consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction

Extensive evaluation of RNA-seq methods have demonstrated that no single algorithm consistently outperforms all others. Removal of unwanted variation (RUV) has also been proposed as a method for stabilizing differential expression (DE) results. Despite this, it remains a challenge to run multiple RNA-seq algorithms to identify significant differences common to multiple algorithms, whilst also integrating and assessing the impact of RUV into all algorithms. consensusDE was developed to automate the process of identifying significant DE by combining the results from multiple algorithms with minimal user input and with the option to automatically integrate RUV. consensusDE only requires a table describing the sample groups, a directory containing BAM files or preprocessed count tables and an optional transcript database for annotation. It supports merging of technical replicates, paired analyses and outputs a compendium of plots to guide the user in subsequent analyses. Herein, we assess the ability of RUV to improve DE stability when combined with multiple algorithms and between algorithms, through application to real and simulated data. We find that, although RUV increased fold change stability between algorithms, it demonstrated improved FDR in a setting of low replication for the intersect, the effect was algorithm specific and diminished with increased replication, reinforcing increased replication for recovery of true DE genes. We finish by offering some rules and considerations for the application of RUV in a consensus-based setting. consensusDE is freely available, implemented in R and available as a Bioconductor package, under the GPL-3 license, along with a comprehensive vignette describing functionality: trup://bioconduaor.org/packagesi consensusDE/

Tapered Fluidized Beds and the Role of Fluidization in Mineral Emplacement

One of the most prominent features of fluidized beds is their ability to mix and segregate. This is of great importance for many industrial processes, but takes on a particular significance for mineral extraction where a small amount of valuable matter is mixed with a large amount of waste. In this study we consider the occurrence of diamonds in the volcanic rock called “kimberlite”. These are often emplaced (erupted and deposited) in large volcanic pipes commonly referred to as “diatremes” (length scale of the order of a kilometre) with a vent at the bottom through which the minerals were introduced along with other fragmental particulate matter and a gas flow. The purpose of this study is to gain an understanding of the processes that led to the dispersal of minerals before their emplacement to allow efficient extraction. The paper describes experimental observations of a tapered fluidized bed. The objective was to identify the physical behaviour of gas and particles; so, of particular interest are the extent to which fluidization takes place within the bed, and the arrangements of particles seen. Gas flow-rate, particle size, and degree of taper were all varied. These observations can be used to identify the structures and processes that can take place; it is then possible to understand field data in terms of the physics that led to the emplacement of material. This will be shown using new data taken from southern Africa. Scale-up of evidence is of obvious difficulty in this system and this is discussed in terms of the possible behaviour of the bubbles that have generated mixing of material before emplacement

Concepts of mental disorders in the United Kingdom : Similarities and differences between the lay public and psychiatrists

BACKGROUND: The lay public often conceptualise mental disorders in a different way to mental health professionals, and this can negatively impact on outcomes when in treatment. AIMS: This study explored which disorders the lay public are familiar with, which theoretical models they understand, which they endorse and how they compared to a sample of psychiatrists. METHODS: The Maudsley Attitude Questionnaire (MAQ), typically used to assess mental health professional's concepts of mental disorders, was adapted for use by a lay community sample (N = 160). The results were compared with a sample of psychiatrists (N = 76). RESULTS: The MAQ appeared to be accessible to the lay public, providing some interesting preliminary findings: in order, the lay sample reported having the best understanding of depression followed by generalised anxiety, schizophrenia and finally antisocial personality disorder. They best understood spiritualist, nihilist and social realist theoretical models of these disorders, but were most likely to endorse biological, behavioural and cognitive models. The lay public were significantly more likely to endorse some models for certain disorders suggesting a nuanced understanding of the cause and likely cure, of various disorders. Ratings often differed significantly from the sample of psychiatrists who were relatively steadfast in their endorsement of the biological model. CONCLUSION: The adapted MAQ appeared accessible to the lay sample. Results suggest that the lay public are generally aligned with evidence-driven concepts of common disorders, but may not always understand or agree with how mental health professionals conceptualise them. The possible causes of these differences, future avenues for research and the implications for more collaborative, patient-clinician conceptualisations are discussed.Peer reviewedFinal Accepted Versio

Hookworm secreted extracellular vesicles interact with host cells and prevent inducible colitis in mice

Gastrointestinal (GI) parasites, hookworms in particular, have evolved to cause minimal harm to their hosts, allowing them to establish chronic infections. This is mediated by creating an immunoregulatory environment. Indeed, hookworms are such potent sup-pressors of inflammation that they have been used in clinical trials to treat inflammatory bowel diseases (IBD) and celiac disease. Since the recent description of helminths (worms) secreting extracellular vesicles (EVs), exosome-like EVs from different helminths have been characterized and their salient roles in parasite-host interactions have been highlighted. Here, we analyze EVs from the rodent parasite Nippostrongylus brasiliensis, which has been used as a model for human hookworm infection. N. brasiliensis EVs (Nb-EVs) are actively internalized by mouse gut organoids, indicating a role in driving parasitism. We used proteomics and RNA-Seq to profile the molecular composition of Nb-EVs. We identified 81 proteins, including proteins frequently present in exosomes (like tetraspanin, enolase, 14-3-3 protein, and heat shock proteins), and 27 sperm-coating protein-like extracellular proteins. RNA-Seq analysis revealed 52 miRNA species, many of which putatively map to mouse genes involved in regulation of inflammation. To determine whether GI nematode EVs had immunomodulatory properties, we assessed their potential to suppress GI inflammation in a mouse model of inducible chemical colitis. EVs from N. brasiliensis but not those from the whipworm Trichuris muris or control vesicles from grapes protected against colitic inflammation in the gut of mice that received a single intraperitoneal injection of EVs. Key cytokines associated with colitic pathology (IL-6, IL-1 beta, IFN gamma, and IL-17a) were significantly suppressed in colon tissues from EV-treated mice. By contrast, high levels of the anti-inflammatory cytokine IL-10 were detected in Nb-EV-treated mice. Proteins and miRNAs contained within helminth EVs hold great potential application in development of drugs to treat helminth infections as well as chronic non-infectious diseases resulting from a dysregulated immune system, such as IBD

Comparison of ecosystem processes in a woodland and prairie pond with different hydroperiods

Shallow lakes and ponds constitute a significant number of water bodies worldwide. Many are heterotrophic, indicating that they are likely net contributors to global carbon cycling. Climate change is likely to have important impacts on these waterbodies. In this study, we examined two small Minnesota ponds; a permanent woodland pond and a temporary prairie pond. The woodland pond had lower levels of phosphorus and phytoplankton than the prairie pond. Using the open water oxygen method, we found the prairie pond typically had a higher level of gross primary production (GPP) and respiration (R) than the woodland pond, although the differences between the ponds varied with season. Despite the differences in GPP and R between the ponds the net ecosystem production was similar with both being heterotrophic. Since abundant small ponds may play an important role in carbon cycling and are likely to undergo changes in temperature and hydroperiod associated with climate change, understanding pond metabolism is critical in predicting impacts and designing management schemes to mitigate changes

Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction.

Mass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes-a major clade of predators comprising over 3,700 living species-remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth's extant vertebrate faunas

Recurrent miscalling of missense variation from short-read genome sequence data

Background: Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases ofgenomic variation. Results: We find that sequence variation from short-read sequence data is subject to recurrent-yet-intermittent miscalling that occurs in a sequence intrinsic manner and is very sensitive to sequence read length. The miscalls arise from difficulties aligning short reads to redundant genomic regions, where the rate of sequencing error approaches the sequence diversity between redundant regions. We find the resultant miscalled variants to be sensitive to small sequence variations between genomes, and thereby are often intrinsic to an individual, pedigree, strain or human ethnic group. In human exome sequences, we identify 2–300 recurrent false positive variants per individual, almost all of which are present in public databases of human genomic variation. From the exomes of non-reference strains of inbred mice, we identify 3–5000 recurrent false positive variants per mouse – the number of which increasing with greater distance between an individual mouse strain and the reference C57BL6 mouse genome. We show that recurrently miscalled variants may be reproduced for a given genome from repeated simulation rounds of read resampling, realignment and recalling. As such, it is possible to identify more than two-thirds of false positive variation from only ten rounds of simulation. Conclusion: Identification and removal of recurrent false positive variants from specific individual variant sets will improve overall data quality. Variant miscalls arising are highly sequence intrinsic and are often specific to an individual, pedigree or ethnicity. Further, read length is a strong determinant of whether given false variants will be called for any given genome – which has profound significance for cohort studies that pool datasets collected and sequenced at different points in time

Functionalized micro-capillary film for the rapid at-line analysis of IgG aggregates in a cell culture bioreactor.

A micro-capillary film has been developed that offers the potential for an at-line analytical tool for rapid aggregate analysis during biopharmaceutical antibody production. A non-porous walled micro-capillary film (NMCF) with cation exchange functionality was demonstrated to act as a chromatography medium that could be operated with high linear fluid velocities and was highly resistant to blockage by entrained particulates, including cells. The NMCF containing 19 parallel microcapillaries was prepared using a melt extrusion process from poly(ethylene-vinyl alcohol) copolymer (EVOH). The NMCF-EVOH was modified to have cation-exchange functionality (NMCF-EVOH-SP) and shown to differentially bind monomer and aggregated species of IgG antibody directly from a bioreactor. The use of NMCF-EVOH-SP to quantify aggregate concentrations in monoclonal antibody preparations in less than 20 minutes was demonstrated.The authors would like to thank the EPSRC for the provision of a CASE Award. This study was sponsored by MedImmune, the global biologics R&D arm of AstraZeneca.This is the final version of the article. It first appeared from Taylor & Francis via http://dx.doi.org/10.1080/19420862.2015.106536

Surrogate model for gravitational wave signals from non-spinning, comparable- to large-mass-ratio black hole binaries built on black hole perturbation theory waveforms calibrated to numerical relativity

We present a reduced-order surrogate model of gravitational waveforms from non-spinning binary black hole systems with comparable to large mass-ratio configurations. This surrogate model, \texttt{BHPTNRSur1dq1e4}, is trained on waveform data generated by point-particle black hole perturbation theory (ppBHPT) with mass ratios varying from 2.5 to 10,000. \texttt{BHPTNRSur1dq1e4} extends an earlier waveform model, \texttt{EMRISur1dq1e4}, by using an updated transition-to-plunge model, covering longer durations up to 30,500 $m_1$ (where $m_1$ is the mass of the primary black hole), includes several more spherical harmonic modes up to $\ell=10$, and calibrates subdominant modes to numerical relativity (NR) data. In the comparable mass-ratio regime, including mass ratios as low as $2.5$, the gravitational waveforms generated through ppBHPT agree surprisingly well with those from NR after this simple calibration step. We also compare our model to recent SXS and RIT NR simulations at mass ratios ranging from $15$ to $32$, and find the dominant quadrupolar modes agree to better than $\approx 10^{-3}$. We expect our model to be useful to study intermediate-mass-ratio binary systems in current and future gravitational-wave detectors.Comment: 20 pages, 15 figure

BAP1 regulates epigenetic switch from pluripotency to differentiation in developmental lineages giving rise to BAP1-mutant cancers

The BAP1 tumor suppressor is mutated in many human cancers such as uveal melanoma, leading to poor patient outcome. It remains unclear how BAP1 functions in normal biology or how its loss promotes cancer progression. Here, we show that Bap1 is critical for commitment to ectoderm, mesoderm, and neural crest lineages during Xenopus laevis development. Bap1 loss causes transcriptional silencing and failure of H3K27ac to accumulate at promoters of key genes regulating pluripotency-to-commitment transition, similar to findings in uveal melanoma. The Bap1-deficient phenotype can be rescued with human BAP1, by pharmacologic inhibition of histone deacetylase (HDAC) activity or by specific knockdown of Hdac4. Similarly, BAP1-deficient uveal melanoma cells are preferentially vulnerable to HDAC4 depletion. These findings show that Bap1 regulates lineage commitment through H3K27ac-mediated transcriptional activation, at least in part, by modulation of Hdac4, and they provide insights into how BAP1 loss promotes cancer progression.Fil: Kuznetsov, Jeffim N.. University of Miami; Estados UnidosFil: Agüero, Tristán Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Investigaciones Biológicas. Universidad Nacional de Tucumán. Instituto Superior de Investigaciones Biológicas; Argentina. University of Miami; Estados UnidosFil: Owens, Dawn A.. University of Miami; Estados UnidosFil: Kurtenbach, Stefan. University of Miami; Estados UnidosFil: Field, Matthew G.. University of Miami; Estados UnidosFil: Durante, Michael A.. University of Miami; Estados UnidosFil: Rodriguez, Daniel A.. University of Miami; Estados UnidosFil: King, Mary Lou. University of Miami; Estados UnidosFil: Harbour, J. William. University of Miami; Estados Unido