A Quantitative Method for the Study of HIV-1 and Mycobacterium tuberculosis Coinfection

Mycobacterium tuberculosis and human immunodeficiency virus-1 (HIV-1) syndemic interactions are a major global health concern. Despite the clinical significance of coinfection, our understanding of the cellular pathophysiology and the therapeutic pharmacodynamic impact of coinfection is limited. Here, we use single-round infectious HIV-1 pseudotyped viral particles expressing green fluorescent protein alongside M. tuberculosis expressing mCherry to study pathogenesis and treatment. We report that HIV-1 infection inhibited intracellular replication of M. tuberculosis and demonstrate the therapeutic activity of antiviral treatment (efavirenz) and antimicrobial treatment (rifampicin). The described method could be applied for detailed mechanistic studies to inform the development of novel treatment strategies.

Remdesivir-ivermectin combination displays synergistic interaction with improved in vitro activity against SARS-CoV-2

A key element for the prevention and management of coronavirus disease 2019 is the development of effective therapeutics. Drug combination strategies offer several advantages over monotherapies. They have the potential to achieve greater efficacy, to increase the therapeutic index of drugs and to reduce the emergence of drug resistance. We assessed the in vitro synergistic interaction between remdesivir and ivermectin, both approved by the US Food and Drug Administration, and demonstrated enhanced antiviral activity against severe acute respiratory syndrome coronavirus-2. Whilst the in vitro synergistic activity reported here does not support the clinical application of this combination treatment strategy due to insufficient exposure of ivermectin in vivo, the data do warrant further investigation. Efforts to define the mechanisms underpinning the observed synergistic action could lead to the development of novel treatment strategies.

Intracellular PD Modelling (PDi) for the Prediction of Clinical Activity of Increased Rifampicin Dosing

Increasing rifampicin (RIF) dosages could significantly reduce tuberculosis (TB) treatment durations. Understanding the pharmacokinetic-pharmacodynamics (PK-PD) of increasing RIF dosages could inform clinical regimen selection. We used intracellular PD modelling (PD_i) to predict clinical outcomes, primarily time to culture conversion, of increasing RIF dosages. PD_i modelling utilizes in vitro-derived measurements of intracellular (macrophage) and extracellular Mycobacterium tuberculosis sterilization rates to predict the clinical outcomes of RIF at increasing doses. We evaluated PD_i simulations against recent clinical data from a high dose (35 mg/kg per day) RIF phase II clinical trial. PD_i-based simulations closely predicted the observed time-to-patient culture conversion status at eight weeks (hazard ratio: 2.04 (predicted) vs. 2.06 (observed)) for high dose RIF-based treatments. However, PD_i modelling was less predictive of culture conversion status at 26 weeks for high-dosage RIF (99% predicted vs. 81% observed). PD_i-based simulations indicate that increasing RIF beyond 35 mg/kg/day is unlikely to significantly improve culture conversion rates, however, improvements to other clinical outcomes (e.g., relapse rates) cannot be ruled out. This study supports the value of translational PD_i-based modelling in predicting culture conversion rates for antitubercular therapies and highlights the potential value of this platform for the improved design of future clinical trials.

Compact laser system for a laser-cooled ytterbium ion microwave frequency standard

The development of a transportable microwave frequency standard based on the ground-state transition of ¹⁷¹Yb⁺ at ∼12.6 GHz requires a compact laser system for cooling the ions, clearing out of long-lived states and also for photoionisation. In this paper, we describe the development of a suitable compact laser system based on a 6U height rack-mounted arrangement with overall dimensions 260 × 194 × 335 mm. Laser outputs at 369 nm (for cooling), 399 nm (photoionisation), 935 nm (repumping), and 760 nm (state clearout) are combined in a fiber arrangement for delivery to our linear ion trap and we demonstrate this system by cooling of ¹⁷¹Yb⁺ ions. Additionally, we demonstrate that the lasers at 935 nm and 760 nm are close in frequency to water vapor and oxygen absorption lines, respectively; specifically, at 760 nm, we show that one ¹⁷¹Yb⁺ transition is within the pressure broadened profile of an oxygen line. These molecular transitions form convenient wavelength references for the stabilization of lasers for a ¹⁷¹Yb⁺ frequency standard.

ANCA-associated vasculitis: a comparison of cases presenting to nephrology and rheumatology services

BACKGROUND

Anti-neutrophil cytoplasmic antibody (ANCA) -associated vasculitis (AAV) is a disease characterized by inflammation of small vessels and detectable ANCA in the circulation. Patients may develop a broad spectrum of clinical features ranging from indolent sino-nasal disease and rashes to fulminant renal failure or acute life-threatening pulmonary haemorrhage. Consequently, patients with AAV present to a variety of specialties including nephrology and rheumatology, whose training and approaches to management of such patients may differ. There is little literature comparing patients presenting to different specialties and their outcomes.

METHODS

We compared two cohorts of patients with ANCA-positive AAV presenting to either the rheumatology or nephrology department at Galway University Hospitals from June 2002 to July 2011. A standardized data collection form was used to collect information regarding baseline demographics, manifestations of AAV, initial management, relapses and complications.

RESULTS

Forty-five patients were included in this study (15 rheumatology/30 nephrology). The nephrology cohort was older, had a higher C-reactive protein, Birmingham Vascular Activity Score and ANCA titer at presentation compared to the rheumatology group. Induction treatment varied between the cohorts with rheumatology patients most commonly receiving a combination of oral corticosteroids (73%) and methotrexate (60%) and nephrology patients receiving a combination of intravenous corticosteroids (93%) and cyclophosphamide (90%). Fifty-three percent of the rheumatology patients who completed induction therapy relapsed compared to 30% of the nephrology patients.

CONCLUSION

This study presents two different cohorts of patients with the same disease that were managed by two different disciplines. It highlights the heterogeneity of AAV and the importance of interdisciplinary communication and cooperation when managing these patients.

Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae)

Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of discordance are rarely investigated. We use species trees from multi-locus data to estimate the species relationships, evolutionary history and timing of diversification among Australian Gehyra-a group renowned for taxonomic uncertainty and showing a large degree of gene tree discordance. We find support for a recent Asian origin and two major clades: a tropically adapted clade and an arid adapted clade, with some exceptions, but no support for allopatric speciation driven by chromosomal rearrangement in the group. Bayesian concordance analysis revealed high gene tree discordance and comparisons of Robinson-Foulds distances showed that discordance between gene trees was significantly higher than that generated by topological uncertainty within each gene. Analysis of gene tree discordance and incomplete taxon sampling revealed that gene tree discordance was high whether terminal taxon or gene sampling was maximized, indicating discordance is due to biological processes, which may be important in contributing to gene tree discordance in many recently diversified organisms.

Fast shuttling of ions in a scalable Penning trap array

We report on the design and testing of an array of Penning ion traps made from printed circuit board. The system enables fast shuttling of ions from one trapping zone to another, which could be of use in quantum information processing. We describe simulations carried out to determine the optimal potentials to be applied to the trap electrodes for enabling this movement. The results of a preliminary experiment with a cloud of laser cooled calcium ions demonstrate a round-trip shuttling efficiency of up to 75%.

Gyrus bipolar electrovaporization vs transurethral resection of the prostate: a randomized prospective single-blind trial with 1 y follow-up

The Gyrus system uses bipolar electrocautery with saline irrigation to vaporize prostatic tissue and is compared to transurethral resection of the prostate (TURP) in a randomized prospective study with 1 y follow-up. Outcomes measured were fluid absorption, blood loss, period of catheterization, hospital stay, symptom scores, quality of life, flow rates, and post-void residual volumes at 3, 6, and 12 months. All measured parameters were similar, although re-catheterization rates were higher (30% vs 5%) in the Gyrus group. Clot evacuation rates were higher in the TURP group (19% vs 0%). The Gyrus device is safe and produces results that are similar to TURP at 1 y.

Molecular discrimination of garfish Hyporhamphus (Beloniformes) larvae in southern Australian waters

A multiplex polymerase chain reaction (PCR) assay developed for discrimination between garfish larvae (family Hemiramphidae, order Beloniformes) found in southern Australian waters was based on species-specific amplification of part of the mitochondrial control region. The species were easily discerned by the number and distinct sizes of PCR products (Hyporhamphus melanochir, 443 bp; H. regularis, 462 and 264 bp). Although based on a single gene, the method will correctly identify the species of individuals in at least 96% of tests for H. melanochir and 94% of tests for H. regularis.

CT analysis of caliceal anatomy in the supine and prone positions

PURPOSE

To assess the effect of patient positioning on the position of the kidneys and their consequent projection onto plain radiographs, thus ascertaining the need for special preoperative imaging.

PATIENTS AND METHODS

Fourteen patients were studied by obtaining fine (5-mm)-cut contrast-enhanced CT scans in the pyelogram phase in both the supine and prone position. The orientation of the kidneys relative to the midsagittal plane of the body and the orientation of the anterior and posterior calices relative to the axis of the kidney were measured from hardcopy images. Comparison was made between prone and supine positions for left and right kidneys separately, as well as overall.

RESULTS

The position of the patient had a small effect on the orientation of the kidneys, with the mean angle changing from 56.6 degrees when supine to 61.6 degrees when prone (p < 0.05). However, no significant change in caliceal orientation or the relative projection of the anterior and posterior calices occurred as a result.

CONCLUSION

There is no need to carry out special preoperative imaging in the operative or prone position.

Phylogenetic relationships of terrestrial Australo-Papuan elapid snakes (subfamily Hydrophiinae) based on cytochrome b and 16S rRNA sequences

Phylogenetic relationships among the venomous Australo-Papuan elapid snake radiation remain poorly resolved, despite the application of diverse data sets. To examine phylogenetic relationships among this enigmatic group, portions of the cytochrome b and 16S rRNA mitochondrial DNA genes were sequenced from 19 of the 20 terrestrial Australian genera and 6 of the 7 terrestrial Melanesian genera, plus a sea krait (Laticauda) and a true sea snake (Hydrelaps). These data clarify several significant issues in elapid phylogeny. First, Melanesian elapids form sister groups to Australian species, indicating that the ancestors of the Australian radiation came via Asia, rather than representing a relict Gondwanan radiation. Second, the two major groups of sea snakes (sea kraits and true sea snakes) represent independent invasions of the marine environment. Third, the radiation of viviparous Australian elapids is much older than has been suggested from immunological data. Parsimony analyses were unable to resolve relationships among the Australian radiation, a problem previously encountered with analyses of other (morphological, electrophoretic, karyotypic, immunological) data sets on these species. These data suggest that the reason for this continued difficulty lies in the timing of speciation events: the elapids apparently underwent a spectacular adaptive radiation soon after reaching Australia, such that divergences are ancient even within genera. Indeed, intrageneric divergences are almost as large as intergeneric divergences. Although this timing means that our sequence data cannot fully resolve phylogenetic relationships among the Australian elapids, the data suggest a close relationship of the following clades: Pseudonaja with Oxyuranus; Ogmodon with Toxicocalamus; Demansia with Aspidomorphus; Echiopsis with Denisonia; the "Notechis" lineage with Drysdalia coronoides; and Rhinoplocephalus and Suta with Drysdalia coronata. At least two of the Australian genera (Drysdalia and Simoselaps) appear to be paraphyletic. These sequence data support many of the conclusions reached by earlier studies using other types of data, but additional information will be needed before the phylogeny of the Australian elapids can be fully resolved.