiseto compute and visualize intersections of multiple sets as clustered heat maps. Intervene, and its interactive web ShinyApp companion, generate publication-quality figures for the interpretation of genomic region and list sets.

Conclusions

Intervene and its web application companion provide an easy command line, and an interactive web interface to compute intersections of multiple genomic and list sets. They also have the capacity to plot intersections using easy-to-interpret visual approaches. Intervene is developed and designed to meet the needs of both computer scientists and biologists. The source code is freely available athttps://bitbucket.org/CBGR/intervene, with the web application available athttps://asntech.shinyapps.io/intervene.
Feedforward inhibition allows input summation to vary in recurrent cortical networks
Authors: Histed Mark H.
Published: February 2017

Brain computations depend on how neurons transform inputs to spike outputs. Here, to understand input-output transformations in cortical networks, we recorded spiking responses from visual cortex (V1) of awake mice of either sex while pairing sensory stimuli with optogenetic perturbation of excitatory and parvalbumin-positive inhibitory neurons. We found V1 neurons’ average responses were primarily additive (linear). We used a recurrent cortical network model to determine if these data, as well as past observations of nonlinearity, could be described by a common circuit architecture. The model showed cortical input-output transformations can be changed from linear to sublinear with moderate (∼20%) strengthening of connections between inhibitory neurons, but this change depends on the presence of feedforward inhibition. Thus, feedforward inhibition, a common feature of cortical circuitry, enables networks to flexibly change their spiking responses via changes in recurrent connectivity.

Significance statement

Brains are made up of neural networks that process information by receiving input activity and transforming those inputs into output activity. We use optogenetic manipulations in awake mice to expose how a transformation in a cortical network depends on internal network activity. Combining numerical simulations with our observations uncovers that transformation depend critically on feedforward inhibition – the fact that inputs to the cortex often make strong connections on both excitatory and inhibitory neurons.
The skin barrier function gene SPINK5 is associated with challenge‐proven IgE‐mediated food allergy in infants
Authors: Ashley S. E. , Tan H.‐T. T. , Vuillermin P. , Dharmage S. C. , Tang M. L. K. , Koplin J. , Gurrin L. C. , Lowe A. , Lodge C. , Ponsonby A.‐L. , Molloy J. , Martin P. , Matheson M. C. , Saffery R. , Allen K. J. , Ellis J. A. , Martino D. ,   the HealthNuts team,   the Barwon Infant Study, the Melbourne Atopy Cohort study, the Peanut Allergen Threshold Study and the Probiotic and Peanut Oral ImmunoTherapy study
Published: February 2017

Background

A defective skin barrier is hypothesized to be an important route of sensitization to dietary antigens and may lead to food allergy in some children. Missense mutations in the serine peptidase inhibitor Kazal type 5 (SPINK5) skin barrier gene have previously been associated with allergic conditions.

Objective

To determine whether genetic variants in and around SPINK5 are associated with IgE‐mediated food allergy.

Method

We genotyped 71 “tag” single nucleotide polymorphisms (tag‐SNPs) within a region spanning ~263 kb including SPINK5 (~61 kb) in n=722 (n=367 food‐allergic, n=199 food‐sensitized‐tolerant and n=156 non‐food‐allergic controls) 12‐month‐old infants (discovery sample) phenotyped for food allergy with the gold standard oral food challenge. Transepidermal water loss (TEWL) measures were collected at 12 months from a subset (n=150) of these individuals. SNPs were tested for association with food allergy using the Cochran‐Mantel‐Haenszel test adjusting for ancestry strata. Association analyses were replicated in an independent sample group derived from four paediatric cohorts, total n=533 (n=203 food‐allergic, n=330 non‐food‐allergic), mean age 2.5 years, with food allergy defined by either clinical history of reactivity, 95% positive predictive value (PPV) or challenge, corrected for ancestry by principal components.

Results

SPINK5 variant rs9325071 (A⟶G) was associated with challenge‐proven food allergy in the discovery sample (P=.001, OR=2.95, CI=1.49‐5.83). This association was further supported by replication (P=.007, OR=1.58, CI=1.13‐2.20) and by meta‐analysis (P=.0004, OR=1.65). Variant rs9325071 is associated with decreased SPINK5 gene expression in the skin in publicly available genotype‐tissue expression data, and we generated preliminary evidence for association of this SNP with elevated TEWL also.

Conclusions

We report, for the first time, association between SPINK5 variant rs9325071 and challenge‐proven IgE‐mediated food allergy.
Dysregulation of metabolic pathways in a mouse model of allergic asthma
Authors: Quinn K. D. , Schedel M. , Nkrumah‐Elie Y. , Joetham A. , Armstrong M. , Cruickshank‐Quinn C. , Reisdorph R. , Gelfand E. W. , Reisdorph N.
Published: February 2017

Background

Asthma is a complex lung disease resulting from the interplay of genetic and environmental factors. To understand the molecular changes that occur during the development of allergic asthma without genetic and environmental confounders, an experimental model of allergic asthma in mice was used. Our goals were to (1) identify changes at the small molecule level due to allergen exposure, (2) determine perturbed pathways due to disease, and (3) determine whether small molecule changes correlate with lung function.

Methods

In this experimental model of allergic asthma, matched bronchoalveolar lavage (BAL) fluid and plasma were collected from three groups of C57BL6 mice (control vs sensitized and/or challenged with ovalbumin, n=3‐5/group) 6 hour, 24 hour, and 48 hour after the last challenge. Samples were analyzed using liquid chromatography‐mass spectrometry‐based metabolomics. Airway hyper‐responsiveness (AHR) measurements and differential cell counts were performed.

Results

In total, 398 and 368 dysregulated metabolites in the BAL fluid and plasma of sensitized and challenged mice were identified, respectively. These belonged to four, interconnected pathways relevant to asthma pathogenesis: sphingolipid metabolism (P=6.6×10−5), arginine and proline metabolism (P=1.12×10−7), glycerophospholipid metabolism (P=1.3×10−10), and the neurotrophin signaling pathway (P=7.0×10−6). Furthermore, within the arginine and proline metabolism pathway, a positive correlation between urea‐1‐carboxylate and AHR was observed in plasma metabolites, while ornithine revealed a reciprocal effect. In addition, agmatine positively correlated with lung eosinophilia.

Conclusion

These findings point to potential targets and pathways that may be central to asthma pathogenesis and can serve as novel therapeutic targets.
Transfusion in critical care – a UK regional audit of current practice
Authors: Plumb J. O. M. , Taylor M. G. , Clissold E. , Grocott M. P. W. , Gill R. ,   the South Coast Peri‐operative Audit and Research Collaboration (SPARC)
Published: February 2017

A consistent message within critical care publications has been that a restrictive transfusion strategy is non‐inferior, and possibly superior, to a liberal strategy for stable, non‐bleeding critically ill patients. Translation into clinical practice has, however, been slow. Here, we describe the degree of adherence to UK best practice guidelines in a regional network of nine intensive care units within Wessex. All transfusions given during a 2‐month period were included (n = 444). Those given for active bleeding or within 24 h of major surgery, trauma or gastrointestinal bleeding were excluded (n = 148). The median (IQR [range]) haemoglobin concentration before transfusion was 73 (68–77 [53–106]) g.l−1, with only 34% of transfusion episodes using a transfusion threshold of < 70 g.l−1. In a subgroup analysis that did not study patients with a history of cardiac disease (n = 42), haemoglobin concentration before transfusion was 72 (68–77 [50–98]) g.l−1, with only 36% of transfusion episodes using a threshold of < 70 g.l−1 (see Fig. 3). Most blood transfusions given to critically ill patients who were not bleeding in this audit used a haemoglobin threshold > 70 g.l−1. The reason why recommendations on transfusion triggers have not translated into clinical practice is unclear. With a clear national drive to decrease usage of blood products and clear evidence that a threshold of 70 g.l−1 is non‐inferior, it is surprising that a scarce and potentially dangerous resource is still being overused within critical care. Simple solutions such as electronic patient records that force pause for thought before blood transfusion, or prescriptions that only allow administration of a single unit in non‐emergency circumstances may help to reduce the incidence of unnecessary blood transfusions.
Novel method to assess intrinsic heart rate recovery in ambulatory ECG recordings tracks cardioprotective effects of chronic autonomic regulation therapy in patients enrolled in the ANTHEM‐HF study
Authors: Carlson Gerrard M. , Libbus Imad , Amurthur Badri , KenKnight Bruce H. , Verrier Richard L.
Published: February 2017

Background

Postexercise heart rate recovery (HRR) is a powerful and independent predictor of mortality. Autonomic regulation therapy (ART) with chronic vagus nerve stimulation (VNS) has been shown to improve ventricular function in patients with chronic heart failure. However, the effect of ART on HRR in patients with heart failure remains unknown.

Methods

A new measure involving quantification of intrinsic HRR was developed for 24‐hr ambulatory ECG (AECG) recordings based on spontaneous heart rate changes observed during daily activity in patients with symptomatic heart failure and reduced ejection fraction. Intrinsic HRR values were compared in 21 patients enrolled in the ANTHEM‐HF study (NCT01823887) before and after 12 months of chronic ART (10 Hz, 250 μs pulse width, 18% duty cycle, maximum tolerable current amplitude after 10 weeks of titration) and to values from normal subjects (PhysioNet database, n = 54).

Results

With chronic ART, average intrinsic HRR was improved as indicated by a shortening of the rate‐recovery time constant by 8.9% (from 12.3 ± 0.1 at baseline to 11.2 ± 0.1 s, p < .0001) among patients receiving high‐intensity stimuli (≥2 mA). In addition, mean heart rate decreased by 8.5 bpm (from 75.9 ± 2.6 to 67.4 ± 2.9 bpm, p = .005) and left ventricular ejection fraction (LVEF) increased by 4.7% (from 32.6 ± 2.0% to 37.3 ± 1.9%, p < .005).

Conclusion

Using a new technique adapted for 24‐hr AECG recordings, intrinsic HRR was found to be impaired in patients with symptomatic HF compared to normal subjects. Chronic ART significantly improved intrinsic HRR, indicating an improvement in autonomic function.
Diagnostic accuracy of Charcot's triad: a systematic review
Authors: Rumsey Steva , Winders Joel , MacCormick Andrew D.
Published: February 2017

Background

Charcot's triad is a well‐established diagnostic tool for acute cholangitis (AC). It has been recognized as an inaccurate test in clinical practice; however, its exact sensitivity and specificity remain unclear. This knowledge is key to informing the value of its continued clinical application. The objectives of this study are to calculate an estimate of the sensitivity and specificity of Charcot's triad based on published research and consider its applicability to clinical practice and medical education.

Methods

Electronic database search for relevant literature and review of reference lists of the subsequent articles for additional resources. Two independent researchers located articles which were qualitatively and quantitatively reviewed. The overall sensitivity and specificity values across all studies were subsequently calculated.

Results

The 16 articles included in the review varied widely in study design and the sensitivity of Charcot's triad was reported for AC. Across the included articles, there were 4288 patients studied. The overall sensitivity for Charcot's triad was calculated as 36.3%. The specificity was only analysed in three studies and had an overall value of 93.2%. Nine of the articles also investigated the sensitivity of Reynold's pentad which was consistently low with an overall value of 4.82%. The specificity of Reynold's pentad was not studied.

Conclusion

Charcot's triad has limited clinical utility as a diagnostic algorithm for AC. It is an effective rule‐in test but a poor rule‐out test and should be applied and taught accordingly. A more sensitive diagnostic tool is required to achieve superior outcomes for AC patients.
Population pharmacokinetic and exposure simulation analysis for cediranib (AZD2171) in pooled Phase I/II studies in patients with cancer
Authors: Li Jianguo , Al‐Huniti Nidal , Henningsson Anja , Tang Weifeng , Masson Eric
Published: February 2017

Aims

A population pharmacokinetic (PK) model was developed for cediranib to simulate cediranib exposure for different doses, including comedication with strong uridine glucuronosyl transferase/P‐glycoprotein inducers such as rifampicin, in cancer patients.

Methods

Plasma concentrations and covariates from 625 cancer patients after single or multiple oral cediranib administrations ranging from 0.5 to 90 mg in 19 Phase I and II studies were included in the analysis. Stepwise covariate modelling was used to develop the population PK model. The final model was used to simulate cediranib exposure in cancer patients to evaluate cediranib target coverage and the need for dose adjustment for covariates or coadministration with rifampicin.

Results

A two‐compartment model with sequential zero‐ and first‐order absorption and first‐order elimination adequately described the cediranib concentration–time courses. Body weight and age were identified as having statistically significant impact on cediranib PK, but only <21% impact on AUC and maximum concentrations. Simulated lower bounds of 90% prediction interval or median of unbound cediranib concentrations after cediranib 15 or 20 mg exceeded the IC50 for vascular endothelial growth factor receptors‐1, ‐2 and ‐3. Exposures of cediranib 20 or 30 mg with coadministration of rifampicin were comparable to those of 15 or 20 mg, respectively, without coadministration.

Conclusions

No covariate was identified to require dose adjustment for cediranib. Cediranib exposure following 15 or 20 mg daily dose administration is adequate overall for inhibition of in vitro estimated vascular endothelial growth factor receptor‐1, ‐2 and ‐3 activities. An increase in cediranib dose may be needed for cediranib coadministered with strong uridine glucuronosyl transferase/P‐glycoprotein inducers such as rifampicin.
A bosentan pharmacokinetic study to investigate dosing regimens in paediatric patients with pulmonary arterial hypertension: FUTURE‐3
Authors: Berger Rolf M. F. , Gehin Martine , Beghetti Maurice , Ivy Dunbar , Kusic‐Pajic Andjela , Cornelisse Peter , Grill Simon , Bonnet Damien ,   the FUTURE‐3 investigators
Published: February 2017

Aim

The aim of the present study was to investigate whether increasing the bosentan dosing frequency from 2 mg kg–1 twice daily (b.i.d.) to 2 mg kg–1 three times daily (t.i.d.) in children with pulmonary arterial hypertension (PAH) (from ≥3 months to <12 years of age) would increase exposure.

Methods

An open‐label, prospective, randomized, multicentre, multiple‐dose, phase III study was conducted. Patients (n = 64) were randomized 1:1 to receive oral doses of bosentan of 2 mg kg–1 b.i.d. or t.i.d. The main pharmacokinetic endpoint was the daily exposure to bosentan over 24 h corrected to the 2 mg kg–1 dose (AUC0–24C). The maximum plasma concentration corrected to the 2 mg kg–1 dose (CmaxC), the time to reach the maximum plasma concentration (tmax) and safety endpoints were also assessed.

Results

The geometric mean [95% confidence interval (CI)] for AUC0–24C was 8535 h.ng ml–1 (6936, 10 504) and 7275 h.ng ml–1 (5468, 9679) for 2 mg kg–1 b.i.d. and t.i.d., respectively [geometric mean ratio (95% CI) 0.85 (0.61, 1.20)]. The geometric mean (95% CI) for CmaxC was 743 ng ml–1 (573, 963) and 528 ng ml–1 (386, 722) for 2 mg kg–1 b.i.d. and t.i.d., respectively [geometric mean ratio (95% CI) 0.71 (0.48, 1.05)]. The median (range) for tmax was 3.0 h (0.0–7.5) and 3.0 h (1.0–8.0) for 2 mg kg–1 b.i.d. and t.i.d., respectively. The proportions of patients who experienced ≥1 adverse event were similar in the b.i.d. (66.7%) and t.i.d. (67.7%) groups.

Conclusions

There appeared to be no clinically relevant difference in exposure to bosentan, or in safety, when increasing the frequency of bosentan dosing from b.i.d. to t.i.d. Therefore, the present study provides no indication that the dosing recommendation should be changed, and 2 mg kg–1 b.i.d. remains the recommended dosing regimen for bosentan in paediatric PAH patients.
Patients with learning disabilities who lack capacity detained under the Mental Health Act in the UK: A case study
Authors: Sawhney Indermeet , Zia Asif , Gates Bob
Published: February 2017

Accessible Summary

In England and Wales, some people with learning disabilities may have to be detained under the Mental Health Act 2007 as patients in a hospital for a period of assessment and or treatment if they are suffering from a mental disorder, and it is for the interests of their own health and safety, or to protect others.

Patients who are detained under Section 2 of the Mental Health Act 2007 can apply to the Mental Health Tribunal to decide whether they should be detained in a psychiatric hospital or be discharged.

The Mental Health Tribunal has the power to discharge these patients after a hearing.

Patients who lack capacity to apply to the tribunal are unable to have a tribunal hearing.

The European Court has ruled that this is unfair to these patients.

There needs to be a system in place to ensure that these patients get a tribunal hearing.

Background

In the UK, the Mental Health Tribunal is a long‐established safeguard for patients detained under the Mental Health Act. This gives such patients an effective appeal mechanism to ensure legal protection of their liberty. This act contains sections that allow for civil detention in the case of mental disorder. The right to apply to the tribunal against such detention is underpinned by the right to liberty under Article 5 of the European Convention of Human Rights (ECHR). Some patients with learning disabilities may lack capacity and the ability to challenge their detention.

Method

This article presents a case study of a woman with Down's syndrome and severe learning disabilities. Whilst this woman was detained under the Mental Health Act, she could have applied for a review of her detention to the Mental Health Tribunal within 14 days. She did not do so because she lacked capacity to instruct solicitors. Subsequently, as a result of appeal, the case proceeded through English and European judicial review.

Results

The European Court of Human Rights, in the case of MH v UK (2013), has ruled that the appeals procedure for patients without capacity detained under Section 2 of the Mental Health Act is not compatible with Article 5(4) of the European Convention of Human Rights. The European Court has ruled that special procedural safeguards are required to enable this cohort of patients to exercise their rights guaranteed by Article 5(4).

Conclusions

Responsible clinicians [treating consultant psychiatrists] need to ensure that all patients detained under section 2 of the Mental Health Act have an assessment of their capacity to apply to the tribunal. There need to be systems in place to alert hospital managers when a patient lacks capacity to apply for a tribunal. Hospital managers should request the Secretary of State to apply for a tribunal in these instances. Knowledge of this ruling is relevant to informing the practice of other interdisciplinary healthcare professionals working with such patients.
Diagnostic red flags: steroid‐treated malignant CNS lymphoma mimicking autoimmune inflammatory demyelination
Authors: Barrantes‐Freer Alonso , Engel Aylin Sophie , Rodríguez‐Villagra Odir Antonio , Winkler Anne , Bergmann Markus , Mawrin Christian , Kuempfel Tania , Pellkofer Hannah , Metz Imke , Bleckmann Annalen , Hernández‐Durán Silvia , Schippling Sven , Rushing Elisabeth J. , Frank Stephan , Glatzel Markus , Matschke Jakob , Hartmann Christian , Reifenberger Guido , Müller Wolf , Schildhaus Hans‐Ulrich , Brück Wolfgang , Stadelmann Christine
Published: February 2017

The presence of inflammation and demyelination in a central nervous system (CNS) biopsy points towards a limited, yet heterogeneous group of pathologies, of which multiple sclerosis (MS) represents one of the principal considerations. Inflammatory demyelination has also been reported in patients with clinically suspected primary central nervous system lymphoma (PCNSL), especially when steroids had been administered prior to biopsy acquisition. The histopathological changes induced by corticosteroid treatment can range from mild reduction to complete disappearance of lymphoma cells. It has been proposed that in the absence of neoplastic B cells, these biopsies are indistinguishable from MS, yet despite the clinical relevance, no histological studies have specifically compared the two entities. In this work, we analyzed CNS biopsies from eight patients with inflammatory demyelination in whom PCNSL was later histologically confirmed, and compared them with nine well defined early active multiple sclerosis lesions. In the patients with steroid‐treated PCNSL (ST‐PCNSL) the interval between first and second biopsy ranged from 3 to 32 weeks; all of the patients had received corticosteroids before the first, but not the second biopsy. ST‐PCNSL patients were older than MS patients (mean age: ST‐PCNSL: 62 ± 4 years, MS: 30 ± 2 years), and histological analysis revealed numerous apoptoses, patchy and incomplete rather than confluent and complete demyelination and a fuzzy lesion edge. The loss of Luxol fast blue histochemistry was more profound than that of myelin proteins in immunohistochemistry, and T cell infiltration in ST‐PCNSL exceeded that in MS by around fivefold (P = 0.005). Our data indicate that in the presence of extensive inflammation and incomplete, inhomogeneous demyelination, the neuropathologist should refrain from primarily considering autoimmune inflammatory demyelination and, even in the absence of lymphoma cells, instigate close clinical follow‐up of the patient to detect recurrent lymphoma.
Calcium signalling through L‐type calcium channels: role in pathophysiology of spinal nociceptive transmission
Authors: Roca‐Lapirot Olivier , Radwani Houda , Aby Franck , Nagy Frédéric , Landry Marc , Fossat Pascal
Published: February 2017

L‐type voltage‐gated calcium channels are ubiquitous channels in the CNS. L‐type calcium channels (LTCs) are mostly post‐synaptic channels regulating neuronal firing and gene expression. They play a role in important physio‐pathological processes such as learning and memory, Parkinson's disease, autism and, as recognized more recently, in the pathophysiology of pain processes. Classically, the fundamental role of these channels in cardiovascular functions has limited the use of classical molecules to treat LTC‐dependent disorders. However, when applied locally in the dorsal horn of the spinal cord, the three families of LTC pharmacological blockers – dihydropyridines (nifedipine), phenylalkylamines (verapamil) and benzothiazepines (diltiazem) – proved effective in altering short‐term sensitization to pain, inflammation‐induced hyperexcitability and neuropathy‐induced allodynia. Two subtypes of LTCs, Cav1.2 and Cav1.3, are expressed in the dorsal horn of the spinal cord, where Cav1.2 channels are localized mostly in the soma and proximal dendritic shafts, and Cav1.3 channels are more distally located in the somato‐dendritic compartment. Together with their different kinetics and pharmacological properties, this spatial distribution contributes to their separate roles in shaping short‐ and long‐term sensitization to pain. Cav1.3 channels sustain the expression of plateau potentials, an input/output amplification phenomenon that contributes to short‐term sensitization to pain such as prolonged after‐discharges, dynamic receptive fields and windup. The Cav1.2 channels support calcium influx that is crucial for the excitation‐transcription coupling underlying nerve injury‐induced dorsal horn hyperexcitability. These subtype‐specific cellular mechanisms may have different consequences in the development and/or the maintenance of pathological pain. Recent progress in developing more specific compounds for each subunit will offer new opportunities to modulate LTCs for the treatment of pathological pain with reduced side‐effects.

Linked Articles

This article is part of a themed section on Recent Advances in Targeting Ion Channels to Treat Chronic Pain. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.12/issuetoc
Opioids and the immune system – friend or foe
Authors: Plein Lisanne Mirja , Rittner Heike L
Published: February 2017

Systemically administered opioids are among the most powerful analgesics for treating severe pain. Several negative side effects (respiratory depression, addiction, nausea and confusion) and the risk of opioid‐induced hyperalgesia accompany opioid administration. One other side effect is the potential of opioids to suppress the immune response and thereby to increase the vulnerability to infections. The link between opioids and immunosuppression has been investigated both in vitro and in vivo as well as in patients. However, the results are inconsistent: Exogenous opioids such as morphine and fentanyl have been found to impair the function of macrophages, natural killer cells and T‐cells and to weaken the gut barrier in vitro and in animal studies. In epidemiological studies, high doses and the initiation of opioid therapy for non‐malignant pain have been correlated with a higher risk of infectious diseases such as pneumonia. However clear randomized controlled studies are missing. Furthermore, immune cells including neutrophils, macrophages and T‐cells have been shown to secrete endogenous opioid peptides, which then bind to peripheral opioid receptors to relieve inflammatory and neuropathic pain. In addition to cytokines, hormones and bacterial products, the release of opioid peptides is stimulated by the application of exogenous opioids. In summary, there is a reciprocal interaction between the immune system and endogenous as well as exogenous opioids. Further to the existing epidemiological studies, controlled clinical studies are needed in the future to elucidate the role of the opioid–immune system interaction in patients and to determine its clinical relevance.

Linked Articles

This article is part of a themed section on Emerging Areas of Opioid Pharmacology. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.14/issuetoc
PGE2/EP4 receptor attenuated mucosal injury via β‐arrestin1/Src/EGFR‐mediated proliferation in portal hypertensive gastropathy
Authors: Tan Siwei , Chen Xiaoliang , Xu Minyi , Huang Xiaoli , Liu Huiling , Jiang Jie , Lu Yu , Peng Xiaojie , Wu Bin
Published: February 2017

Background and Purpose

Portal hypertensive gastropathy (PHG) is a serious complication of liver cirrhosis and a potential cause of bleeding in patients with cirrhosis. Suppressed mucosal epithelial proliferation is a crucial pathological characteristic of PHG. Our studies demonstrated an important role for PGE2 and its EP4 receptor in the promotion of mucosal proliferation. However, whether β‐arrestin1 (β‐arr1), a well‐established mediator of GPCRs, is involved in the PGE2/EP4 receptor‐mediated mucosal proliferation complex in PHG remains unclear. The aim of the study was to investigate whether β‐arr1 participated in PGE2/EP4 receptor‐mediated mucosal proliferation by recruiting the Src/EGF receptor (EGFR) complex to activate Akt/proliferating cell nuclear antigen (PCNA) signalling in PHG.

Experimental Approach

Gastric mucosal proliferation was examined in patients with PHG and the PHG model of β‐arr1‐knockout (β‐arr1‐KO) and β‐arr1‐wild type (β‐arr1‐WT) mice. The induction of β‐arr1 and EP4 receptor expression and the Src/EGFR signalling elements was investigated, and the mechanisms underlying PGE2‐regulated gastric mucosal proliferation were analysed.

Key Results

Portal hypertension suppressed COX‐1 but not COX‐2, which was accompanied by a down‐regulation of PGE2 generation and EP4 receptor levels in the mucosa of patients with PHG. PGE2 administration markedly promoted mucosal proliferation in a mouse model of PHG. Targeted deletion of β‐arr1 abolished PGE2/EP4 receptor‐mediated gastric proliferation in PHG by repressing the Src/EGFR/Akt/PCNA signalling network.

Conclusions and Implications

These results indicate that β‐arr1 regulates PGE2/EP4 receptor‐mediated mucosal proliferation by promoting activation of the Src/EGFR/Akt/PCNA signalling pathway, and thus, this network is a potential therapeutic target for PHG.
Protective antibodies against Clostridium difficile are present in intravenous immunoglobulin and are retained in humans following its administration
Authors: Negm O H , MacKenzie B , Hamed M R , Ahmad O A J , Shone C C , Humphreys D P , Ravi Acharya K , Loscher C E , Marszalowska I , Lynch M , Wilcox M H , Monaghan T M
Published: February 2017

The prevalence of serum antibodies against Clostridium difficile (CD) toxins A and B in healthy populations have prompted interest in evaluating the therapeutic activity of intravenous immunoglobulin (IVIg) in individuals experiencing severe or recurrent C. difficile infection (CDI). Despite some promising case reports, a definitive clinical role for IVIg in CDI remains unclear. Contradictory results may be attributed to a lack of consensus regarding optimal dose, timing of administration and patient selection as well as variability in specific antibody content between commercial preparations. The purpose of this study was to investigate retrospectively the efficacy of three commercial preparations of IVIg for treating severe or recurrent CDI. In subsequent mechanistic studies using protein microarray and toxin neutralization assays, all IVIg preparations were analysed for specific binding and neutralizing antibodies (NAb) to CD antigens in vitro and the presence of anti-toxin NAbs in vivo following IVIg infusion. A therapeutic response to IVIg was observed in 41% (10 of 17) of the CDI patients. Significant variability in multi-isotype specific antibodies to a 7-plex panel of CD antigens and toxin neutralization efficacies were observed between IVIg preparations and also in patient sera before and after IVIg administration. These results extend our current understanding of population immunity to CD and support the inclusion of surface layer proteins and binary toxin antigens in CD vaccines. Future strategies could enhance IVIg treatment response rates by using protein microarray to preselect donor plasma/serum with the highest levels of anti-CD antibodies and/or anti-toxin neutralizing capacities prior to fractionation.