Made-to-Measure Modelling of Globular Clusters

We present the first application of the made-to-measure method for modelling dynamical systems to globular clusters. Through the made-to-measure algorithm, the masses of individual particles within a model cluster are adjusted while the system evolves forward in time via a gravitational $N$-body code until the model cluster is able to reproduce select properties of an observed cluster. The method is first applied to observations of mock isotropic and anisotropic clusters while fitting against the cluster's three dimensional or projected density profile, density weighted mean-squared velocity profile, or its density profile with individual mean-squared velocity profiles. We find that a cluster's three-dimensional density profile can easily be reproduced by the made-to-measure method, with minor discrepancies in the outer regions if fitting against a cluster's projected surface density or projected kinematic properties. If an observed cluster is anisotropic, only fitting against the cluster's density profile and individual mean-squared velocity profiles will fully recover the full degree of anisotropy. Partial anisotropy can be recovered as long as two kinematic properties are included in the fit. We further apply the method to observations of the Galactic globular cluster M4 and generate a complete six-dimensional representation of the cluster that reproduces observations of its surface density profile, mean-squared proper motion velocity profile, and mean-squared line of sight velocity profile. The M2M method predicts M4 is primarily isotropic with a mass of $9.2 \pm 0.4 \times 10^4\, M_{\odot}$ and a half-mass radius of $3.7 \pm 0.1$ pc.Comment: 11 pages, 10 figures, submitted to MNRAS for publicatio

Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli

Polyketides are a class of specialised metabolites synthesised by both eukaryotes and prokaryotes. These chemically and structurally diverse molecules are heavily used in the clinic and include frontline antimicrobial and anticancer drugs such as erythromycin and doxorubicin. To replenish the clinicians’ diminishing arsenal of bioactive molecules, a promising strategy aims at transferring polyketide biosynthetic pathways from their native producers into the biotechnologically desirable host Escherichia coli. This approach has been successful for type I modular polyketide synthases (PKSs); however, despite more than 3 decades of research, the large and important group of type II PKSs has until now been elusive in E. coli. Here, we report on a versatile polyketide biosynthesis pipeline, based on identification of E. coli–compatible type II PKSs. We successfully express 5 ketosynthase (KS) and chain length factor (CLF) pairs—e.g., from Photorhabdus luminescens TT01, Streptomyces resistomycificus, Streptoccocus sp. GMD2S, Pseudoalteromonas luteoviolacea, and Ktedonobacter racemifer—as soluble heterodimeric recombinant proteins in E. coli for the first time. We define the anthraquinone minimal PKS components and utilise this biosynthetic system to synthesise anthraquinones, dianthrones, and benzoisochromanequinones (BIQs). Furthermore, we demonstrate the tolerance and promiscuity of the anthraquinone heterologous biosynthetic pathway in E. coli to act as genetically applicable plug-and-play scaffold, showing it to function successfully when combined with enzymes from phylogenetically distant species, endophytic fungi and plants, which resulted in 2 new-to-nature compounds, neomedicamycin and neochaetomycin. This work enables plug-and-play combinatorial biosynthesis of aromatic polyketides using bacterial type II PKSs in E. coli, providing full access to its many advantages in terms of easy and fast genetic manipulation, accessibility for high-throughput robotics, and convenient biotechnological scale-up. Using the synthetic and systems biology toolbox, this plug-and-play biosynthetic platform can serve as an engine for the production of new and diversified bioactive polyketides in an automated, rapid, and versatile fashion

WebTraceMiner: a web service for processing and mining EST sequence trace files

Expressed sequence tags (ESTs) remain a dominant approach for characterizing the protein-encoding portions of various genomes. Due to inherent deficiencies, they also present serious challenges for data quality control. Before GenBank submission, EST sequences are typically screened and trimmed of vector and adapter/linker sequences, as well as polyA/T tails. Removal of these sequences presents an obstacle for data validation of error-prone ESTs and impedes data mining of certain functional motifs, whose detection relies on accurate annotation of positional information for polyA tails added posttranscriptionally. As raw DNA sequence information is made increasingly available from public repositories, such as NCBI Trace Archive, new tools will be necessary to reanalyze and mine this data for new information. WebTraceMiner (www.conifergdb.org/software/wtm) was designed as a public sequence processing service for raw EST traces, with a focus on detection and mining of sequence features that help characterize 3′ and 5′ termini of cDNA inserts, including vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites and polyA or polyT tails. WebTraceMiner complements other public EST resources and should prove to be a unique tool to facilitate data validation and mining of error-prone ESTs (e.g. discovery of new functional motifs)

On the Clustering of Sub-millimeter Galaxies

We measure the angular two-point correlation function of sub-millimeter galaxies (SMGs) from 1.1-millimeter imaging of the COSMOS field with the AzTEC camera and ASTE 10-meter telescope. These data yields one of the largest contiguous samples of SMGs to date, covering an area of 0.72 degrees^2 down to a 1.26 mJy/beam (1-sigma) limit, including 189 (328) sources with S/N greater than 3.5 (3). We can only set upper limits to the correlation length r_0, modeling the correlation function as a power-law with pre-assigned slope. Assuming existing redshift distributions, we derive 68.3% confidence level upper limits of r_0 < 6-8 h^-1 Mpc at 3.7 mJy, and r_0 < 11-12 h^-1 Mpc at 4.2 mJy. Although consistent with most previous estimates, these upper limits imply that the real r_0 is likely smaller. This casts doubts on the robustness of claims that SMGs are characterized by significantly stronger spatial clustering, (and thus larger mass), than differently selected galaxies at high-redshift. Using Monte Carlo simulations we show that even strongly clustered distributions of galaxies can appear unclustered when sampled with limited sensitivity and coarse angular resolution common to current sub-millimeter surveys. The simulations, however, also show that unclustered distributions can appear strongly clustered under these circumstances. From the simulations, we predict that at our survey depth, a mapped area of two degrees^2 is needed to reconstruct the correlation function, assuming smaller beam sizes of future surveys (e.g. the Large Millimeter Telescope's 6" beam size). At present, robust measures of the clustering strength of bright SMGs appear to be below the reach of most observations.Comment: 23 pages, 8 figures, accepted for publication in The Astrophysical Journa

TIGIT Marks Exhausted T Cells, Correlates with Disease Progression, and Serves as a Target for Immune Restoration in HIV and SIV Infection.

HIV infection induces phenotypic and functional changes to CD8+ T cells defined by the coordinated upregulation of a series of negative checkpoint receptors that eventually result in T cell exhaustion and failure to control viral replication. We report that effector CD8+ T cells during HIV infection in blood and SIV infection in lymphoid tissue exhibit higher levels of the negative checkpoint receptor TIGIT. Increased frequencies of TIGIT+ and TIGIT+ PD-1+ CD8+ T cells correlated with parameters of HIV and SIV disease progression. TIGIT remained elevated despite viral suppression in those with either pharmacological antiretroviral control or immunologically in elite controllers. HIV and SIV-specific CD8+ T cells were dysfunctional and expressed high levels of TIGIT and PD-1. Ex-vivo single or combinational antibody blockade of TIGIT and/or PD-L1 restored viral-specific CD8+ T cell effector responses. The frequency of TIGIT+ CD4+ T cells correlated with the CD4+ T cell total HIV DNA. These findings identify TIGIT as a novel marker of dysfunctional HIV-specific T cells and suggest TIGIT along with other checkpoint receptors may be novel curative HIV targets to reverse T cell exhaustion

Orientation cues for high-flying nocturnal insect migrants: do turbulence-induced temperature and velocity fluctuations indicate the mean wind flow?

Migratory insects flying at high altitude at night often show a degree of common alignment, sometimes with quite small angular dispersions around the mean. The observed orientation directions are often close to the downwind direction and this would seemingly be adaptive in that large insects could add their self-propelled speed to the wind speed, thus maximising their displacement in a given time. There are increasing indications that high-altitude orientation may be maintained by some intrinsic property of the wind rather than by visual perception of relative ground movement. Therefore, we first examined whether migrating insects could deduce the mean wind direction from the turbulent fluctuations in temperature. Within the atmospheric boundary-layer, temperature records show characteristic ramp-cliff structures, and insects flying downwind would move through these ramps whilst those flying crosswind would not. However, analysis of vertical-looking radar data on the common orientations of nocturnally migrating insects in the UK produced no evidence that the migrants actually use temperature ramps as orientation cues. This suggests that insects rely on turbulent velocity and acceleration cues, and refocuses attention on how these can be detected, especially as small-scale turbulence is usually held to be directionally invariant (isotropic). In the second part of the paper we present a theoretical analysis and simulations showing that velocity fluctuations and accelerations felt by an insect are predicted to be anisotropic even when the small-scale turbulence (measured at a fixed point or along the trajectory of a fluid-particle) is isotropic. Our results thus provide further evidence that insects do indeed use turbulent velocity and acceleration cues as indicators of the mean wind direction

COVID 19 and its effects on pediatric orthopaedic clinical trials

Background: Clinical trials for the treatment of pediatric orthopaedics are critical to enhance the quality of life of these children. In response to the COVID-19 pandemic, the FDA updated guidance on conducting clinical trials to prioritize patient safety; however the degree to which the pandemic disrupted pediatric orthopaedic-related clinical trials is unknown. Thus, our objective is to quantify the number of these trials disrupted due to the COVID-19 pandemic.Methods: We searched ClinicalTrials.gov for ongoing and discontinued trials between 01/01/2020 - 10/31/2021. Trials were screened for relevance to the study and the number of participants, trial location, funding source, and reason for discontinuation. Associations between reasons for termination, funding source, trial location, and the number of participants enrolled were evaluated using MannWhitney U tests or ANOVA, where appropriate.Results: Our search returned 544 trials, of which 128 were included with a total of 15,194 participants. Of the included Pediatric trials of orthopaedic conditions, 9 were discontinued with a total of 497 participants. Of the 9 discontinued trials, 1 of 3 stated COVID-19 as a reason. Mann-Whitney U tests and ANOVA showed no statistically significant difference in enrollment between trials discontinued due to COVID-19 compared to other discontinued trials, nor among funding or location.Conclusion: Our study shows 33% of discontinued pediatric orthopaedic-related clinical trials cited COVID-19 as a reason for discontinuation; however, only 12% of all children enrolled in discontinued trials. Findings from this study highlight the importance of developing strategies for safely continuing clinical research amid global emergencies that will almost certainly arise in the future

Clinical and cost effectiveness of single stage compared with two stage revision for hip prosthetic joint infection (INFORM):pragmatic, parallel group, open label, randomised controlled trial

OBJECTIVES: To determine whether patient reported outcomes improve after single stage versus two stage revision surgery for prosthetic joint infection of the hip, and to determine the cost effectiveness of these procedures. DESIGN: Pragmatic, parallel group, open label, randomised controlled trial. SETTING: High volume tertiary referral centres or orthopaedic units in the UK (n=12) and in Sweden (n=3), recruiting from 1 March 2015 to 19 December 2018. PARTICIPANTS: 140 adults (aged ≥18 years) with a prosthetic joint infection of the hip who required revision (65 randomly assigned to single stage and 75 to two stage revision). INTERVENTIONS: A computer generated 1:1 randomisation list stratified by hospital was used to allocate participants with prosthetic joint infection of the hip to a single stage or a two stage revision procedure. MAIN OUTCOME MEASURES: The primary intention-to-treat outcome was pain, stiffness, and functional limitations 18 months after randomisation, measured by the Western Ontario and McMasters Universities Osteoarthritis Index (WOMAC) score. Secondary outcomes included surgical complications and joint infection. The economic evaluation (only assessed in UK participants) compared quality adjusted life years and costs between the randomised groups. RESULTS: The mean age of participants was 71 years (standard deviation 9) and 51 (36%) were women. WOMAC scores did not differ between groups at 18 months (mean difference 0.13 (95% confidence interval -8.20 to 8.46), P=0.98); however, the single stage procedure was better at three months (11.53 (3.89 to 19.17), P=0.003), but not from six months onwards. Intraoperative events occurred in five (8%) participants in the single stage group and 20 (27%) in the two stage group (P=0.01). At 18 months, nine (14%) participants in the single stage group and eight (11%) in the two stage group had at least one marker of possible ongoing infection (P=0.62). From the perspective of healthcare providers and personal social services, single stage revision was cost effective with an incremental net monetary benefit of £11 167 (95% confidence interval £638 to £21 696) at a £20 000 per quality adjusted life years threshold (£1.0; $1.1; €1.4). CONCLUSIONS: At 18 months, single stage revision compared with two stage revision for prosthetic joint infection of the hip showed no superiority by patient reported outcome. Single stage revision had a better outcome at three months, fewer intraoperative complications, and was cost effective. Patients prefer early restoration of function, therefore, when deciding treatment, surgeons should consider patient preferences and the cost effectiveness of single stage surgery. TRIAL REGISTRATION: ISRCTN registry ISRCTN10956306.RD&E staff can access the full-text of this article by clicking on the 'Additional Link' above and logging in with NHS OpenAthens if prompted.Unknow