A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Adult 'PICC' Device May be Used as a Tunnelled Central Venous Catheter in Children

Purpose: Central venous access in children, in particular small children and infants, is challenging. We have developed a technique employing adult peripherally inserted central venous catheters (PICCs) as tunnelled central venous catheters (TCVCs) in children. The principal advantage of this novel technique is that the removal technique is less complex than that of conventional cuffed TCVCs. The catheter can be removed simply by being pulled out and does not require general anaesthesia. The purpose of this study is to determine the success, safety and utility of this technique and to identify the rate of late complications. We describe the 6-year experience in our unit.Materials and methods: Electronic and paper medical records were reviewed for consecutive paediatric patients who had a PICC device inserted as a TCVC over a 6-year period (September 2009 through July 2015). The following data were recorded-patient demographics, setting for PICC as TCVC insertion, use of ultrasound and fluoroscopy, PICC device type, early or late complications and date of and reason for removal.Results: Twenty-one PICCs were inserted as TCVCs in 19 children, all aged less than 10 years. Mean patient age at the time of placement was 3.7 years. Average patient weight was 15.7 kg. All insertions were successful with no significant immediate complications recorded. The most common indication for insertion in our patient sample was pseudo-obstruction secondary to gastrointestinal dysmotility disorder (24%), with cystic fibrosis infective exacerbation being the second most frequent diagnosis (14%). Suspected catheter-related infection led to early device removal in one case (4.8%). Inadvertent dislodgement occurred in one case (4.8%). Nineteen of the 21 devices (90.4%) lasted for the total intended duration of use.Conclusion: Using a PICC device as a TCVC in small children appears to be a safe technique, with an acceptable complication profile.</p

Introduction to Configuration Path Integral Monte Carlo

In low-temperature high-density plasmas quantum effects of the electrons are becoming increasingly important. This requires the development of new theoretical and computational tools. Quantum Monte Carlo methods are among the most successful approaches to first-principle simulations of many-body quantum systems. In this chapter we present a recently developed method---the configuration path integral Monte Carlo (CPIMC) method for moderately coupled, highly degenerate fermions at finite temperatures. It is based on the second quantization representation of the $N$-particle density operator in a basis of (anti-)symmetrized $N$-particle states (configurations of occupation numbers) and allows to tread arbitrary pair interactions in a continuous space. We give a detailed description of the method and discuss the application to electrons or, more generally, Coulomb-interacting fermions. As a test case we consider a few quantum particles in a one-dimensional harmonic trap. Depending on the coupling parameter (ratio of the interaction energy to kinetic energy), the method strongly reduces the sign problem as compared to direct path integral Monte Carlo (DPIMC) simulations in the regime of strong degeneracy which is of particular importance for dense matter in laser plasmas or compact stars. In order to provide a self-contained introduction, the chapter includes a short introduction to Metropolis Monte Carlo methods and the second quantization of quantum mechanics.Comment: chapter in book "Introduction to Complex Plasmas: Scientific Challenges and Technological Opportunities", Michael Bonitz, K. Becker, J. Lopez and H. Thomsen (Eds.) Springer Series "Atomic, Optical and Plasma Physics", vol. 82, Springer 2014, pp. 153-194 ISBN: 978-3-319-05436-0 (Print) 978-3-319-05437-7 (Online

Colour variations in the GRB 120327A afterglow

Aims. We present a comprehensive temporal and spectral analysis of the long Swift GRB 120327A afterglow data to investigate possible causes of the observed early-time colour variations. Methods. We collected data from various instruments and telescopes in X-ray, ultraviolet, optical, and near-infrared bands, and determined the shapes of the afterglow early-time light curves. We studied the overall temporal behaviour and the spectral energy distributions from early to late times. Results. The ultraviolet, optical, and near-infrared light curves can be modelled with a single power-law component between 200 and 2 × 10 4 s after the burst event. The X-ray light curve shows a canonical steep-shallow-steep behaviour that is typical of long gamma-ray bursts. At early times a colour variation is observed in the ultraviolet/optical bands, while at very late times a hint of a re-brightening is visible. The observed early-time colour change can be explained as a variation in the intrinsic optical spectral index, rather than an evolution of the optical extinction. © 2017 ESO

The BRG1 transcriptional coregulator

The packaging of genomic DNA into chromatin, often viewed as an impediment to the transcription process, plays a fundamental role in the regulation of gene expression. Chromatin remodeling proteins have been shown to alter local chromatin structure and facilitate recruitment of essential factors required for transcription. Brahma-related gene-1 (BRG1), the central catalytic subunit of numerous chromatin-modifying enzymatic complexes, uses the energy derived from ATP-hydrolysis to disrupt the chromatin architecture of target promoters. In this review, we examine BRG1 as a major coregulator of transcription. BRG1 has been implicated in the activation and repression of gene expression through the modulation of chromatin in various tissues and physiological conditions. Outstanding examples are studies demonstrating that BRG1 is a necessary component for nuclear receptor-mediated transcriptional activation. The remodeling protein is also associated with transcriptional corepressor complexes which recruit remodeling activity to target promoters for gene silencing. Taken together, BRG1 appears to be a critical modulator of transcriptional regulation in cellular processes including transcriptional regulation, replication, DNA repair and recombination

The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response

The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1Δ and sro9Δ mutant strains indicated altered gene expression in similar functional classes of mRNAs following loss of each factor. The loss of SLF1 had a greater impact on the transcriptome, and in particular, revealed changes in genes involved in the oxidative stress response. slf1Δ cells are more sensitive to oxidants and RIP-Seq analysis of oxidatively stressed cells enriched Slf1p targets encoding antioxidants and other proteins required for oxidant tolerance. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1Δ strains following oxidative stress. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1Δ mutant. Importantly, a significant number of the mRNAs encoding these targets were also identified as Slf1p-mRNA targets. We show that Slf1p remains associated with the few translating ribosomes following hydrogen peroxide stress and that Slf1p co-immunoprecipitates ribosomes and members of the eIF4E/eIF4G/Pab1p ‘closed loop’ complex suggesting that Slf1p interacts with actively translated mRNAs following stress. Finally, mutational analysis of SLF1 revealed a novel ribosome interacting domain in Slf1p, independent of its RNA binding La-motif. Together, our results indicate that Slf1p mediates a translational response to oxidative stress via mRNA-specific translational control

Generation of human vascular smooth muscle subtypes provides insight into embryological origin-dependent disease susceptibility.

Heterogeneity of embryological origins is a hallmark of vascular smooth muscle cells (SMCs) and may influence the development of vascular disease. Differentiation of human pluripotent stem cells (hPSCs) into developmental origin-specific SMC subtypes remains elusive. Here we describe a chemically defined protocol in which hPSCs were initially induced to form neuroectoderm, lateral plate mesoderm or paraxial mesoderm. These intermediate populations were further differentiated toward SMCs (>80% MYH11(+) and ACTA2(+)), which displayed contractile ability in response to vasoconstrictors and invested perivascular regions in vivo. Derived SMC subtypes recapitulated the unique proliferative and secretory responses to cytokines previously documented in studies using aortic SMCs of distinct origins. Notably, this system predicted increased extracellular matrix degradation by SMCs derived from lateral plate mesoderm, which was confirmed using rat aortic SMCs from corresponding origins. This differentiation approach will have broad applications in modeling origin-dependent disease susceptibility and in developing bioengineered vascular grafts for regenerative medicine

B Part Of It School Leaver protocol: an observational repeat cross-sectional study to assess the impact of a meningococcal serogroup B (4CMenB) vaccine program on carriage of Neisseria meningitidis

Introduction: Invasive meningococcal disease is uncommon but associated with a high-case fatality rate. Carriage prevalence of the causative bacteria, Neisseria meningitidis, is high in adolescents. A large (n=34 500) cluster randomised controlled trial (RCT) to assess the impact of a meningococcal B (MenB) vaccine on meningococcal carriage was implemented in the state of South Australia (SA) for year 10, 11 and 12 senior school students in 2017–2018. This study will assess the impact of MenB vaccine (4CMenB) on carriage prevalence in school leavers in SA, 1 and 2 years after implementation of the cluster RCT in adolescents. Measuring the impact of population programmes on carriage can assist in informing future meningococcal immunisation programmes such as targeted age groups and use of catch-up campaigns.Methods and analysis: This repeat cross-sectional study will assess carriage prevalence in 2018 and 2019. All school leavers who attended year 12 in any school in SA in 2018 or 2019 will be invited to participate in this study. An oropharyngeal swab will be taken from each participating student and a risk factor questionnaire completed by the student following informed consent. Students will attend clinics at SA universities, technical colleges, and metropolitan, rural and remote government council clinics. Confirmed vaccination history will allow a comparison in carriage prevalence between vaccinated and unvaccinated school leavers. A sample size of 4096 students per year will provide 80% power to detect a 20% difference in carriage prevalence of disease-causing meningococci (defined as genogroup A, B, C, W, X or Y) between years.Ethics and dissemination: The study was approved by the Women’s and Children’s Health Network Human Research Ethics Committee. Results will be published in international peer review journals and presented at national and international conferences

Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study.

Background: Acute illness, existing co-morbidities and surgical stress response can all contribute to postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. The aim of this study was prospectively to develop a pragmatic prognostic model to stratify patients according to risk of developing AKI after major gastrointestinal surgery. Methods: This prospective multicentre cohort study included consecutive adults undergoing elective or emergency gastrointestinal resection, liver resection or stoma reversal in 2-week blocks over a continuous 3-month period. The primary outcome was the rate of AKI within 7 days of surgery. Bootstrap stability was used to select clinically plausible risk factors into the model. Internal model validation was carried out by bootstrap validation. Results: A total of 4544 patients were included across 173 centres in the UK and Ireland. The overall rate of AKI was 14·2 per cent (646 of 4544) and the 30-day mortality rate was 1·8 per cent (84 of 4544). Stage 1 AKI was significantly associated with 30-day mortality (unadjusted odds ratio 7·61, 95 per cent c.i. 4·49 to 12·90; P < 0·001), with increasing odds of death with each AKI stage. Six variables were selected for inclusion in the prognostic model: age, sex, ASA grade, preoperative estimated glomerular filtration rate, planned open surgery and preoperative use of either an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Internal validation demonstrated good model discrimination (c-statistic 0·65). Discussion: Following major gastrointestinal surgery, AKI occurred in one in seven patients. This preoperative prognostic model identified patients at high risk of postoperative AKI. Validation in an independent data set is required to ensure generalizability